Browsing by Author "Costa, Rodrigo"
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- Assessing the genomic composition, putative ecological relevance and biotechnological potential of plasmids from sponge bacterial symbiontsPublication . Oliveira, Vanessa; Polónia, Ana R. M.; Cleary, Daniel F. R.; Huang, Yusheng M.; de Voogd, Nicole J.; Keller-Costa, Tina; Costa, Rodrigo; Gomes, Newton C. M.Plasmid-mediated transfer of genes can have direct consequences in several biological processes within sponge microbial communities. However, very few studies have attempted genomic and functional characterization of plasmids from marine host-associated microbial communities in general and those of sponges in particular. In the present study, we used an endogenous plasmid isolation method to obtain plasmids from bacterial symbionts of the marine sponges Stylissa carteri and Paratetilla sp. and investigated the genomic composition, putative ecological relevance and biotechnological potential of these plasmids. In total, we isolated and characterized three complete plasmids, three plasmid prophages and one incomplete plasmid. Our results highlight the importance of plasmids to transfer relevant genetic traits putatively involved in microbial symbiont adaptation and host-microbe and microbe-microbe interactions. For example, putative genes involved in bacterial response to chemical stress, competition, metabolic versatility and mediation of bacterial colonization and pathogenicity were detected. Genes coding for enzymes and toxins of biotechnological potential were also detected. Most plasmid prophage coding sequences were, however, hypothetical proteins with unknown functions. Overall, this study highlights the ecological relevance of plasmids in the marine sponge microbiome and provides evidence that plasmids of sponge bacterial symbionts may represent an untapped resource of genes of biotechnological interest.
- Cloning, characterization, in vitro and in planta expression of a necrosis-inducing Phytophthora protein 1 gene npp1 from Phytophthora cinnamomiPublication . Martins, Ivone M.; Meirinho, Sofia; Costa, Rodrigo; Cravador, Alfredo; Choupina, AltinoThe soil-borne oomycete Phytophthora cinnamomi is a highly destructive Phytophthora species associated with the decline of forest. This pathogen secretes a novel class of necrosis-inducing proteins known as Nep1-like proteins (NLPs). In this work, we report the sequencing and molecular characterization of one of these proteins, more specifically the necrosis-inducing Phytophthora protein 1 (NPP1). The ORF of the npp1 gene (EMBL database AM403130) has 768 bp encoding a putative peptide of 256 amino acids with a molecular weight of approximately 25 kD. In order to understand its function, in vitro gene expression was studied during growth in different carbon sources (glucose, cellulose, and sawdust), and at different times of infection, in vivo by RT-qPCR. The highest expression of the npp1 gene occurred in glucose medium followed by sawdust. In vivo infection of Castanea sativa roots with P. cinnamomi revealed a decrease in npp1 expression from 12 to 24 h; at 36 h its expression increased suggesting the existence of a complex mechanism of defense/attack interaction between the pathogen and the host. Expression of recombinant npp1 gene was achieved in Pichia pastoris and assessed by SDS-PAGE analysis of the protein secreted into the culture supernatant, revealing the presence of the NPP1 protein.
- Clostridia Initiate Heavy Metal Bioremoval in Mixed Sulfidogenic CulturesPublication . Alexandrino, Maria; Costa, Rodrigo; Canario, Adelino V. M.; Costa, Maria ClaraSulfate reducing bacteria (SRB) are widely used for attenuating heavy metal pollution by means of sulfide generation. Due to their low metal tolerance, several SRB species depend on associated bacteria in mixed cultures to cope with metal-induced stress. Yet the identity of the SRB protecting bacteria is largely unknown. We aimed to identify these associated bacteria and their potential role in two highly metal-resistant mixed SRB cultures by comparing bacterial community composition and SRB activity between these cultures and two sensitive ones. The SRB composition in the resistant and sensitive consortia was similar. However, whereas the SRB in the sensitive cultures were strongly inhibited by a mixture of copper, zinc, and iron, no influence of these metals was detected on SRB growth and activity in the resistant cultures. In the latter, a Gram-positive population mostly assigned to Clostridium spp.initiated heavy metal bioremoval based on sulfide generation from components of the medium (mainly sulfite) but not from sulfate. After metal levels were lowered by the Clostridium spp. populations, SRB started sulfate reduction and raised the pH of the medium. The combination of sulfite reducing Clostridium spp. with SRB may improve green technologies for removal of heavy metals.
