Biosynthetic gene clusters with biotechnological applications in novel Antarctic isolates from Actinomycetota

Actinomycetota have been widely described as valuable sources for the acquisition of secondary metabolites. Most microbial metabolites are produced via metabolic pathways encoded by biosynthetic gene clusters (BGCs). Although many secondary metabolites are not essential for the survival of bacteria, they play an important role in their adaptation and interactions within microbial communities. This is how bacteria isolated from extreme environments such as Antarctica could facilitate the discovery of new BGCs with biotechnological potential. This study aimed to isolate rare Actinomycetota strains from Antarctic soil and sediment samples and identify their metabolic potential based on genome mining and exploration of biosynthetic gene clusters. To this end, the strains were sequenced using Illumina and Oxford Nanopore Technologies platforms. The assemblies were annotated and subjected to phylogenetic analysis. Finally, the BGCs present in each genome were identified using the antiSMASH tool, and the biosynthetic diversity of the Micrococcaceae family was evaluated. Taxonomic annotation revealed that seven strains were new and two were previously reported in the NCBI database. Additionally, BGCs encoding type III polyketide synthases (T3PKS), beta-lactones, siderophores, and non-ribosomal peptide synthetases (NRPS) have been identified, among others. In addition, the sequence similarity network showed a predominant type of BGCs in the family Micrococcaceae, and some genera were distinctly grouped. The BGCs identified in the isolated strains could be associated with applications such as antimicrobials, anticancer agents, and plant growth promoters, among others, positioning them as excellent candidates for future biotechnological applications and innovations. KEY POINTS: • Novel Antarctic rare Actinomycetota strains were isolated from soil and sediments • Genome-based taxonomic affiliation revealed seven potentially novel species • Genome mining showed metabolic potential for novel natural products.

Marine Actinomycetes Associated with Stony Corals: A Potential Hotspot for Specialized Metabolites

Microbial secondary metabolites are an important source of antibiotics currently available for combating drug-resistant pathogens. These important secondary metabolites are produced by various microorganisms, including Actinobacteria. Actinobacteria have a colossal genome with a wide array of genes that code for several bioactive metabolites and enzymes. Numerous studies have reported the isolation and screening of millions of strains of actinomycetes from various habitats for specialized metabolites worldwide. Looking at the extent of the importance of actinomycetes in various fields, corals are highlighted as a potential hotspot for untapped secondary metabolites and new bioactive metabolites. Unfortunately, knowledge about the diversity, distribution and biochemistry of marine actinomycetes compared to hard corals is limited. In this review, we aim to summarize the recent knowledge on the isolation, diversity, distribution and discovery of natural compounds from marine actinomycetes associated with hard corals. A total of 11 new species of actinomycetes, representing nine different families of actinomycetes, were recovered from hard corals during the period from 2007 to 2022. In addition, this study examined a total of 13 new compounds produced by five genera of actinomycetes reported from 2017 to 2022 with antibacterial, antifungal and cytotoxic activities. Coral-derived actinomycetes have different mechanisms of action against their competitors.

Susceptibility pattern of methicillin resistance Staphylococcus aureus (MRSA) by flow cytometry analysis and characterization of novel lead drug molecule from Streptomyces species

BACKGROUND

Actinomycetes particularly, Streptomyces species are producing wide variety of natural products with potential bioactivities. The microbial-derived metabolites hold a strong position to combat emerging and re-emerging antimicrobial drug-resistant pathogens.

OBJECTIVES

A diverse group of actinomycetes strains were isolated from unexplored regions of mangrove sediment. Further, a polyphasic approach based on 16S rRNA gene sequence analysis and to evaluate their antibacterial potential against a panel of bacterial pathogens and methicillin resistance Staphylococcus aureus (MRSA).

METHODS

The mangrove sediment samples were serially diluted with sterile water and plated on inorganic starch agar medium. A total of 20 isolates were pure cultured and 16S rRNA gene sequences were deposited in the public nucleotide databases (GenBank, NCBI). All the isolates were screened for the antibacterial activity by agar overlay method. Further, the susceptibility pattern of MRSA by flow cytometry and fluorescence microscopy was analysed.

RESULTS

These twenty different isolates were grouped under nine major clad and they shared 95-99% sequence identity to the 16S rRNA gene sequences of the genus Streptomyces in the public nucleotide databases. Among these strains, the isolates namely JRG-02, JRG-03, JRG-04, JRG-10 and JRG-12 exhibited a broad-spectrum antibacterial activity against Methicillin-resistant Staphylococcus aureus(MRSA) and Gram negative bacteria Klebsiella pneumoniae MTCC109. Furthermore, we have characterized the antibacterial compound production and its properties from the isolate JRG-02, a potential drug candidate. The culture conditions and various nutrient components of strain Streptomyces sp. JRG-02 were optimized for enhanced antibiotics production of the isolate. The FT-IR and LCMS spectrum analysis envisaged the chemical nature of the substance. The effect of antibacterial compound on the viability of MRSA was alone examined by flow cytometry (FACS) and fluorescence microscopy analysis.

CONCLUSIONS

The present study clearly shows that the survival of diverse inhabitants of Streptomyces in the mangrove sediments. Hence, the mangrove sediment inhabiting strain Streptomyces sp. JRG-02 has potential pharmaceutical activity and genetic diversity.

Marine Actinomycetes, New Sources of Biotechnological Products

The Actinomycetales order is one of great genetic and functional diversity, including diversity in the production of secondary metabolites which have uses in medical, environmental rehabilitation, and industrial applications. Secondary metabolites produced by actinomycete species are an abundant source of antibiotics, antitumor agents, anthelmintics, and antifungals. These actinomycete-derived medicines are in circulation as current treatments, but actinomycetes are also being explored as potential sources of new compounds to combat multidrug resistance in pathogenic bacteria. Actinomycetes as a potential to solve environmental concerns is another area of recent investigation, particularly their utility in the bioremediation of pesticides, toxic metals, radioactive wastes, and biofouling. Other applications include biofuels, detergents, and food preservatives/additives. Exploring other unique properties of actinomycetes will allow for a deeper understanding of this interesting taxonomic group. Combined with genetic engineering, microbial experimental evolution, and other enhancement techniques, it is reasonable to assume that the use of marine actinomycetes will continue to increase. Novel products will begin to be developed for diverse applied research purposes, including zymology and enology. This paper outlines the current knowledge of actinomycete usage in applied research, focusing on marine isolates and providing direction for future research.

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.