Publications

  • Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) species

    Sandra G. Silva, Jochen Blom, Tina Keller-Costa and Rodrigo Costa

     

    This study determines the natural product biosynthesis and full coding potential within the bacterial genus Aquimarina. Using comprehensive phylogenomics and functional genomics, we reveal that phylogeny instead of isolation source [host-associated (HA) vs. free-living (FL) habitats] primarily shape the inferred metabolism of Aquimarina species. These can be coherently organized into three major functional clusters, each presenting distinct natural product biosynthesis profiles suggesting that evolutionary trajectories strongly underpin their secondary metabolite repertoire and presumed bioactivities. Aquimarina spp. are highly versatile bacteria equipped to colonize HA and FL microniches, eventually displaying opportunistic behaviour, owing to their shared ability to produce multiple glycoside hydrolases from diverse families. We furthermore uncover previously underestimated, and highly complex secondary metabolism for the genus by detecting 928 biosynthetic gene clusters (BGCs) across all genomes, grouped in 439 BGC families, with polyketide synthases (PKSs), terpene synthases and non-ribosomal peptide synthetases (NRPSs) ranking as the most frequent BGCs encoding drug-like candidates. We demonstrate that the recently described cuniculene (trans-AT PKS) BGC is conserved among, and specific to, the here delineated A. megaterium-macrocephali-atlantica phylogenomic clade. Our findings provide a timely and in-depth perspective of an under-explored yet emerging keystone taxon in the cycling of organic matter and secondary metabolite production in marine ecosystems.

     

    https://doi.org/10.1111/1462-2920.14747

  • Endozoicomonas lisbonensis sp. nov., a novel marine bacterium isolated from the soft coral Litophyton sp. at Oceanário de Lisboa in Portugal

    Daniela M. G. da Silva, Matilde Marques, Joana F. Couceiro, Elsa Santos, Núria Baylina, Rodrigo Costa and Tina Keller-Costa

     

    This study describes a Gram-stain-negative, rod-shaped, facultatively anaerobic bacterial species isolated from the octocoral Litophyton sp. inhabiting the live coral aquarium at Oceanário de Lisboa in Portugal. Four strains, NE35, NE40T, NE41 and NE43, were classified into the genus Endozoicomonas by means of 16S rRNA gene and whole-genome sequence homologies. We then performed phylogenetic, phylogenomic and biochemical analyses to examine their novel species status within the Endozoicomonas genus, based on comparisons with the designated novel type strain NE40T. The closest 16S rRNA gene relatives to strain NE40T are Endozoicomonas montiporae CL-33T (98.2%), Endozoicomonas euniceicola EF212T (97.6%) and Endozoicomonas gorgoniicola PS125T (97.2%). The four strains show genome-wide average nucleotide identity scores above the species level cut-off (95%) with one another and below the cut-off with all Endozoicomonas type strains with publicly available genomes. Digital DNA–DNA hybridization further supported the classification of the strains as a novel species, showing values below 70% when compared with other Endozoicomonas type strains. The DNA G+C content of NE40T was 49.0 mol%, and its genome size was 5.45 Mb. Strain NE40T grows from 15 to 37 °C, with 1–5% (w/v) NaCl, and between pH 6.0 and 8.0 in marine broth and shows optimal growth at 28–32 °C, 2–3% NaCl and pH 7.0–8.0. The predominant cellular fatty acids are summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c), C16 :0 and C14 :0. Strain NE40T presents oxidase, catalase and β-galactosidase activities and can reduce nitrates to nitrites and degrade cellulose, chitin, agarose and xylan. Based on the polyphasic approach employed in this study, we propose the novel species name Endozoicomonas lisbonensis sp. nov. (type strain NE40T=DSM 118084T=UCCCB 212T).

     

    https://doi.org/10.1099/ijsem.0.006696

  • Aquimarina aquimarini sp. nov. and Aquimarina spinulae sp. nov., novel bacterial species with versatile natural product biosynthesis potential isolated from marine sponges

    Joana F. Couceiro​, Matilde Marques, Sandra G. Silva​, Tina Keller-Costa​ and Rodrigo Costa

     

    This study describes two Gram-negative, flexirubin-producing, biofilm-forming, motile-by-gliding and rod-shaped bacteria, isolated from the marine sponges Ircinia variabilis and Sarcotragus spinosulus collected off the coast of Algarve, Portugal. Both strains, designated Aq135T and Aq349T, were classified into the genus Aquimarina by means of 16S rRNA gene sequencing. We then performed phylogenetic, phylogenomic and biochemical analyses to determine whether these strains represent novel Aquimarina species. Whereas the closest 16S rRNA gene relatives to strain Aq135T were Aquimarina macrocephali JAMB N27T (97.8 %) and Aquimarina sediminis w01T (97.1 %), strain Aq349T was more closely related to Aquimarina megaterium XH134T (99.2 %) and Aquimarina atlantica 22II-S11-z7T (98.1 %). Both strains showed genome-wide average nucleotide identity scores below the species level cut-off (95 %) with all Aquimarina type strains with publicly available genomes, including their closest relatives. Digital DNA–DNA hybridization further suggested a novel species status for both strains since values lower than 70 % hybridization level with other Aquimarina type strains were obtained. Strains Aq135T and Aq349T grew from 4 to 30°C and with between 1–5 % (w/v) NaCl in marine broth. The most abundant fatty acids were iso-C17 : 03-OH and iso-C15 : 0 and the only respiratory quinone was MK-6. Strain Aq135T was catalase-positive and β-galactosidase-negative, while Aq349T was catalase-negative and β-galactosidase-positive. These strains hold unique sets of secondary metabolite biosynthetic gene clusters and are known to produce the peptide antibiotics aquimarins (Aq135T) and the trans-AT polyketide cuniculene (Aq349T), respectively. Based on the polyphasic approach employed in this study, we propose the novel species names Aquimarina aquimarini sp. nov. (type strain Aq135T=DSM 115833T=UCCCB 169T=ATCC TSD-360T) and Aquimarina spinulae sp. nov. (type strain Aq349T=DSM 115834T=UCCCB 170T=ATCC TSD-361T).

     

    https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.006228

  • Marine Sponge and Octocoral-Associated Bacteria Show Versatile Secondary Metabolite Biosynthesis Potential and Antimicrobial Activities against Human Pathogens

    João F. Almeida, Matilde Marques, Vanessa Oliveira, Conceição Egas, Dalila Mil-Homens, Romeu Viana, Daniel F. R. Cleary, Yusheng M. Huang, Arsénio M. Fialho, Miguel C. Teixeira, Newton C. M. Gomes, Rodrigo Costa andTina Keller-Costa

     

    Marine microbiomes are prolific sources of bioactive natural products of potential pharmaceutical value. This study inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several thus-far unclassified lineages to identify isolates with potentially rich secondary metabolism and antimicrobial activities. Seventy representative isolates had their genomes mined for secondary metabolite biosynthetic gene clusters (SM-BGCs) and were screened for antimicrobial activities against four pathogenic bacteria and five pathogenic Candida strains. In total, 466 SM-BGCs were identified, with antimicrobial peptide- and polyketide synthase-related SM-BGCs being frequently detected. Only 38 SM-BGCs had similarities greater than 70% to SM-BGCs encoding known compounds, highlighting the potential biosynthetic novelty encoded by these genomes. Cross-streak assays showed that 33 of the 70 genome-sequenced isolates were active against at least one Candida species, while 44 isolates showed activity against at least one bacterial pathogen. Taxon-specific differences in antimicrobial activity among isolates suggested distinct molecules involved in antagonism against bacterial versus Candida pathogens. The here reported culture collections and genome-sequenced isolates constitute a valuable resource of understudied marine bacteria displaying antimicrobial activities and potential for the biosynthesis of novel secondary metabolites, holding promise for a future sustainable production of marine drug leads.

     

    https://doi.org/10.3390/md21010034