Molecular and biotechnological aspects of secondary metabolites in actinobacteria

Drivers of the Sisrè berry plant [Synsepalum dulcificum (Schumach & Thonn.) Daniell] rhizosphere bacterial communities in Benin

Each plant species has its own rhizobacteriome, whose activities determine both soil biological quality and plant growth. Little knowledge exists of the rhizosphere bacterial communities associated with opportunity crops with high economic potential such as Synsepalum dulcificum. Native to West Africa, this shrub is famous for its red berries representing the only natural source of miraculin, a glycoprotein, with sweetening properties, but also playing a role in the treatment of cancer and diabetes. This study aimed to characterize the structure and diversity of rhizobacterial communities associated with S. dulcificum and to identify the parameters determining this diversity. An initial sampling stage allowed the collection of rhizosphere soils from 29 S. dulcificum accessions, belonging to three distinct phenotypes, from 16 municipalities of Benin, located either on farms or in home gardens. The bacterial diversity of these rhizosphere soils was assessed by Illumina sequencing of the 16S rRNA gene after DNA extraction from these soils. Furthermore, an analysis of the physicochemical properties of these soils was carried out. All accessions combined, the most represented phylum appeared to be Actinobacteriota, with an average relative abundance of 43.5 %, followed by Proteobacteria (14.8 %), Firmicutes (14.3 %) and Chloroflexi (12.2 %), yet the relative abundance of dominant phyla varied significantly among accessions (p < 0.05). Plant phenotype, habitat, climate and soil physicochemical properties affected the bacterial communities, but our study pointed out that soil physicochemical parameters were the main driver of rhizobacterial communities' structure and diversity. Among them, the assimilable phosphorus, lead, potassium, arsenic and manganese contents, texture and cation exchange capacity of rhizosphere soils were the major determinants of the composition and diversity of rhizosphere bacterial communities. These results suggested the possibility of improving the growth conditions and productivity of S. dulcificum, by harnessing its associated bacteria of interest and better managing soil physicochemical properties.

A Genomics-Based Discovery of Secondary Metabolite Biosynthetic Gene Clusters in the Potential Novel Strain Streptomyces sp. 21So2-11 Isolated from Antarctic Soil

Streptomyces species are attractive sources of secondary metabolites that serve as major sources of antibiotics and other drugs. In this study, genome mining was used to determine the biosynthetic potential of Streptomyces sp. 21So2-11 isolated from Antarctic soil. 16S rRNA gene sequencing revealed that this strain is most closely related to Streptomyces drozdowiczii NBRC 101007T, with a similarity of 98.02%. Genome comparisons based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) showed that strain 21So2-11 represents a novel species of the genus Streptomyces. In addition to a large number of genes related to environmental adaptation and ecological function, a total of 28 putative biosynthetic gene clusters (BGCs) responsible for the biosynthesis of known and/or novel secondary metabolites, including terpenes, lantipeptides, polyketides, nonribosomal peptides, RiPPs and siderophores, were detected in the genome of strain 21So2-11. In addition, a total of 1456 BGCs were predicted to contribute to the biosynthesis of more than 300 secondary metabolites based on the genomes of 47 Streptomyces strains originating from polar regions. The results indicate the potential of Streptomyces sp. 21So2-11 for bioactive secondary metabolite production and are helpful for understanding bacterial adaptability and ecological function in cold terrestrial environments.

Antiproliferative and antimicrobial compounds from Streptomyces levis: supported by in vitro and in silico molecular docking approach

The present work describes the investigation of secondary metabolites produced by rhizospheric soil isolate Streptomyces levis with respect to partial purification, bioactivity, structural elucidation, and docking study. MIC (Minimum Inhibitory Concentration) of the fraction was found to be 16 µg/mL, 32 µg/mL, and 8 µg/mL against S. aureus, E. coli, and C. albicans respectively. The fraction exhibited an IC50 of 90.48 μg/mL and 59.10 µg/mL against L929 and HeLa cell lines respectively. Spectroscopic analysis showed abundant of Isofucosterol 3-O-[6-O-(9-Octadecanoyl)-b-D-glucopyranoside], and Viniferal. These compounds were docked against receptor molecules E6, E7, Caspase-3, and Bcl2. The in-silico results suggested that all the secondary metabolites showed higher docking scores than the standard compound 5-Fluorouracil. Molecular docking study and published literature suggested that Isofucosterol 3-O-[6-O-(9-Octadecanoyl)-b-D-glucopyranoside] inactivated viral oncoprotein E7 and arrested the cell cycle from entering in S phase. Viniferal induced apoptosis by inactivation of Bcl2.

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

Secondary metabolites produced by actinomycete strains undoubtedly have great potential for use in applied research areas such as drug discovery. However, it is becoming difficult to obtain novel compounds because of repeated isolation around the world. Therefore, a new strategy for discovering novel secondary metabolites is needed. Many researchers believe that actinomycetes have as yet unanalyzed secondary metabolic activities, and the associated undiscovered secondary metabolite biosynthesis genes are called "silent" genes. This review outlines several approaches to further activate the metabolic potential of actinomycetes.

Enhancement of Streptomyces thinghirensis WAE1 for production of bioactive metabolites under different optimization strategies

Isolation of novel bioactive metabolites from Streptomyces strains is a promising source for drug discovery. However, conventional screening approaches have limitations in identifying new leads due to redundant discoveries. Optimization of culture conditions is important but traditionally optimized one factor at a time, failing to consider interactions. This study addressed these gaps by enhancing metabolite production from Streptomyces thinghirensis WAE1 through statistical optimization. Various chemical and physical factors impacting metabolite production were identified. Response surface methodology with a central composite design was applied to optimize significant factors like carbon source, nitrogen source, inoculum size, pH, temperature and incubation period. This optimized production against Streptococcus pneumoniae, increasing antibacterial activity by 74.92%. Gas chromatography-mass spectrometry revealed 19 bioactive compounds, including 1,25-dihydroxyvitamin D3 inhibiting cell wall development. This highlights S. thinghirensis WAE1's potential as a bioresource and emphasizes studying metabolite production from novel Streptomyces strains to discover new antibacterial drugs.

Screening biosurfactant-producing actinomycetes: Identification of Streptomyces sp. RP1 as a potent species for bioremediation

This study aimed to isolate biosurfactant-producing and hydrocarbon-degrading actinomycetes from different soils using glycerol-asparagine and starch-casein media with an antifungal agent. The glycerol-asparagine agar exhibited the highest number of actinomycetes, with a white, low-opacity medium supporting pigment production and high growth. Biosurfactant analyses, such as drop collapse, oil displacement, emulsification, tributyrin agar test, and surface tension measurement, were conducted. Out of 25 positive isolates, seven could utilize both olive oil and black oil for biosurfactant production, and only isolate RP1 could produce biosurfactant when grown in constrained conditions with black oil as the sole carbon source and inducer, demonstrating in situ bioremediation potential. Isolate RP1 from oil-spilled garden soil is Gram-staining-positive with a distinct earthy odor, melanin formation, and white filamentous colonies. It has a molecular size of ~621 bp and 100% sequence similarity to many Streptomyces spp. Morphological, biochemical, and 16 S rRNA analysis confirmed it as Streptomyces sp. RP1, showing positive results in all screenings, including high emulsification activity against kerosene (27.2%) and engine oil (95.8%), oil displacement efficiency against crude oil (7.45 cm), and a significant reduction in surface tension (56.7 dynes/cm). Streptomyces sp. RP1 can utilize citrate as a carbon source, tolerate sodium chloride, resist lysozyme, degrade petroleum hydrocarbons, and produce biosurfactant at 37°C in a 15 mL medium culture, indicating great potential for bioremediation and various downstream industrial applications with optimization.