- Comparative genomics reveals complex natural product biosynthesis capacities and carbon metabolism across host-associated and free-living Aquimarina (Bacteroidetes, Flavobacteriaceae) speciesPublication . Silva, Sandra G.; Blom, Jochen; Keller-Costa, Tina; Costa, RodrigoThis 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.
- Comparative metagenomics reveals the distinctive adaptive features of the Spongia officinalis endosymbiotic consortiumPublication . Karimi, Elham; Ramos, Miguel; Gonçalves, Jorge Manuel Santos; Xavier, Joana R.; Reis, Margarida; Costa, RodrigoCurrent knowledge of sponge microbiome functioning derives mostly from comparative analyses with bacterioplankton communities. We employed a metagenomics-centered approach to unveil the distinct features of the Spongia officinalis endosymbiotic consortium in the context of its two primary environmental vicinities. Microbial metagenomic DNA samples (n = 10) from sponges, seawater, and sediments were subjected to Hiseq Illumina sequencing (c. 15 million 100 bp reads per sample). Totals of 10,272 InterPro (IPR) predicted protein entries and 784 rRNA gene operational taxonomic units (OTUs, 97% cut-off) were uncovered from all metagenomes. Despite the large divergence in microbial community assembly between the surveyed biotopes, the S. officinalis symbiotic community shared slightly greater similarity (p < 0.05), in terms of both taxonomy and function, to sediment than to seawater communities. The vast majority of the dominant S. officinalis symbionts (i.e., OTUs), representing several, so-far uncultivable lineages in diverse bacterial phyla, displayed higher residual abundances in sediments than in seawater. CRISPR-Cas proteins and restriction endonucleases presented much higher frequencies (accompanied by lower viral abundances) in sponges than in the environment. However, several genomic features sharply enriched in the sponge specimens, including eukaryotic-like repeat motifs (ankyrins, tetratricopeptides, WD-40, and leucine-rich repeats), and genes encoding for plasmids, sulfatases, polyketide synthases, type IV secretion proteins, and terpene/terpenoid synthases presented, to varying degrees, higher frequencies in sediments than in seawater. In contrast, much higher abundances of motility and chemotaxis genes were found in sediments and seawater than in sponges. Higher cell and surface densities, sponge cell shedding and particle uptake, and putative chemical signaling processes favoring symbiont persistence in particulate matrices all may act as mechanisms underlying the observed degrees of taxonomic connectivity and functional convergence between sponges and sediments. The reduced frequency of motility and chemotaxis genes in the sponge microbiome reinforces the notion of a prevalent mutualistic mode of living inside the host. This study highlights the S. officinalis "endosymbiome" as a distinct consortium of uncultured prokaryotes displaying a likely "sit-and-wait" strategy to nutrient foraging coupled to sophisticated anti-viral defenses, unique natural product biosynthesis, nutrient utilization and detoxification capacities, and both microbe-microbe and host-microbe gene transfer amenability.
- Development and validation of an experimental life support system for assessing the effects of global climate change and environmental contamination on estuarine and coastal marine benthic communitiesPublication . Coelho, Francisco J. R. C.; Rocha, Rui J. M.; Pires, Ana C. C.; Ladeiro, Bruno; Castanheira, Jose M.; Costa, Rodrigo; Almeida, Adelaide; Cunha, Angela; Lillebo, Ana Isabel; Ribeiro, Rui; Pereira, Ruth; Lopes, Isabel; Marques, Catarina; Moreira-Santos, Matilde; Calado, Ricardo; Cleary, Daniel F. R.; Gomes, Newton C. M.An experimental life support system (ELSS) was constructed to study the interactive effects of multiple stressors on coastal and estuarine benthic communities, specifically perturbations driven by global climate change and anthropogenic environmental contamination. The ELSS allows researchers to control salinity, pH, temperature, ultraviolet radiation (UVR), tidal rhythms and exposure to selected contaminants. Unlike most microcosms previously described, our system enables true independent replication (including randomization). In addition to this, it can be assembled using commercially available materials and equipment, thereby facilitating the replication of identical experimental setups in different geographical locations. Here, we validate the reproducibility and environmental quality of the system by comparing chemical and biological parameters recorded in our ELSS with those prevalent in the natural environment. Water, sediment microbial community and ragworm (the polychaete Hediste diversicolor) samples were obtained from four microcosms after 57days of operation. In general, average concentrations of dissolved inorganic nutrients (NO3-; NH4+ and PO4-3) in the water column of the ELSS experimental control units were within the range of concentrations recorded in the natural environment. While some shifts in bacterial community composition were observed between in situ and ELSS sediment samples, the relative abundance of most metabolically active bacterial taxa appeared to be stable. In addition, ELSS operation did not significantly affect survival, oxidative stress and neurological biomarkers of the model organism Hediste diversicolor. The validation data indicate that this system can be used to assess independent or interactive effects of climate change and environmental contamination on benthic communities. Researchers will be able to simulate the effects of these stressors on processes driven by microbial communities, sediment and seawater chemistry and to evaluate potential consequences to sediment toxicity using model organisms such as Hediste diversicolor.
