Análise da diversidade taxonômica e funcional da microbiota presente no sedimento marinho da praia de Lucena-PB através da abordagem metagenômica e cultivo convencional

Abstract

Marine bacteria may represent an important source of bioactive compounds and antimicrobials. The objective of this work was to prospect microorganisms from the marine sediment using the 16S rRNA gene as a phylogenetic marker, and to cultivate polyketide-producing bacterial strains. Expeditions were conducted at Praia de Lucena, located in the metropolitan region of João Pessoa, State of Paraíba, Brazil. A Van Veen dredge was used for collection of samples of marine sediment (n = 21) at depth of 10 meters from December/ 2016 to September/ 2017. Extraction of metagenomic DNA was carried out with 0.25 grams of each sample. The SC-Act-235-aS-20 and S-CAct-878-aA19 primers were used to amplify the regions between V3 to V5 of the 16S rRNA gene by PCR. After construction of the 16S rRNA library, the data analysis after sequencing was performed using One Codex platform. Shotgun sequencing was carried out through the MiSeq System. Alpha and beta diversity were determined using the q2- diversity plugin in QIIME2 at a sampling depth of 6,060. Paired-end DNA sequencing 34 reads were assembled into metagenomes and compared with different database. One sample of marine sediment was selected for bacterial culture in laboratory. Gas chromatography-mass spectrometry was used for identification of compounds of polyketide class. The results showed greater abundance of the phyla Actinobacteria, Planctomycetes and Proteobacteria in the samples, including genera of bacteria associated with production of bioactives, such as: Nocardioides, Streptomyces, Blastopirellula and, Myxococcus. In silico analyses revealed genes involved in two metabolism pathways in the genus Streptomyces: 1) terpenoids, polyketides and carotenoids; and 2) other secondary metabolites, including stilbene. In addition, we found 179 antibiotic-resistant genes associated to 17 antibiotic classes from other bacteria in marine sediment. Four polyketide-producing Pseudomonas spp. were identified. The mass spectra obtained from fermented extracts leaded to identification of a polyketide metabolic precursor: Orselinic acid; and four chemical compounds of the polyketide class: 4-tert-Butylphenol, Triacetic acid lactone, 5,7-Dihydroxy-2-ethylchromone, Phylloquinone. We conclude that cultivation of marine Actinobacteria from the genus Streptomyces can lead to production of novel broad-spectrum antimicrobials. However, attention should be paid to marine bacteria that carry antibiotic resistance genes to hospital-restricted drugs and marine Pseudomonas strains represent a rich source of polyketides of pharmaceutical interest.