Isolation of Secondary Metabolites From Marine Actinobacterium of Microbispora sp.T3S11 and Their Antibacterial Activities

Introduction Marine actinobacteria are promising sources of novel bioactive compounds due to their distinct ecological niches and diverse secondary metabolite production capabilities. Among these, Microbispora sp. T3S11 is notable for its unique spore chain structure, which allows for both morphological and genetic identification. Despite its potential, little is understood about the secondary metabolites produced by this strain. In this study, we hope to fill this gap by extracting and analyzing the antibacterial activities of secondary metabolites from Microbispora sp. T3S11, which will be the first time its bioactive compound profile is investigated. Aim To evaluate the antibacterial activity of secondary metabolites isolated from the marine actinobacterium Microbispora sp. T3S11. Materials and methods The antibacterial assays were carried out on agar plates containing the appropriate media for each pathogen. Sterile filter paper disks were impregnated with secondary metabolites extracted from Microbispora sp. T3S11 and placed on the surface of agar plates inoculated with the appropriate pathogens. Similarly, disks containing tetracycline were used as a positive control. The plates were then incubated at the appropriate temperature for each pathogen, and the zones of inhibition around the disks were measured to determine the extracted metabolites' antibacterial activity. Result Secondary metabolites had antimicrobial activity against Streptococcus mutans, Klebsiella pneumonia, and methicillin-resistant Staphylococcus aureus (MRSA). The inhibition of S. mutans was 7.5 mm and 8.5 mm at 75 μg/mL and 100 μg/mL, respectively. Klebsiella pneumonia zones measured 7 mm and 7.5 mm, while MRSA zones measured 7.6 mm and 8.5 mm at the same concentrations. Tetracycline, the standard antibiotic, had larger inhibition zones: 22 mm for S. mutans and Klebsiella pneumonia and 16 mm for MRSA, indicating variable susceptibility. Conclusion We conclude that the secondary metabolites extracted from Microbispora sp. T3S11 exhibits high antibacterial activity. This could be attributed to the presence of various active compounds.

Insights into additional lactone-based signaling circuits in Streptomyces: existence of acyl-homoserine lactones and LuxI/LuxR homologs in six Streptomyces species

Acyl-homoserine lactones (AHLs), mediating pivotal physiological activities through quorum sensing (QS), have conventionally been considered limited to Gram-negative bacteria. However, few reports on the existence of AHLs in Gram-positive bacteria have questioned this conception. Streptomyces, as Gram-positive bacteria already utilizing a lactone-based QS molecule (i.e., gamma-butyrolactones), are yet to be explored for producing AHLs, considering their metabolic capacity and physiological distinction. In this regard, our study examined the potential production of AHLs within Streptomyces by deploying HPLC-MS/MS methods, which resulted in the discovery of multiple AHL productions by S. griseus, S. lavendulae FRI-5, S. clavuligerus, S. nodosus, S. lividans, and S. coelicolor A3(2). Each of these Streptomyces species possesses a combination of AHLs of different size ranges, possibly due to their distinct properties and regulatory roles. In light of additional lactone molecules, we further confirm that AHL- and GBL-synthases (i.e., LuxI and AfsA enzyme families, respectively) and their receptors (i.e., LuxR and ArpA) are evolutionarily distinct. To this end, we searched for the components of the AHL signaling circuit, i.e., AHL synthases and receptors, in the Streptomyces genus, and we have identified multiple potential LuxI and LuxR homologs in all 2,336 Streptomyces species included in this study. The 6 Streptomyces of interest in this study also had at least 4 LuxI homologs and 97 LuxR homologs. In conclusion, AHLs and associated gene regulatory systems could be more widespread within the prokaryotic realm than previously believed, potentially contributing to the control of secondary metabolites (e.g., antibiotics) and their complex life cycle, which leads to substantial industrial and clinical applications.

Biosynthesis of Silver Nanoparticles From Marine Actinobacterium Micromonospora sp. and Their Bioactive Potential

Background The biosynthesis of nanoparticles represents a rapid, environmentally friendly, cost-effective, and straightforward technology. This approach allows for the production of nanoparticles with a wide range of chemical compositions, sizes, shapes, high uniformity, and scalability. One of the principal advantages of biogenic nanoparticles is their water solubility and compatibility with biological systems. Biologically synthesized nanoparticles have demonstrated superior efficiency compared to conventionally synthesized particles. Among biosynthesis, microbial-mediated biosynthesis is a promising one that has a selectively reducing ability on specific metal ions through electron transfer.  Objectives Evaluation of antimicrobial and antioxidant activity of silver nanoparticle synthesized by actinobacteria Micromonospora sp. which is isolated from marine environment. Materials and methods In this study, actinobacteria were isolated from the marine sediment using the spread plate method. The isolates were identified based on morphological observation, cell wall amino acids, sugar analysis, and micromorphological analysis. The silver nanoparticle synthesis from microbes and their inhibition against clinical pathogens have been evaluated by the disc diffusion method. Antioxidant efficiency was evaluated in terms of total antioxidant activity through ammonium molybdenum assay. Results A total of five isolates were isolated from the sediment sample. The cell-free extract of MBIT-MSA4 can synthesize silver nanoparticles that have potential antimicrobial activity against the clinical pathogens Streptococcus mutans at a zone of inhibition 6 mm, 10 mm inhibition zone of Klebsiella pneumonia, and 8 mm zone of inhibition of Staphylococcus aureus. Also, it has significant antioxidant activity up to 73% of free radical inhibition. Conclusion Marine microbial-mediated biosynthesized silver nanoparticles have potential antimicrobial activity against S. mutans and methicillin-resistant Staphylococcus aureus (MRSA) and inhibit the oxidation process through antioxidant activity. This enhanced efficient biosynthesised nanoparticle has significantly reduced the concentration of free radicals caused by pathogens.

