Bioprospecting from cultivable bacterial communities of marine sediment and invertebrates from the underexplored Ubatuba region of Brazil

Abstract

Shrimp fisheries along the Brazilian coast have significant environmental impact due to high by-catch rates (21 kg per kilogram of shrimp). Typically discarded, by-catch contains many invertebrates that may host a great variety of bacterial genera, some of which may produce bioactive natural products with biotechnological applications. Therefore, to utilize by-catch that is usually discarded we explored the biotechnological potential of culturable bacteria of two abundant by-catch invertebrate species, the snail Olivancillaria urceus and the sea star Luidia senegalensis. Sediment from the collection area was also investigated. Utilizing multiple isolation approaches, 134 isolates were obtained from the invertebrates and sediment. Small-subunit rRNA (16S) gene sequencing revealed that the isolates belonged to Proteobacteria, Firmicutes and Actinobacteria phyla and were distributed among 28 genera. Several genera known for their capacity to produce bioactive natural products (Micromonospora, Streptomyces, Serinicoccus and Verrucosispora) were retrieved from the invertebrate samples. To query the bacterial isolates for their ability to produce bioactive metabolites, all strains were fermented and fermentation extracts profiled by UP LC-HRMS and tested for antimicrobial activity. Four strains exhibited antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus warneri.

Biotechnological Potential of Bacteria Isolated from the Sea Cucumber Holothuria leucospilota and Stichopus vastus from Lampung, Indonesia

“…A detailed compilation of all isolated bacterial strains from HL and SV are shown in Table S1. Our results of the identified phyla are in line with previous studies that attempted to isolate cultivable bacteria from marine macroorganisms and environments [30,31,32]. However, as determined by next generation sequencing studies, the cultivable bacteria still only represent about 1% of the estimated microbial diversity [33].…”

“…Several media were prepared including Marine Agar 100% (MA, made from Marine Broth (MB, Carl Roth, Karlsruhe, Germany) according to manufacturer’s instruction with addition of 9 g/L agar (Agar-agar Bacteriological, Carl Roth, Karlsruhe, Germany)), Marine Agar 10% (MA2, was made by a 10-fold dilution of MA with distilled water) and M1 media (1.8% agar, 1% starch, 0.4% yeast extract, 0.2% peptone and filtered seawater). We choose the rich nutrient media MA and M1 for the isolation as it was used in the previous publications [30,31,68]. While the lower nutrient MA2 media was provided to allow slow growing bacteria more time to form colonies before the agar plates were eventually covered by fast growing bacteria like in the MA media.…”

Insights into the Variation in Bioactivities of Closely Related Streptomyces Strains from Marine Sediments of the Visayan Sea against ESKAPE and Ovarian Cancer

“…Actinomycetes dwell in terrestrial soil, but evidence indicates that they are common in the marine ecosystem [ 17 , 18 , 37 , 38 , 39 ]. The strategy of using marine microorganisms as a source of new therapeutic agents is not unfeasible as it has been the focus of many recent investigations in other countries [ 5 , 13 , 20 , 40 , 41 , 42 , 43 , 44 , 45 ] and has led to the discovery of bioactive compounds with unique chemical entities. These include antitubercular sporalactam A and B [ 46 ] and dumulmycin [ 47 ], anticancer nahuoic acids [ 48 , 49 ] and kenalactams [ 50 ], and antibiotics bisanhydroaklavinone and 1-hydroxyaklavinone [ 11 ].…”

Marine Actinomycetes, New Sources of Biotechnological Products

“…Preventing adhesion also hinders biofilms, which are virulence factors in conditions such as pneumonia caused by P. aeruginosa [ 221 , 222 ]. In a study that used bycatch discards to isolate bioactive compounds from invertebrates and sediment, the researchers were able to use small subunit rRNA sequencing to obtain isolates (including Actinomycetales members such as Streptomyces ) that exhibited activity against MRSA as well as Staphylococcus warneri [ 223 ]. Sponges and other invertebrates may be viable sources for the continued isolation of novel marine actinomycete species (including marine mycobacteria) and products [ 224 ].…”