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  • Draft genome sequence of Vibrio chagasii 18LP, isolated from Gilthead Seabream (Sparus aurata) larvae reared in aquaculture
    Publication . Sanches-Fernandes, Gracinda M. M.; Califano, Gianmaria; Keller-Costa, Tina; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão-Ferreira, Pedro; Mata, Leonardo; Costa, Rodrigo
    We 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.
  • Resistance of seagrass habitats to ocean acidification via altered interactions in a tri-trophic chain
    Publication . Martínez-Crego, Begoña; Vizzini, Salvatrice; Califano, Gianmaria; Massa-Gallucci, Alexia; Andolina, Cristina; Gambi, Maria Cristina; Santos, Rui
    Despite the wide knowledge about prevalent effects of ocean acidification on single species, the consequences on species interactions that may promote or prevent habitat shifts are still poorly understood. Using natural CO2 vents, we investigated changes in a key tri-trophic chain embedded within all its natural complexity in seagrass systems. We found that seagrass habitats remain stable at vents despite the changes in their tri-trophic components. Under high pCO2, the feeding of a key herbivore (sea urchin) on a less palatable seagrass and its associated epiphytes decreased, whereas the feeding on higher-palatable green algae increased. We also observed a doubled density of a predatory wrasse under acidified conditions. Bottom-up CO2 effects interact with top-down control by predators to maintain the abundance of sea urchin populations under ambient and acidified conditions. The weakened urchin herbivory on a seagrass that was subjected to an intense fish herbivory at vents compensates the overall herbivory pressure on the habitat-forming seagrass. Overall plasticity of the studied system components may contribute to prevent habitat loss and to stabilize the system under acidified conditions. Thus, preserving the network of species interactions in seagrass ecosystems may help to minimize the impacts of ocean acidification in near-future oceans.
  • Effects of live feed manipulation with algal‐derived antimicrobial metabolites on fish larvae microbiome assembly: a molecular‐based assessment
    Publication . Sanches‐Fernandes, Gracinda M. M.; Califano, Gianmaria; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão‐Ferreira, Pedro; Mata, Leonardo; Costa, Rodrigo
    Opportunistic microorganisms acquired through rearing water or live feed ingestion are believed to underpin high mortality rates of fish larvae, constituting a production bottleneck for the aquaculture industry. We employed 16S rRNA gene sequencing to determine whether treatment of live feed (rotifers and Artemia) with algal-derived, antibacterial metabolites could alter bacterial community structure of gilthead seabream (Sparus aurata) larvae in a larviculture facility. Owing to a large degree of sample-to-sample variation, pronounced 'legacy effects' of live feed manipulation on the total fish larvae bacterial community could not be verified. Notwithstanding, the approach induced shifts in relative abundance of specific bacterial phylotypes in both the live feed and fish larvae. Some phylotypes representing opportunistic taxa such as Stenotrophomonas, Pseudomonas and Klebsiella displayed reduced abundances in the bacterial community of fish larvae fed metabolite-treated vs. control live feed. Conversely, potentially beneficial phylotypes in the Alphaproteobacteria clade were consistently-although not significantly-promoted in the treated larval samples. These outcomes encourage future microbiome manipulation attempts to improve fish larviculture. However, successful host colonization and competition with resident symbionts are primary barriers that need to be overcome if live feeds are to be used as effective delivery systems of beneficial bacteria to fish larvae.
  • Draft genome sequence of vibrio jasicida 20LP, an opportunistic bacterium isolated from fish larvae
    Publication . Sanches-Fernandes, Gracinda M. M.; Califano, Gianmaria; Keller-Costa, Tina; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão-Ferreira, Pedro; Mata, Leonardo; Costa, Rodrigo
    We 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.