Combatting Sugar Beet Root Rot: Streptomyces Strains' Efficacy against Fusarium oxysporum

Sugar beet root rot disease triggered by Fusarium oxysporum f. sp. radicis-betae is a destructive disease and dramatically affects the production and quality of the sugar beet industry. Employing beneficial microorganisms as a biocontrol strategy represents an eco-friendly and sustainable approach to combat various plant diseases. The distinct aspect of this study was to assess the antifungal and plant growth-promoting capabilities of recently isolated Streptomyces to treat sugar beet plants against infection with the phytopathogen F. oxysporum. Thirty-seven actinobacterial isolates were recovered from the rhizosphere of healthy sugar beet plants and screened for their potential to antagonize F. oxysporum in vitro. Two isolates SB3-15 and SB2-23 that displayed higher antagonistic effects were morphologically and molecularly identified as Streptomyces spp. Seed treatment with the fermentation broth of the selected Streptomyces strains SB3-15 and SB2-23 significantly reduced disease severity compared to the infected control in a greenhouse experiment. Streptomyces SB2-23 exhibited the highest protective activity with high efficacy ranging from 91.06 to 94.77% compared to chemical fungicide (86.44 to 92.36%). Furthermore, strain SB2-23 significantly increased plant weight, root weight, root length, and diameter. Likewise, it improves sucrose percentage and juice purity. As a consequence, the strain SB2-23's intriguing biocontrol capability and sugar beet root growth stimulation present promising prospects for its utilization in both plant protection and enhancement strategies.

Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria

Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.

The untapped potential of actinobacterial lanthipeptides as therapeutic agents

The increase in bacterial resistance generated by the indiscriminate use of antibiotics in medical practice set new challenges for discovering bioactive natural products as alternatives for therapeutics. Lanthipeptides are an attractive natural product group that has been only partially explored and shows engaging biological activities. These molecules are small peptides with potential application as therapeutic agents. Some members show antibiotic activity against problematic drug-resistant pathogens and against a wide variety of viruses. Nevertheless, their biological activities are not restricted to antimicrobials, as their contribution to the treatment of cystic fibrosis, cancer, pain symptoms, control of inflammation, and blood pressure has been demonstrated. The study of biosynthetic gene clusters through genome mining has contributed to accelerating the discovery, enlargement, and diversification of this group of natural products. In this review, we provide insight into the recent advances in the development and research of actinobacterial lanthipeptides that hold great potential as therapeutics.

Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens

Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.

Exploring Antibacterial Properties of Bioactive Compounds Isolated from Streptomyces sp. in Bamboo Rhizosphere Soil

The increasing concern over multidrug resistance in pathogens has led to an ongoing search for novel antibiotics derived from soil actinobacteria. In this current investigation, actinobacteria were isolated from the rhizosphere of bamboo plants collected within the Megamalai forest of the Western Ghats in the Theni zone of Tamil Nadu, India. These actinobacteria were subjected to characterization, and their growth conditions were optimized to enhance the production of bioactive compounds. To assess antibacterial properties, the isolated Actinobacteria underwent testing using the agar plug method. The strain exhibiting notable antibacterial activity underwent further characterization through 16s rRNA gene sequencing and subsequent phylogenetic analysis. Employing response surface methodology (RSM), cultural conditions were fine-tuned. Bioactive compounds were extracted from the culture medium using ethyl acetate, and their antibacterial and antioxidant effects were evaluated through disc diffusion and DPPH radical scavenging methods, respectively. Ethyl acetate extracts were analyzed by using FT-IR and GC-MS techniques. In total, nine strains of Actinobacteria were isolated from the rhizosphere soil of bamboo. Among these, strain BS-16 displayed remarkable antibacterial activity against three strains: Staphylococcus aureus (19 mm), Bacillus subtilis (12 mm), and Streptococcus pyogenes (10 mm). This strain was identified as Streptomyces sp. The optimal conditions for bioactive compound production were determined as follows: malt extract (10 g), yeast extract (5 g), dextrose (5 g), pH 6.5, and temperature 30 °C. After a 7-day incubation period, the results showed a 6% increase in production. The ethyl acetate fraction derived from strain BS-16 exhibited dose-dependent antibacterial and antioxidant activities. FT-IR and GC-MS analyses revealed the presence of active compounds with antibacterial effects within the extract. Consequently, further investigation into the BS-16 strain holds promise for scaling up the production of bioactive compounds possessing antibacterial and antioxidant properties.

Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles

More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.

Structural insights into the transcription activation mechanism of the global regulator GlnR from actinobacteria

In actinobacteria, an OmpR/PhoB subfamily protein called GlnR acts as an orphan response regulator and globally coordinates the expression of genes responsible for nitrogen, carbon, and phosphate metabolism in actinobacteria. Although many researchers have attempted to elucidate the mechanisms of GlnR-dependent transcription activation, progress is impeded by lacking of an overall structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a co-crystal structure of the C-terminal DNA-binding domain of GlnR (GlnR_DBD) in complex with its regulatory cis-element DNA and a cryo-EM structure of GlnR-TAC which comprises Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures illustrate how four GlnR protomers coordinate to engage promoter DNA in a head-to-tail manner, with four N-terminal receiver domains of GlnR (GlnR-RECs) bridging GlnR_DBDs and the RNAP core enzyme. Structural analysis also unravels that GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved β flap, σAR4, αCTD, and αNTD domains of RNAP, which are further confirmed by our biochemical assays. Taken together, these results reveal a global transcription activation mechanism for the master regulator GlnR and other OmpR/PhoB subfamily proteins and present a unique mode of bacterial transcription regulation.

Penicillium citrinum, a Drought-Tolerant Endophytic Fungus Isolated from Wheat (Triticum aestivum L.) Leaves with Plant Growth-Promoting Abilities

Endophytic fungi have recently garnered significant attention as next-generation bioinoculants due to their plausible role in ameliorating abiotic and biotic stresses. This adaptation is achieved via various signalling molecules and mechanisms established by these symbionts with their hosts. The present study screened 61 endophytic isolates of culturable mycobiome associated with wheat variety PBW725 during their crop cycle. Three endophytic isolates exhibited a minimum reduction in their growth and maximum biomass production during the drought stress developed using polyethylene glycol 6000. Further, these isolates also exhibited plant growth promoting properties by virtue of the production of indole acetic acid, gibberellic acid and ammonia. These isolates also exhibited the propensity to solubilise phosphate and zinc, produce siderophores and further exhibit extracellular enzymatic activities, contributing to plants' adaptability to abiotic stresses. The best isolate amongst the three was #5TAKL-3a, identified as Penicillium citrinum based on multilocus phylogenetic analysis. The isolate as a bioinoculant enhances various biochemical and physiological properties in planta. Hence our studies indicate that Penicillium citrinum #5TAKL-3a is a potential candidate bioinoculant for field trials to improve the adaptability of the wheat plant under drought stress.

Strain Streptomyces sp. P-56 Produces Nonactin and Possesses Insecticidal, Acaricidal, Antimicrobial and Plant Growth-Promoting Traits

Streptomycetes produce a huge variety of bioactive metabolites, including antibiotics, enzyme inhibitors, pesticides and herbicides, which offer promise for applications in agriculture as plant protection and plant growth-promoting products. The aim of this report was to characterize the biological activities of strain Streptomyces sp. P-56, previously isolated from soil as an insecticidal bacterium. The metabolic complex was obtained from liquid culture of Streptomyces sp. P-56 as dried ethanol extract (DEE) and possessed insecticidal activity against vetch aphid (Medoura viciae Buckt.), cotton aphid (Aphis gossypii Glov.), green peach aphid (Myzus persicae Sulz.), pea aphid (Acyrthosiphon pisum Harr.) and crescent-marked lily aphid (Neomyzus circumflexus Buckt.), as well as two-spotted spider mite (Tetranychus urticae). Insecticidal activity was associated with production of nonactin, which was purified and identified using HPLC-MS and crystallographic techniques. Strain Streptomyces sp. P-56 also showed antibacterial and antifungal activity against various phytopathogenic bacteria and fungi (mostly for Clavibacfer michiganense, Alternaria solani and Sclerotinia libertiana), and possessed a set of plant growth-promoting traits, such as auxin production, ACC deaminase and phosphate solubilization. The possibilities for using this strain as a biopesticide producer and/or biocontrol and a plant growth-promoting microorganism are discussed.

