Isolation, phylogenetic analysis and anti-infective activity screening of marine sponge-associated actinomycetes

Abstract

Terrestrial actinomycetes are noteworthy producers of a multitude of antibiotics, however the marine representatives are much less studied in this regard. In this study, 90 actinomycetes were isolated from 11 different species of marine sponges that had been collected from offshore Ras Mohamed (Egypt) and from Rovinj (Croatia). Phylogenetic characterization of the isolates based on 16S rRNA gene sequencing supported their assignment to 18 different actinomycete genera representing seven different suborders. Fourteen putatively novel species were identified based on sequence similarity values below 98.2% to other strains in the NCBI database. A putative new genus related to Rubrobacter was isolated on M1 agar that had been amended with sponge extract, thus highlighting the need for innovative cultivation protocols. Testing for anti-infective activities was performed against clinically relevant, Gram-positive (Enterococcus faecalis, Staphylococcus aureus) and Gram-negative (Escherichia coli, Pseudomonas aeruginosa) bacteria, fungi (Candida albicans) and human parasites (Leishmania major, Trypanosoma brucei). Bioactivities against these pathogens were documented for 10 actinomycete isolates. These results show a high diversity of actinomycetes associated with marine sponges as well as highlight their potential to produce anti-infective agents.

Keywords: actinomycetes; anti-infective; anti-parasitic; marine sponges; phylogenetic analysis.

Figure 1

Number of actinomycete isolates (A) per sponge species, (B) per actinomycete genera and (C) per cultivation media.

Figure 1

Number of actinomycete isolates (A) per sponge species, (B) per actinomycete genera and (C) per cultivation media.

Figure 2

Neighbor-joining tree of the strains and representative species of the suborder Micrococcineae based on nearly complete 16S rRNA gene sequences. Numbers at the nodes indicate the levels of bootstrap support based on 1000 resampled data sets. Only values greater than 50% are shown. The arrow points to the outgroup consisting of five species belonging to Enterobacteriaceae. The scale bar indicates 0.01 substitution per nucleotide position.

Figure 3

Neighbor-joining tree of the strains and representative species of the suborders Corynebacterineae, Pseudonocardineae, Streptomycineae and Rubrobacterineae based on nearly complete 16S rRNA gene sequences. Numbers at the nodes indicate the levels of bootstrap support based on 1000 resampled data sets. Only values greater than 50% are shown. The arrow points to the outgroup consisting of five species belonging to Enterobacteriaceae. The scale bar indicates 0.01 substitution per nucleotide position.