- Diversity of Bacteria in the Marine Sponge Aplysina fulva in Brazilian Coastal Waters (vol 75, pg 3331, 2009)Publication . Hardoim, C. C. P.; Costa, Rodrigo; Araujo, F. V.; Hajdu, E.; Peixoto, R.; Lins, U.; Rosado, A. S.; van Elsas, J. D.Author's correction of Diversity of Bacteria in the Marine SpongeAplysina fulvain BrazilianCoastal Waters
- Diversity, structure and convergent evolution of the global sponge microbiomePublication . Thomas, Torsten; Moitinho-Silva, Lucas; Lurgi, Miguel; Bjoerk, Johannes R.; Easson, Cole; Astudillo-Garcia, Carmen; Olson, Julie B.; Erwin, Patrick M.; Lopez-Legentil, Susanna; Luter, Heidi; Chaves-Fonnegra, Andia; Costa, Rodrigo; Schupp, Peter J.; Steindler, Laura; Erpenbeck, Dirk; Gilbert, Jack; Knight, Rob; Ackermann, Gail; Lopez, Jose Victor; Taylor, Michael W.; Thacker, Robert W.; Montoya, Jose M.; Hentschel, Ute; Webster, Nicole S.Sponges (phylum Porifera) are early-diverging metazoa renowned for establishing complex microbial symbioses. Here we present a global Porifera microbiome survey, set out to establish the ecological and evolutionary drivers of these host-microbe interactions. We show that sponges are a reservoir of exceptional microbial diversity and major contributors to the total microbial diversity of the world's oceans. Little commonality in species composition or structure is evident across the phylum, although symbiont communities are characterized by specialists and generalists rather than opportunists. Core sponge microbiomes are stable and characterized by generalist symbionts exhibiting amensal and/or commensal interactions. Symbionts that are phylogenetically unique to sponges do not disproportionally contribute to the core microbiome, and host phylogeny impacts complexity rather than composition of the symbiont community. Our findings support a model of independent assembly and evolution in symbiont communities across the entire host phylum, with convergent forces resulting in analogous community organization and interactions.
- Draft genome sequence of Vibrio chagasii 18LP, isolated from Gilthead Seabream (Sparus aurata) larvae reared in aquaculturePublication . Sanches-Fernandes, Gracinda M. M.; Califano, Gianmaria; Keller-Costa, Tina; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão-Ferreira, Pedro; Mata, Leonardo; Costa, RodrigoWe report the draft genome sequence of Vibrio chagasii strain 18LP, isolated from gilthead seabream larvae at a fish hatchery research station in Portugal. The genome presents numerous features underlying opportunistic behavior, including genes coding for toxin biosynthesis and tolerance, host cell invasion, and heavy metal resistance.
- Draft genome sequence of vibrio jasicida 20LP, an opportunistic bacterium isolated from fish larvaePublication . Sanches-Fernandes, Gracinda M. M.; Califano, Gianmaria; Keller-Costa, Tina; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão-Ferreira, Pedro; Mata, Leonardo; Costa, RodrigoWe present the genome sequence of Vibrio jasicida 20LP, a bacterial strain retrieved from larvae of gilthead seabream (Sparus aurata), a highly valuable, model fish species in land-based aquaculture. Annotation of the V. jasicida 20LP genome reveals multiple genomic features potentially underpinning opportunistic associations with diverse marine animals.