Secondary metabolic profiling of Serratia marcescens NP10 reveals new stephensiolides and glucosamine derivatives with bacterial membrane activity

Secondary metabolic profiling, using UPLC-MS^E and molecular networking, revealed the secondary metabolites produced by Serratia marcescens NP10. The NP10 strain co-produced cyclic and open-ring stephensiolides (i.e., fatty acyl chain linked to Thr-Ser-Ser-Ile/Leu-Ile/Leu/Val) and glucosamine derivatives (i.e., fatty acyl chain linked to Val-glucose-butyric/oxo-hexanoic acid), with the structures of sixteen new stephensiolides (L-Y) and three new glucosamine derivatives (L-N) proposed. Genome mining identified sphA (stephensiolides) and gcd (glucosamine derivatives) gene clusters within Serratia genomes available on NBCI using antiSMASH, revealing specificity scores of the adenylation-domains within each module that corroborates MS^E data. Of the nine RP-HPLC fractions, two stephensiolides and two glucosamine derivatives exhibited activity against Staphylococcus aureus (IC₅₀ of 25-79 µg/mL). ¹H NMR analysis confirmed the structure of the four active compounds as stephensiolide K, a novel analogue stephensiolide U, and glucosamine derivatives A and C. Stephensiolides K and U were found to cause membrane depolarisation and affect the membrane permeability of S. aureus, while glucosamine derivatives A and C primarily caused membrane depolarisation. New members of the stephensiolide and glucosamine derivative families were thus identified, and results obtained shed light on their antibacterial properties and mode of membrane activity.

Nonribosomal peptide synthetase gene clusters and characteristics of predicted NRPS-dependent siderophore synthetases in Armillaria and other species in the Physalacriaceae

Fungal secondary metabolites are often pathogenicity or virulence factors synthesized by genes contained in secondary metabolite gene clusters (SMGCs). Nonribosomal polypeptide synthetase (NRPS) clusters are SMGCs which produce peptides such as siderophores, the high affinity ferric iron chelating compounds required for iron uptake under aerobic conditions. Armillaria spp. are mostly facultative necrotrophs of woody plants. NRPS-dependent siderophore synthetase (NDSS) clusters of Armillaria spp. and selected Physalacriaceae were investigated using a comparative genomics approach. Siderophore biosynthesis by strains of selected Armillaria spp. was evaluated using CAS and split-CAS assays. At least one NRPS cluster and other clusters were detected in the genomes studied. No correlation was observed between the number and types of SMGCs and reported pathogenicity of the species studied. The genomes contained one NDSS cluster each. All NDSSs were multi-modular with the domain architecture (ATC)₃(TC)₂. NDSS clusters of the Armillaria spp. showed a high degree of microsynteny. In the genomes of Desarmillaria spp. and Guyanagaster necrorhizus, NDSS clusters were more syntenic with NDSS clusters of Armillaria spp. than to those of the other Physalacriaceae species studied. Three A-domain orthologous groups were identified in the NDSSs, and atypical Stachelhaus codes were predicted for the A3 orthologous group. In vitro biosynthesis of mainly hydroxamate and some catecholate siderophores was observed. Hence, Armillaria spp. generally contain one highly conserved, NDSS cluster although some interspecific variations in the products of these clusters is expected. Results from this study lays the groundwork for future studies to elucidate the molecular biology of fungal phyto-pathogenicity.

Harnessing Novel Soil Bacteria for Beneficial Interactions with Soybean

It is claimed that one g of soil holds ten billion bacteria representing thousands of distinct species. These bacteria play key roles in the regulation of terrestrial carbon dynamics, nutrient cycles, and plant productivity. Despite the overwhelming diversity of bacteria, most bacterial species remain largely unknown. Here, we used an oligotrophic medium to isolate novel soil bacteria for positive interaction with soybean. Strictly 22 species of bacteria from the soybean rhizosphere were selected. These isolates encompass ten genera (Kosakonia, Microbacterium, Mycobacterium, Methylobacterium, Monashia, Novosphingobium, Pandoraea, Anthrobacter, Stenotrophomonas, and Rhizobium) and have potential as novel species. Furthermore, the novel bacterial species exhibited plant growth-promoting traits in vitro and enhanced soybean growth under drought stress in a greenhouse experiment. We also reported the draft genome sequences of Kosakonia sp. strain SOY2 and Agrobacterium sp. strain SOY23. Along with our analysis of 169 publicly available genomes for the genera reported here, we demonstrated that these bacteria have a repertoire of genes encoding plant growth-promoting proteins and secondary metabolite biosynthetic gene clusters that directly affect plant growth. Taken together, our findings allow the identification novel soil bacteria, paving the way for their application in crop production.

Bioaugmentation with a defined bacterial consortium: A key to degrade high molecular weight polylactic acid during traditional composting

Polylactic acid (PLA) is commercialized as a compostable bio-thermoplastic. PLA degrades under industrial composting conditions where elevated temperatures are maintained for a long timeframe. However, these conditions cannot be achieved in a non-industrial compost pile. Therefore, this study aims to degrade high molecular weight PLA films by adding a PLA-degrading bacterial consortium (EAc) comprised of Nocardioides zeae EA12, Stenotrophomonas pavanii EA33, Gordonia desulfuricans EA63, and Chitinophaga jiangningensis EA02 during traditional composting. With EAc-bioaugmentation, PLA films (5-30% w/w) had complete disintegration (35 d), 77-82% molecular weight reduction (16 d), and higher CO₂ liberation and mineralization than non-bioaugmented composting. Bacterial community analyses showed that EAc-bioaugmentation increased the relative abundance of Schlegelella, a known polymer degrader, and interacted positively with beneficial indigenous microbes like Bacillus, Schlegelella and Thermopolyspora. The bioaugmentation also decreased compost phytotoxicity. Hence, consortium EAc shows potential in PLA-waste treatment applications, such as backyard and small-scale composting.

Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential

Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.

