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- Molecular richness and biotechnological potential of bacteria cultured from Irciniidae sponges in the north-east AtlanticPublication . Esteves, Ana; Hardoim, Cristiane; Xavier, Joana R.; Gonçalves, Jorge Manuel Santos; Costa, RodrigoSeveral bioactive compounds originally isolated from marine sponges have been later ascribed or suggested to be synthesized by their symbionts. The cultivation of sponge-associated bacteria provides one possible route to the discovery of these metabolites. Here, we determine the bacterial richness cultured from two irciniid sponge species, Sarcotragus spinosulus and Ircinia variabilis, and ascertain their biotechnological potential. A total of 279 isolates were identified from 13 sponge specimens. These were classified into 17 genera - with Pseudovibrio, Ruegeria and Vibrio as the most dominant - and 3 to 10 putatively new bacterial species. While 16S rRNA gene sequencing identified 29 bacterial phylotypes at the 'species' level (97% sequence similarity), whole-genome BOX-PCR fingerprinting uncovered 155 genotypes, unveiling patterns of specimen-dependent occurrence of prevailing bacterial genomes across sponge individuals. Among the BOX-PCR genotypes recovered, 34% were active against clinically relevant strains, with Vibrio isolates producing the most active antagonistic effect. Several Pseudovibrio genotypes showed the presence of polyketide synthase (PKS) genes, and these were for the first time detected in isolates of the genus Aquimarina (Bacteroidetes). Our results highlight great biotechnological potential and interest for the Irciniidae sponge family and their diversified bacterial genomes.
- Effects of sample handling and cultivation bias on the specificity of bacterial communities in keratose marine spongesPublication . