Selective isolation and characterisation of novel members of the family Nocardiopsaceae and other actinobacteria from a marine sediment of Tioman Island

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.

Red Sea Atlas of Coral-Associated Bacteria Highlights Common Microbiome Members and Their Distribution across Environmental Gradients-A Systematic Review

The Red Sea is a suitable model for studying coral reefs under climate change due to its strong environmental gradient that provides a window into future global warming scenarios. For instance, corals in the southern Red Sea thrive at temperatures predicted to occur at the end of the century in other biogeographic regions. Corals in the Red Sea thrive under contrasting thermal and environmental regimes along their latitudinal gradient. Because microbial communities associated with corals contribute to host physiology, we conducted a systematic review of the known diversity of Red Sea coral-associated bacteria, considering geographic location and host species. Our assessment comprises 54 studies of 67 coral host species employing cultivation-dependent and cultivation-independent techniques. Most studies have been conducted in the central and northern Red Sea, while the southern and western regions remain largely unexplored. Our data also show that, despite the high diversity of corals in the Red Sea, the most studied corals were Pocillopora verrucosa, Dipsastraea spp., Pleuractis granulosa, and Stylophora pistillata. Microbial diversity was dominated by bacteria from the class Gammaproteobacteria, while the most frequently occurring bacterial families included Rhodobacteraceae and Vibrionaceae. We also identified bacterial families exclusively associated with each of the studied coral orders: Scleractinia (n = 125), Alcyonacea (n = 7), and Capitata (n = 2). This review encompasses 20 years of research in the Red Sea, providing a baseline compendium for coral-associated bacterial diversity.

Salt tolerance of halotolerant bacteria from coastal soils and sediments near saltern field of Hainan Island, China

Understanding the salt tolerance of microbial communities may help to elucidate the effects of salt concentration and other environmental factors on soil biodiversity. Here, high-throughput sequencing of 16S rDNA and ITS was combined to investigate the distribution and salt tolerance of microbial communities in coastal soils and sediments near the Yinggehai saltern field of Hainan Island, China. The microbial communities in the soils and sediments of the land zone (YGHLS), the intertidal zone (YGHIS), and the inshore zone (YGHWS) were compared. PCoA of weighted and unweighted UniFrac distance revealed obvious differences in soil microbial community among different samples. ANOSIM analysis could clearly separate the three samples from each other. Three halotolerant bacteria, including Halomonas, Halobacillus and Wallemia, were found in the samples, which accounted for 0.0335 ± 0.0586%, 0.0241 ± 0.0304%, and 0.0308 ± 0.0445% of the total microbial community, respectively. The relative abundance of Trk system potassium uptake protein, Kdp operon response regulator, and Na⁺/H⁺ antiporter in the samples exceeded 0.09%, 0.06%, and 0.02%, respectively, indicating that the Trk system plays a major role in the salt tolerance of halotolerant bacteria in Yinggehai coastal soils and sediments.

Actinobacteria in natural products research: Progress and prospects

Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.

Marinitenerispora sediminis gen. nov., sp. nov., a member of the family Nocardiopsaceae isolated from marine sediment

Three novel actinobacterial strains, designated as TPS16^T, TPS81 and TPS83, were isolated from a sample of marine sediment collected from Tioman Island, Malaysia. The strains formed abundant branched substrate mycelia without fragmentation along with production of blue spores and blue diffusible pigment on soybean meal agar. The strains could grow at pH ranging from pH 6 to 12 and in 0-8 % (w/v) NaCl. Cell-wall hydrolysis showed the presence of meso-diaminopimelic acid. The strains were closely related to Marinactinospora thermotolerans SCSIO 00652^T (97.60 %) and Marinactinospora endophytica YIM 690053^T (96.87 %) based on phylogenetic analysis of 16S rRNA gene sequences. Multilocus sequence analysis including gyrB, recA and rpoB genes further confirmed that strain TPS16^T represented a distinct branch within the family Nocardiopsaceae. The predominant menaquinones were MK-11(H₂), MK-10(H₂), MK-11(H₄) and MK-10(H₄), while the major fatty acids were found to be iso-C_16 : 0, anteiso-C_17 : 0, iso-C_15 : 0 and C_18 : 1ω9c. Genome sequencing revealed genome sizes of approximately 6 Mb and G+C contents of 73.8 mol%. A new genus, Marinitenerispora gen. nov., is proposed within the family Nocardiopsaceae based on polyphasic data and the type species is Marinitenerispora sediminis gen. nov., sp. nov. The type strain is TPS16^T (=DSM 46825^T=TBRC 5138^T).

Metabolomic Fingerprinting of Salinispora From Atlantic Oceanic Islands

Salinispora (Micromonosporaceae) is an obligate marine bacterium genus consisting of three species that share over 99% 16S rRNA identity. The genome and biosynthetic pathways of the members of this genus have been widely investigated due to their production of species-specific metabolites. However, despite the species’ high genetic similarity, site-specific secondary metabolic gene clusters have been found in Salinispora strains collected at different locations. Therefore, exploring the metabolic expression of Salinispora recovered from different sites may furnish insights into their environmental adaptation or their chemical communication and, further, may lead to the discovery of new natural products. We describe the first occurrence of Salinispora strains in sediments from the Saint Peter and Saint Paul Archipelago (a collection of islets in Brazil) in the Atlantic Ocean, and we investigate the metabolic profiles of these strains by employing mass-spectrometry-based metabolomic approaches, including molecular networking from the Global Natural Products Social Molecular Networking platform. Furthermore, we analyze data from Salinispora strains recovered from sediments from the Madeira Archipelago (Portugal, Macaronesia) in order to provide a wider metabolomic investigation of Salinispora strains from the Atlantic Oceanic islands. Overall, our study evidences a broader geographic influence on the secondary metabolism of Salinispora than was previously proposed. Still, some biosynthetic gene clusters, such as those corresponding to typical chemical signatures of S. arenicola, like saliniketals and rifamycins, are highly conserved among the assessed strains.