Mixed culture chain elongation for consumption of acetate and ethanol in anaerobic fermentation: The impact of salt type, dosage and acclimation

Microbial chain elongation is a newly developed carboxylate platform-based bioprocess, which often encounters high salinity stress due to saline feedstock and pH adjustment. In this study, we systematically investigated the effects of salt types (Na⁺, K⁺, and NH₄⁺), dosage, and salinity acclimation on microbial chain elongation, and identified the microbial community by high throughput 16S rRNA gene sequencing. The results showed that a high level of Na⁺ and NH₄⁺ (12.5 g/L of cations) exerted seriously inhibitory effects without chain elongating activity, while K⁺ had the slightest inhibition only with a little longer lag phase and lower products yield. The chain elongating products yields and the selectivity of caproate decreased with the increasing Na⁺ concentration, and 8.6 g/L of Na⁺ was found to be the threshold value for un-acclimated inoculum used for chain elongation. The acclimation to high saline conditions greatly promoted the consumption of acetate and ethanol with a shorter lag phase, and recovered a robust elongating activity for butyrate production. Furthermore, the high throughput 16S rRNA gene sequencing analysis results indicated that six genera, such as Clostridium IV and Clostridium sensu stricto, closely relating chain elongation process were depressed by high salinity, and the salinity acclimation helped to enrich the functional microbes. These findings could provide useful information for engineering microbial chain elongation process under saline conditions.

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.

Biological Dark Matter Exploration using Data Mining for the Discovery of Antimicrobial Natural Products

The discovery of novel antimicrobials has significantly slowed down over the last three decades. At the same time, humans rely increasingly on antimicrobials because of the progressive antimicrobial resistance in medical practices, human communities, and the environment. Data mining is currently considered a promising option in the discovery of new antibiotics. Some of the advantages of data mining are the ability to predict chemical structures from sequence data, anticipation of the presence of novel metabolites, the understanding of gene evolution, and the corroboration of data from multiple omics technologies. This review analyzes the state-of-the-art for data mining in the fields of bacteria, fungi, and plant genomic data, as well as metabologenomics. It also summarizes some of the most recent research accomplishments in the field, all pinpointing to innovation through uncovering and implementing the next generation of antimicrobials.

Unraveling the tripartite interaction of volatile compounds of Streptomyces rochei with grain mold pathogens infecting sorghum

Sorghum is a major grain crop used in traditional meals and health drinks, and as an efficient fuel. However, its productivity, value, germination, and usability are affected by grain mold, which is a severe problem in sorghum production systems, which reduces the yield of harvested grains for consumer use. The organic approach to the management of the disease is essential and will increase consumer demand. Bioactive molecules like mVOC (volatile organic compound) identification are used to unravel the molecules responsible for antifungal activity. The Streptomyces rochei strain (ASH) has been reported to be a potential antagonist to many pathogens, with high levels of VOCs. The present study aimed to study the inhibitory effect of S. rochei on sorghum grain mold pathogens using a dual culture technique and via the production of microbial volatile organic compounds (mVOCs). mVOCs inhibited the mycelial growth of Fusarium moniliforme by 63.75 and Curvularia lunata by 68.52%. mVOCs suppressed mycelial growth and inhibited the production of spores by altering the structure of mycelia in tripartite plate assay. About 45 mVOCs were profiled when Streptomyces rochei interacted with these two pathogens. In the present study, several compounds were upregulated or downregulated by S. rochei, including 2-methyl-1-butanol, methanoazulene, and cedrene. S. rochei emitted novel terpenoid compounds with peak areas, such as myrcene (1.14%), cymene (6.41%), and ç-terpinene (7.32%) upon interaction with F. moniliforme and C. lunata. The peak area of some of the compounds, including furan 2-methyl (0.70%), benzene (1.84%), 1-butanol, 2-methyl-(8.25%), and myrcene (1.12)%, was increased during tripartite interaction with F. moniliforme and C. lunata, which resulted in furan 2-methyl (6.60%), benzene (4.43%), butanol, 2-methyl (18.67%), and myrcene (1.14%). These metabolites were implicated in the sesquiterpenoid and alkane biosynthetic pathways and the oxalic acid degradation pathway. The present study shows how S. rochei exhibits hyperparasitism, competition, and antibiosis via mVOCs. In addition to their antimicrobial functions, these metabolites could also enhance plant growth.

Paradigms of actinorhizal symbiosis under the regime of global climatic changes: New insights and perspectives

Nitrogen occurs as inert and inaccessible dinitrogen gaseous form (N₂ ) in the atmosphere. Biological nitrogen fixation is a chief process that makes this dinitrogen (N₂ ) accessible and bioavailable in the form of ammonium (NH₄ ⁺ ) ions. The key organisms to fix nitrogen are certain prokaryotes, called diazotrophs either in the free-living form or establishing significant mutual relationships with a variety of plants. On such examples is ~95-100 MY old incomparable symbiosis between dicotyledonous trees and a unique actinobacterial diazotroph in diverse ecosystems. In this association, the root of the certain dicotyledonous tree (~25 genera and 225 species) belonging to three different taxonomic orders, Fagales, Cucurbitales, and Rosales (FaCuRo) known as actinorhizal trees can host a diazotroph, Frankia of order Frankiales. Frankia is gram-positive, branched, filamentous, sporulating, and free-living soil actinobacterium. It resides in the specialized, multilobed, and coralloid organs (lateral roots but without caps), the root nodules of actinorhizal tress. This review aims to provide systematic information on the distribution and the phylogenetic diversity of hosts from FaCuRo and their micro-endosymbionts (Frankia spp.), colonization mechanisms, and signaling pathways. We also aim to provide details on developmental and physiological imperatives for gene regulation and functional genomics of symbiosis, phenomenal restoration ecology, influences of contemporary global climatic changes, and anthropogenic impacts on plant-Frankia interactions for the functioning of ecosystems and the biosphere.

The Use of Baikal Psychrophilic Actinobacteria for Synthesis of Biologically Active Natural Products from Sawdust Waste

One of the relevant areas in microbiology and biotechnology is the study of microorganisms that induce the destruction of different materials, buildings, and machines and lead to negative effects. At the same time, the positive ecological effects of degradation can be explained by the detoxication of industrial and agricultural wastes, chemical substances, petroleum products, xenobiotics, pesticides, and other chemical pollutants. Many of these industrial wastes include hard-to-degrade components, such as lignocellulose or plastics. The biosynthesis of natural products based on the transformation of lignocellulosic wastes is of particular interest. One of the world’s unique ecosystems is presented by Lake Baikal. This ecosystem is characterized by the highest level of biodiversity, low temperatures, and a high purity of the water. Here, we studied the ability of several psychrophilic representatives of Baikal Actinobacteria to grow on sawdust wastes and transform them into bioactive natural products. Different strains of both widely spread genus of Actinobacteria and rare genera of Actinobacteria were tested. We used the LC-MS methods to show that Actinobacteria living in sawmill wastes can produce both known and novel natural products with antibiotic activity. We demonstrated that the type of sawmill wastes and their concentration influence the Actinobacteria biosynthetic potential. We have shown for the first time that the use of Baikal psychrophilic microorganisms as a factory for biodegradation is applicable for the transformation of lignocellulosic wastes. Thus, the development of techniques for screening novel natural products leads to an elaboration on the active ingredients for novel drugs.

Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches

Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.

