Lekha Menon Margassery

Diversity and antimicrobial activities of microbes from two Irish marine sponges, Suberites carnosus and Leucosolenia sp.

Aims:  To evaluate the diversity and antimicrobial activity of bacteria from the marine sponges Suberites carnosus and Leucosolenia sp.

Diversity and antibacterial activity of bacteria isolated from the coastal marine sponges Amphilectus fucorum and Eurypon major

Aims:  To assess the diversity and antimicrobial activity of culturable bacteria associated with two temperate‐water marine sponges, Amphilectus fucorum and Eurypon major.

Metabolomic Profiling and Genomic Study of a Marine Sponge-Associated Streptomyces sp.

Metabolomics and genomics are two complementary platforms for analyzing an organism as they provide information on the phenotype and genotype, respectively. These two techniques were applied in the dereplication and identification of bioactive compounds from a Streptomyces sp. (SM8) isolated from the sponge Haliclona simulans from Irish waters. Streptomyces strain SM8 extracts showed antibacterial and antifungal activity. NMR analysis of the active fractions proved that hydroxylated saturated fatty acids were the major components present in the antibacterial fractions. Antimycin compounds were initially putatively identified in the antifungal fractions using LC-Orbitrap. Their presence was later confirmed by comparison to a standard. Genomic analysis of Streptomyces sp. SM8 revealed the presence of multiple secondary metabolism gene clusters, including a gene cluster for the biosynthesis of the antifungal antimycin family of compounds. The antimycin gene cluster of Streptomyces sp. SM8 was inactivated by disruption of the antimycin biosynthesis gene antC. Extracts from this mutant strain showed loss of antimycin production and significantly less antifungal activity than the wild-type strain. Three butenolides, 4,10-dihydroxy-10-methyl-dodec-2-en-1,4-olide (1), 4,11-dihydroxy-10-methyl-dodec-2-en-1,4-olide (2), and 4-hydroxy-10-methyl-11-oxo-dodec-2-en-1,4-olide (3) that had previously been reported from marine Streptomyces species were also isolated from SM8. Comparison of the extracts of Streptomyces strain SM8 and its host sponge, H. simulans, using LC-Orbitrap revealed the presence of metabolites common to both extracts, providing direct evidence linking sponge metabolites to a specific microbial symbiont.

Aquimarina amphilecti sp. nov., isolated from the sponge Amphilectus fucorum

A Gram-stain-negative, rod-shaped, orange-coloured, catalase- and oxidase-positive, non-motile bacterium, designated strain 92V(T), was isolated from the marine sponge Amphilectus fucorum, collected from Lough Hyne, County Cork, Ireland. 16S rRNA gene sequence analysis revealed that strain 92V(T) clustered with members of the family Flavobacteriaceae, the closest member being Aquimarina latercula NCIMB 1399(T), with a gene sequence similarity of 97.5%. Strain 92V(T) required seawater for growth with optimal growth occurring at 25 °C, at pH 6-7 and with 3% (w/v) NaCl. MK-6 was the sole respiratory quinone present and the major fatty acids were iso-C(17 : 0) 3-OH, iso-C(15 : 0), iso-C(17 : 1)ω9c and iso-C(15 : 0) 3-OH. The DNA G+C content was 36.1 mol%. Combined phenotypic differences and phylogenetic analysis indicate that strain 92V(T) represents a novel species of the genus Aquimarina, for which the name Aquimarina amphilecti sp. nov. is proposed. The type strain is 92V(T) ( = NCIMB 14723(T) = DSM 25232(T)).

Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates

The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches. We have sequenced the genomes of 13 Streptomyces spp. strains isolated from shallow water and deep-sea sponges that display antimicrobial activities against a number of clinically relevant bacterial and yeast species. Draft genomes have been assembled and smBGCs have been identified using the antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) web platform. We have compared the smBGCs amongst strains in the search for novel sequences conferring the potential to produce novel bioactive secondary metabolites. The strains in this study recruit to four distinct clades within the genus Streptomyces. The marine strains host abundant smBGCs which encode polyketides, NRPS, siderophores, bacteriocins and lantipeptides. The deep-sea strains appear to be enriched with gene clusters encoding NRPS. Marine adaptations are evident in the sponge-derived strains which are enriched for genes involved in the biosynthesis and transport of compatible solutes and for heat-shock proteins. Streptomyces spp. from marine environments are a promising source of novel bioactive secondary metabolites as the abundance and diversity of smBGCs show high degrees of novelty. Sponge derived Streptomyces spp. isolates appear to display genomic adaptations to marine living when compared to terrestrial strains.

