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- The microbial rare biosphere: current concepts, methods and ecological principlesPublication . Pascoal, Francisco; Costa, Rodrigo; Magalhaes, CatarinaOur ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.
- Effects of live feed manipulation with algal‐derived antimicrobial metabolites on fish larvae microbiome assembly: a molecular‐based assessmentPublication . Sanches‐Fernandes, Gracinda M. M.; Califano, Gianmaria; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão‐Ferreira, Pedro; Mata, Leonardo; Costa, RodrigoOpportunistic 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.
- Vibriosis outbreaks in aquaculture: addressing environmental and public health concerns and preventive therapies using gilthead seabream farming as a model systemPublication . Sanches-Fernandes, Gracinda M. M.; Sá-Correia, Isabel; Da Silva Costa, RodrigoBacterial and viral diseases in aquaculture result in severe production and economic losses. Among pathogenic bacteria, species belonging to the Vibrio genus are one of the most common and widespread disease-causing agents. Vibrio infections play a leading role in constraining the sustainable growth of the aquaculture sector worldwide and, consequently, are the target of manifold disease prevention strategies. During the early, larval stages of development, Vibrio species are a common cause of high mortality rates in reared fish and shellfish, circumstances under which the host organisms might be highly susceptible to disease preventive or treatment strategies such as vaccines and antibiotics use, respectively. Regardless of host developmental stage, Vibrio infections may occur suddenly and can lead to the loss of the entire population reared in a given aquaculture system. Furthermore, the frequency of Vibrio-associated diseases in humans is increasing globally and has been linked to anthropic activities, in particular human-driven climate change and intensive livestock production. In this context, here we cover the current knowledge of Vibrio infections in fish aquaculture, with a focus on the model species gilthead seabream (Sparus aurata), a highly valuable reared fish in the mediterranean climatic zone. Molecular methods currently used for fast detection and identification of Vibrio pathogens and their antibiotic resistance profiles are addressed. Targeted therapeutic approaches are critically examined. They include vaccination, phage therapy and probiotics supplementation, which bear promise in supressing vibriosis in land-based fish rearing and in mitigating possible threats to human health and the environment. This literature review suggests that antibiotic resistance is increasing among Vibrio species, with the use of probiotics constituting a promising, sustainable approach to prevent Vibrio infections in aquaculture.
- 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.