  • Cultivating the macroalgal holobiont: effects of integrated multi-trophic aquaculture on the microbiome of Ulva rigida (chlorophyta)
    Publication . Califano, Gianmaria; Kwantes, Michiel; Abreu, Maria Helena; Da Silva Costa, Rodrigo; Wichard, Thomas
    Ulva is a ubiquitous macroalgal genus of commercial interest. Integrated Multi-Trophic Aquaculture (IMTA) systems promise large-scale production of macroalgae due to their high productivity and environmental sustainability. Complex host-microbiome interactions play a decisive role in macroalgal development, especially in Ulva spp. due to algal growth- and morphogenesis-promoting factors released by associated bacteria. However, our current understanding of the microbial community assembly and structure in cultivated macroalgae is scant. We aimed to determine (i) to what extent IMTA settings influence the microbiome associated with U. rigida and its rearing water, (ii) to explore the dynamics of beneficial microbes to algal growth and development under IMTA settings, and (iii) to improve current knowledge of host-microbiome interactions. We examined the diversity and taxonomic composition of the prokaryotic communities associated with wild versus IMTA-grown Ulva rigida and surrounding seawater by using 16S rRNA gene amplicon sequencing. With 3141 Amplicon Sequence Variants (ASVs), the prokaryotic richness was, overall, higher in water than in association with U. rigida. Bacterial ASVs were more abundant in aquaculture water samples than water collected from the lagoon. The beta diversity analysis revealed distinct prokaryotic communities associated with Ulva collected in both aquacultures and coastal waters. Aquaculture samples (water and algae) shared 22% of ASVs, whereas natural, coastal lagoon samples only 9%. While cultivated Ulva selected 239 (8%) host-specific ASVs, wild specimens possessed more than twice host-specific ASVs (17%). Cultivated U. rigida specimens enriched the phyla Cyanobacteria, Planctomycetes, Verrucomicrobia, and Proteobacteria. Within the Gammaproteobacteria, while Glaciecola mostly dominated the microbiome in cultivated algae, the genus Granulosicoccus characterized both Ulva microbiomes. In both wild and IMTA settings, the phylum Bacteroidetes was more abundant in the bacterioplankton than in direct association with U. rigida. However, we observed that the Saprospiraceae family within this phylum was barely present in lagoon water but very abundant in aquaculture water. Aquaculture promoted the presence of known morphogenesis-inducing bacteria in water samples. Our study suggests that IMTA significantly shaped the structure and composition of the microbial community of the rearing water and cultivated U. rigida. Detailed analysis revealed the presence of previously undetected taxa associated with Ulva, possessing potentially unknown functional traits.
  • Macroalgal–bacterial interactions: identification and role of thallusin in morphogenesis of the seaweed Ulva (Chlorophyta)
    Publication . Wichard, Thomas; Ulrich, Johann F; Mohr, Jan Frieder; Kwantes, Michiel; Engelen, Aschwin; Weiss, Anne; Grueneberg, Jan; Deicke, Michael; Califano, Gianmaria; Alsufyani, Taghreed
    Macroalgal microbiomes have core functions related to biofilm formation, growth, and morphogenesis of seaweeds. In particular, the growth and development of the sea lettuce Ulva spp. (Chlorophyta) depend on bacteria releasing morphogenetic compounds. Under axenic conditions, the macroalga Ulva mutabilis develops a callus-like phenotype with cell wall protrusions. However, co-culturing with Roseovarius sp. (MS2) and Maribacter sp. (MS6), which produce various stimulatory chemical mediators, completely recovers morphogenesis. This ecological reconstruction forms a tripartite community which can be further studied for its role in cross-kingdom interactions. Hence, our study sought to identify algal growth- and morphogenesis-promoting factors (AGMPFs) capable of phenocopying the activity of Maribacter spp. We performed bioassay-guided solid-phase extraction in water samples collected from U. mutabilis aquaculture systems. We uncovered novel ecophysiological functions of thallusin, a sesquiterpenoid morphogen, identified for the first time in algal aquaculture. Thallusin, released by Maribacter sp., induced rhizoid and cell wall formation at a concentration of 11 pmol l-1. We demonstrated that gametes acquired the iron complex of thallusin, thereby linking morphogenetic processes with intracellular iron homeostasis. Understanding macroalgae-bacteria interactions permits further elucidation of the evolution of multicellularity and cellular differentiation, and development of new applications in microbiome-mediated aquaculture systems.