Effects of treatment processes on AOC removal and changes of bacterial diversity in a water treatment plant

The effectiveness of different treatment processes on assimilable organic carbon (AOC) removal and bacterial diversity variations was evaluated in a water treatment plant. The van der Kooij technique was applied for AOC analysis and responses of bacterial communities were characterized by the metagenomics assay. Results show that the AOC concentrations were about 93, 148, 43, 51, 37, and 38 μg acetate-C/L in effluents of raw water basin, preozonation, rapid sand filtration (RSF), ozonation, biofiltration [biological activated carbon (BAC) filtration], and chlorination (clear water), respectively. Increased AOC concentrations were observed after preozonation, ozonation, and chlorination units due to the production of biodegradable organic matters after the oxidation processes. Results indicate that the oxidation processes were the main causes of AOC formation, which resulted in significant increases in AOC concentrations (18-59% increment). The AOC removal efficiencies were 47, 28, and 60% in the RSF, biofiltration, and the whole system, respectively. RSF and biofiltration were responsible for the AOC treatment and both processes played key roles in AOC removal. Thus, both RSF and biofiltration processes would contribute to AOC treatment after oxidation. Sediments from the raw water basin and filter samples from RSF and BAC units were collected and analyzed for bacterial communities. Results from scanning electron microscope analysis indicate that bacterial colonization was observed in filter materials. This indicates that the surfaces of the filter materials were beneficial to bacterial growth and AOC removal via the adsorption and biodegradation mechanisms. Next generation sequencing analyses demonstrate that water treatment processes resulted in the changes of bacterial diversity and community profiles in filters of RSF and BAC. According to the findings of bacterial composition and interactions, the dominant bacterial phyla were Proteobacteria (41% in RSF and 56% in BAC) followed by Planctomycetes and Acidobacteria in RSF and BAC systems, which might affect the AOC biodegradation efficiency. Results would be useful in developing AOC treatment and management processes in water treatment plants.

Volatiles produced by Streptomyces spp. delay rot in apples caused by Colletotrichum acutatum

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Volatile organic compounds (VOCs) produced by Streptomyces have antifungal properties.

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Streptomyces VOCs reduced growth of the fungus Colletotrichum acutatum biomass.

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Apples infected by C. acutatum had reduced rot when incubated with Streptomyces.

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Biofumigation by Streptomyces VOCs may help inhibit postharvest rot in fruits.

Volatile organic compounds (VOCs) produced by microorganisms may prevent postharvest rot in fruits. Here, it was examined if VOCs from different species of Streptomyces can control infection in apples caused by the fungal pathogen Colletotrichum acutatum. Incubation of C. acutatum-infected apples in semi-closed boxes with actively growing strains of three Streptomyces (S. coelicolor, S. diastatochromogenes and Streptomyces strain 2R) showed that VOCs reduced rot areas of the apples by 45-66% after 8 days and 39-57% after 10 days, relative to infected apples incubated without Streptomyces. No differences in inhibition among the three strains were seen. In contrast, a mutant strain of Streptomyces that lacks major genes involved in biosynthesis of secondary metabolites, did not reduce development of rot in the apples. Furthermore, Streptomyces VOCs reduced radial hyphal growth of C. acutatum on agar. Several of the VOCs produced by three Streptomyces strains have previously shown fungicidal properties. Although the specific VOCs being active in inhibition of C. acutatum remain to be determined, VOCs may have a great potential as biofumigants to minimize postharvest diseases in fruits.

Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use

Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.

Phylogenetic affiliation of endophytic actinobacteria associated with selected orchid species and their role in growth promotion and suppression of phytopathogens

Endophytic actinobacteria aid in plant development and disease resistance by boosting nutrient uptake or producing secondary metabolites. For the first time, we investigated the culturable endophytic actinobacteria associated with ten epiphytic orchid species of Assam, India. 51 morphologically distinct actinobacteria were recovered from surface sterilized roots and leaves of orchids and characterized based on different PGP and antifungal traits. According to the 16S rRNA gene sequence, these isolates were divided into six families and eight genera, where Streptomyces was most abundant (n=29, 56.86%), followed by Actinomadura, Nocardia, Nocardiopsis, Nocardioides, Pseudonocardia, Microbacterium, and Mycolicibacterium. Regarding PGP characteristics, 25 (49.01%) isolates demonstrated phosphate solubilization in the range of 61.1±4.4 - 289.7±11.9 µg/ml, whereas 27 (52.94%) isolates biosynthesized IAA in the range of 4.0 ± 0.08 - 43.8 ± 0.2 µg/ml, and 35 (68.62%) isolates generated ammonia in the range of 0.9 ± 0.1 - 5.9 ± 0.2 µmol/ml. These isolates also produced extracellular enzymes, viz. protease (43.13%), cellulase (23.52%), pectinase (21.56%), ACC deaminase (27.45%), and chitinase (37.25%). Out of 51 isolates, 27 (52.94%) showed antagonism against at least one test phytopathogen. In molecular screening, most isolates with antifungal and chitinase producing traits revealed the presence of 18 family chitinase genes. Two actinobacterial endophytes, Streptomyces sp. VCLA3 and Streptomyces sp. RVRA7 were ranked as the best strains based on PGP and antifungal activity on bonitur scale. GC-MS examination of ethyl acetate extract of these potent strains displayed antimicrobial compound phenol, 2,4-bis-(1,1-dimethylethyl) as the major metabolite along with other antifungal and plant growth beneficial bioactive chemicals. SEM analysis of fungal pathogen F. oxysporum (MTCC 4633) affected by Streptomyces sp. VCLA3 revealed significant destruction in the spore structure. An in vivo plant growth promotion experiment with VCLA3 and RVRA7 on chili plants exhibited statistically significant (p<0.05) improvements in all of the evaluated vegetative parameters compared to the control. Our research thus gives insight into the diversity, composition, and functional significance of endophytic actinobacteria associated with orchids. This research demonstrates that isolates with multiple plant development and broad-spectrum antifungal properties are beneficial for plant growth. They may provide a viable alternative to chemical fertilizers and pesticides and a sustainable solution for chemical inputs in agriculture.

Understanding the potential of root microbiome influencing salt-tolerance in plants and mechanisms involved at the transcriptional and translational level

Soil salinity severely affects plant growth and development and imparts inevitable losses to crop productivity. Increasing the concentration of salts in the vicinity of plant roots has severe consequences at the morphological, biochemical, and molecular levels. These include loss of chlorophyll, decrease in photosynthetic rate, reduction in cell division, ROS generation, inactivation of antioxidative enzymes, alterations in phytohormone biosynthesis and signaling, and so forth. The association of microorganisms, viz. plant growth-promoting rhizobacteria, endophytes, and mycorrhiza, with plant roots constituting the root microbiome can confer a greater degree of salinity tolerance in addition to their inherent ability to promote growth and induce defense mechanisms. The mechanisms involved in induced stress tolerance bestowed by these microorganisms involve the modulation of phytohormone biosynthesis and signaling pathways (including indole acetic acid, gibberellic acid, brassinosteroids, abscisic acid, and jasmonic acid), accumulation of osmoprotectants (proline, glycine betaine, and sugar alcohols), and regulation of ion transporters (SOS1, NHX, HKT1). Apart from this, salt-tolerant microorganisms are known to induce the expression of salt-responsive genes via the action of several transcription factors, as well as by posttranscriptional and posttranslational modifications. Moreover, the potential of these salt-tolerant microflora can be employed for sustainably improving crop performance in saline environments. Therefore, this review will briefly focus on the key responses of plants under salinity stress and elucidate the mechanisms employed by the salt-tolerant microorganisms in improving plant tolerance under saline environments.