A high-throughput screen to identify novel calcineurin inhibitors

Calcineurin is a eukaryotic protein phosphatase important for many signalling and developmental processes in cells. Inhibitors of this enzyme are used clinically and there is interest in identifying novel inhibitors for therapeutic applications. This report describes a high-throughput assay that can be used to screen natural or chemical libraries of compounds to identify new calcineurin inhibitors. The microtitre plate assay is based on a yeast reporter strain and was validated with known inhibitors and tested in a pilot screen of bacterial extracts.

Marine Sponges – Molecular Biology and Biotechnology

Marine sponges are an ancient and diverse animal phylum that host well-established symbiotic microbial communities. The vast majority of the microbial genetic diversity in sponges is, however, currently inaccessible by traditional methods. This large genetic resource may be of use for biotechnological applications, particularly as the physicochemical parameters under which the genes within these microbes function are likely to dictate that they may be significantly different from similar genes or gene products currently in use in industry, offering in some instances improved performance. Emerging tools and technologies in the field of metagenomics offer enormous potential for the discovery and exploitation of new biosynthetic entities. Both sequence-based and function-based technologies have to date been employed to identify genes with novel or improved functions. Marine sponges, as well-recognized sources of novel marine natural products with varied applications, are the ideal target for the implementation of these new technologies. We detail here some successes in the discovery and development of marine natural products for industrial or pharmaceutical applications and we also highlight some technical impediments to gene and gene product exploitation which as yet still need to be overcome.

Metagenomic strategies for the discovery of novel enzymes with biotechnological application from marine ecosystems

: As a consequence of its geochemical and geophysical variability, the marine environment, which is dominated by microorganisms and their viruses, also possesses the greatest diversity of biological life on the planet. The habitats of these microbes range from the harshest of environments in the deep ocean to intimate symbiotic associations with other marine organisms. This ecological diversity leads, in turn, to metabolic diversity and it is now accepted that marine microbes contain a vast reservoir of novel enzymes and metabolites that can be of benefit to society. The challenge is in accessing, exploring, and ultimately exploiting this potential reservoir. A major obstacle to date has been the limited capacity to culture marine microbes but genomic and metagenomic technologies now offer promising new strategies for marine biodiscovery. In this chapter, the different sequence and function-based approaches that can be taken are described and assessed. There have been some modest successes in identifying new enzymes but significant hurdles remain. This is, however, a field in its infancy and one which is moving rapidly. It is likely, however, that on-going and future development of new methodologies for screening and expressing marine bacterial genes is likely to yield many new enzymes with novel properties.

Draft Genome Sequence of the Antimycin-Producing Bacterium Streptomyces sp. Strain SM8, Isolated from the Marine Sponge Haliclona simulans

ABSTRACT Streptomyces sp. strain SM8, isolated from Haliclona simulans, possesses antifungal and antibacterial activities and inhibits the calcineurin pathway in yeast. The draft genome sequence is 7,145,211 bp, containing 5,929 predicted coding sequences. Several secondary metabolite biosynthetic gene clusters are present, encoding known and novel metabolites, including antimycin.

Draft Genome Sequence of Pseudomonas putida CA-3, a Bacterium Capable of Styrene Degradation and Medium-Chain-Length Polyhydroxyalkanoate Synthesis

ABSTRACT Pseudomonas putida strain CA-3 is an industrial bioreactor isolate capable of synthesizing biodegradable polyhydroxyalkanoate polymers via the metabolism of styrene and other unrelated carbon sources. The pathways involved are subject to regulation by global cellular processes. The draft genome sequence is 6,177,154 bp long and contains 5,608 predicted coding sequences.