Pollution impact on microbial communities composition in natural and anthropogenically modified soils of Southern Russia

Metagenomic studies of soil microbocenoses are extremely relevant nowadays. The study of pollution impact on soil microbiomes is of particular interest. The structure of microbial communities in soils with different levels of pollution by polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) was studied. High bacterial biodiversity was found in all the studied soil samples, but its lowest values are found in soil samples taken on the territory of technogenically polluted Lake Atamanskoye. Assessment of soil pollution showed the highest content of polycyclic aromatic hydrocarbons (PAHs) and potentially toxic elements (PTEs) for the soils Lake Atamanskoye. The high content of pollutants negatively affects the abundance of representatives of the phyla Actinobacteria, Planctomycetes, Verrucomicrobia, and Nitrospirae. Such phyla as Proteobacteria, Candidate Divisions TM7, OD1, WPS-2, Chlamydiae, Cyanobacteria are characterized by positive direct correlation with the content of pollutants, especially with PAHs. A cooperative effect of decrease in the number of Actinobacteria and Proteobacteria with an increase in Armatimonadetes probably corresponds to PTEs contamination. The proportion of Candidate Division OD1, Chlamydiae, Cyanobacteria, and Candidate Division WPS-2 was increased in the soil microbiome under the influence of severe combined pollution. Pollutants negatively affect the abundance of dominant unclassified_o__Gaiellales and unclassified_o__WD2101 genera. Iamia, Salinibacterium, Arthrobacter, Kaistobacter, Thiobacillus genera are characterized by a low abundance, but they are presumably the most resistant to soil pollution. It was revealed that the level of soil pollution largely determines the composition and diversity of bacterial communities in the soils of the studied territories. Operating taxonomic units have been established that have prognostic value for assessing the state, level of soil pollution, and their biological safety.

Genomic Organization of Streptomyces flavotricini NGL1 and Streptomyces erythrochromogenes HMS4 Reveals Differential Plant Beneficial Attributes and Laccase Production Capabilities

The genus Streptomyces has been explored in industrial sectors due to its endurance to environmental stresses, the production of a plethora of biomolecules, the biological remediation of soils, and alleviating plant stresses. The whole genome of NGL1 and HMS4 was sequenced due to the specific laccase activity against 2,6-dimethoxyphenol (2,6-DMP) and differential plant beneficial attributes. The deduced genome of 8.85 Mbp and 7.73 Mbp in size with a G+C content of 72.03% and 72.3% was obtained for NGL1 and HMS4, respectively. A total of 8438 and 7322 protein coding genes, 155 (130 tRNA, 25 rRNA) and 145 tRNA (121 tRNA, 24 rRNA) coding genes were predicted in NGL1 and HMS4, respectively. The comparative genomics of NGL1 and HMS4 showed 185 and 162 genes encoding for carbohydrate-active enzymes, respectively. The genomic ability of these strains to encode carbohydrate-active enzymes, laccase, and diversity of BGCs, along with plant beneficial attributes to suppress the plant pathogens can be used for several industrial and agricultural applications.

Vaccination of Gilthead Seabream After Continuous Xenoestrogen Oral Exposure Enhances the Gut Endobolome and Immune Status via GPER1

In fish culture settings, the exogenous input of steroids is a matter of concern. Recently, we unveiled that in the gilthead seabream (Sparus aurata), the G protein-coupled estrogen receptor agonist G-1 (G1) and the endocrine disruptor 17α-ethinylestradiol (EE₂) are potent modulators in polyreactive antibody production. However, the integral role of the microbiota upon immunity and antibody processing in response to the effect of EE₂ remains largely unexplored. Here, juvenile seabreams continuously exposed for 84 days to oral G1 or EE₂ mixed in the fish food were intraperitoneally (i.p.) immune primed on day 42 with the model antigen keyhole limpet hemocyanin (KLH). A critical panel of systemic and mucosal immune markers, serum VTG, and humoral, enzymatic, and bacteriolytic activities were recorded and correlated with gut bacterial metagenomic analysis 1 day post-priming (dpp). Besides, at 15 dpp, animals received a boost to investigate the possible generation of specific anti-KLH antibodies at the systemic and mucosal interphases by the end of the trial. On day 43, EE₂ but not G1 induced a significant shift in the serum VTG level of naive fish. Simultaneously, significant changes in some immune enzymatic activities in the serum and gut mucus of the EE₂-treated group were recorded. In comparison, the vaccine priming immunization resulted in an attenuated profile of most enzymatic activities in the same group. The gut genes qPCR analysis exhibited a related pattern, only emphasized by a significant shift in the EE₂ group's il1b expression. The gut bacterial microbiome status underwent 16S rRNA dynamic changes in alpha diversity indices, only with the exposure to oral G1, supporting functional alterations on cellular processes, signaling, and lipid metabolism in the microbiota. By the same token, the immunization elevated the relative abundance of Fusobacteria only in the control group, while this phylum was depleted in both the treated groups. Remarkably, the immunization also promoted changes in the bacterial class Betaproteobacteria and the estrogen-associated genus Novosphingobium. Furthermore, systemic and mucosal KLH-specific immunoglobulin (Ig)M and IgT levels in the fully vaccinated fish showed only slight changes 84 days post-estrogenic oral administration. In summary, our results highlight the intrinsic relationship among estrogens, their associated receptors, and immunization in the ubiquitous fish immune regulation and the subtle but significant crosstalk with the gut endobolome.

Genome mining of biosynthetic gene clusters intended for secondary metabolites conservation in actinobacteria

Evolution of genome sequencing technology, on the one hand, and advancement of computational genome mining tools, on the other hand, paves way for improvement in predicting secondary metabolites. In past, numerous efforts were made concerning genome mining for recognizing secondary metabolites within the genus, but only a negligible quantity of comparative genomic reports had carried out among species of different genera. In this study, we explored potential of 24 actinobacteria species belonging to the genera, including Streptomyces, Nocardia, Micromonospora, and Saccharomonospora, to traverse diversity and distribution of Biosynthetic Gene Clusters (BGCs). Investigating results obtained from antiSMASH (Antibiotics and Secondary Metabolites Analysis Shell), NaPDoS (Natural Product Domain Seeker), and NP.searcher revealed conservation of genus-specific gene clusters among various species. E.g., NAGGN (n-acetyl glutaminyl glutamine amide) is present in Micromonospora, furan in Nocardia, melanin, and lassopeptide occur in Streptomyces. Bioactive compounds like alkyl-O-dihydro geranyl methoxy hydroquinone, SapB, desferrioxamine E, 2-Methylisoborneol, mayamycin, cyclodipeptide synthase, diisonitrile, salinichelin, hopene, ectoine and isorenieratene are highly conserved among diverse genera. Furthermore, pharmacological activity of actinobacterial derived metabolites against bacterial and fungal pathogens were illustrated. We need to accomplish large-scale analysis of natural products, including various genera of actinobacteria to deliver comprehensive intuition to overcome antibiotic resistance.

Extracellular Polymeric Substances (EPS) produced by Streptomyces sp. biofilms: Chemical composition and anticancer properties

The extracellular polymeric substances (EPS) have shown free radical scavenging and antitumor activity against both breast and colon cell lines. In this regard, actinobacteria have become an increasingly popular sources of EPS. Therefore, in this study four Streptomyces strains isolated from contaminated soil (M7, A5, A14 and MC1) were evaluated for determining its biofilm-forming capacity including under pesticide stress. In addition, chemical composition of EPS and its cytotoxic effects over 4T1 breast cancer cell and Caco-2 human tumor colon cells were evaluated. The results demonstrated that Streptomyces sp. A5 had the highest capability to develop biofilm more than other strains tested, even under pesticide stress. Moreover, this strain produced EPS with a total protein/total polysaccharide rate of 1.59 ± 0.05. On the other hand, cytotoxicity assays of EPS showed that Streptomyces sp. A5 display a higher toxic effect against 4T1 Breast cancer cells (96.2 ± 13.5 %), Caco-2 (73.9 ± 6.4 %) and low toxicity (29.9 % ± 9.1 %) against non-transformed intestinal cells (IEC-18). Data do not show cytotoxic effect relationship with biofilm-forming capabilities of strains, nor the chemical composition of EPS matrix. The gene that codes for polysaccharide deacetylase, parB-like and transRDD proteins, were identified. These results contribute to the knowledge about the variability of chemical composition and potential cytotoxic properties of EPS produced by Streptomyces biofilms. It proposes interesting future challenges for linking Streptomyces-based pesticide remediation technology with the development of new antitumor drugs.

Exogenous N-acyl-homoserine lactones accelerate resuscitation of starved anaerobic granular sludge after long-term stagnation

So as to accelerate the resuscitation of starved anaerobic granular sludge after long-term stagnation, an innovative method was tried derived from the regulation of N-acyl-homoserine lactones (AHLs)-mediated quorum sensing (QS). The mixture of four AHLs was added to the starved anaerobic granular sludge system in this research. The results confirmed that the exogenous AHLs shortened the recovery time of the granular sludge, and improved the treatment performance and methanogenic capacity of the recovered anaerobic sludge to the level before stagnation. At the same time, exogenous AHLs enhanced the synthesis of extracellular polymeric substances (EPS) during the resuscitation period of starved anaerobic granular sludge. The outcomes of microbial composition detection showed that the change of bacterial and methanogenic bacteria communities towards accelerated performance recovery was significantly correlated with exogenous AHLs. This exploration provided a new technical idea for speeding up the recovery of starved anaerobic granular sludge.

A bioprocess perspective on the production of secondary metabolites by Streptomyces in submerged co-cultures

Filamentous microorganisms are potent sources of bioactive secondary metabolites, the molecules formed in response to complex environmental signals. The chemical diversity encoded in microbial genomes is only partially revealed by following the standard microbiological approaches. Mimicking the natural stimuli through laboratory co-cultivation is one of the most effective methods of awakening the formation of high-value metabolic products. Whereas the biosynthetic outcomes of co-cultures are reviewed extensively, the bioprocess aspects of such efforts are often overlooked. The aim of the present review is to discuss the submerged co-cultivation strategies used for triggering and enhancing secondary metabolites production in Streptomyces, a heavily investigated bacterial genus exhibiting an impressive repertoire of secondary metabolites, including a vast array of antibiotics. The previously published studies on influencing the biosynthetic capabilities of Streptomyces through co-cultivation are comparatively analyzed in the bioprocess perspective, mainly with the focus on the approaches of co-culture initiation, the experimental setup, the design of experimental controls and the ways of influencing the outcomes of co-cultivation processes. These topics are discussed in the general context of secondary metabolites production in submerged microbial co-cultures by referring to the Streptomyces-related studies as illustrative examples.

Tapping Into Actinobacterial Genomes for Natural Product Discovery

The presence of secondary metabolite biosynthetic gene clusters (BGCs) makes actinobacteria well-known producers of diverse metabolites. These ubiquitous microbes are extensively exploited for their ability to synthesize diverse secondary metabolites. The extent of their ability to synthesize various molecules is yet to be evaluated. Current advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about the mechanism of synthesis of these bioactive molecules. Accessing the biosynthetic gene cluster responsible for the production of metabolites has always been a challenging assignment. The genomic approach developments have opened a new gateway for examining and manipulating novel antibiotic gene clusters. These advancements have now developed a better understanding of actinobacterial physiology and their genetic regulation for the prolific production of natural products. These new approaches provide a unique opportunity to discover novel bioactive compounds that might replenish antibiotics’ exhausted stock and counter the microbes’ resistance crisis.

Secondary metabolites and biodiversity of actinomycetes

BACKGROUND

The ability to produce microbial bioactive compounds makes actinobacteria one of the most explored microbes among prokaryotes. The secondary metabolites of actinobacteria are known for their role in various physiological, cellular, and biological processes.

MAIN BODY

Actinomycetes are widely distributed in natural ecosystem habitats such as soil, rhizosphere soil, actinmycorrhizal plants, hypersaline soil, limestone, freshwater, marine, sponges, volcanic cave-hot spot, desert, air, insects gut, earthworm castings, goat feces, and endophytic actinomycetes. The most important features of microbial bioactive compounds are that they have specific microbial producers: their diverse bioactivities and their unique chemical structures. Actinomycetes represent a source of biologically active secondary metabolites like antibiotics, biopesticide agents, plant growth hormones, antitumor compounds, antiviral agents, pharmacological compounds, pigments, enzymes, enzyme inhibitors, anti-inflammatory compounds, single-cell protein feed, and biosurfactant.

SHORT CONCLUSIONS

Further highlight that compounds derived from actinobacteria can be applied in a wide range of industrial applications in biomedicines and the ecological habitat is under-explored and yet to be investigated for unknown, rare actinomycetes diversity.

Ecosystem Functions of Microbial Consortia in Sustainable Agriculture

Knowledge of the agricultural soil microbiota, of the microbial consortia that comprise it, and the promotion of agricultural practices that maintain and encourage them, is a promising way to improve soil quality for sustainable agriculture and to provide food security. Although numerous studies have demonstrated the positive effects of beneficial soil microorganisms on crop yields and quality, the use of microbial consortia in agriculture remains low. Microbial consortia have more properties than an individual microbial inoculum, due to the synergy of the microorganisms that populate them. This review describes the main characteristics, ecosystem functions, crop benefits, and biotechnological applications of microbial consortia composed of arbuscular mycorrhizal fungi (AMF), plant growth-promoting rhizobacteria (PGPR), and Actinobacteria, to promote the restoration of agricultural soils and, consequently, the quality and health of agricultural crops. The aim is to provide knowledge that will contribute to the development of sustainable and sufficiently productive agriculture, which will adapt in a good way to the pace of the growing human population and to climate change.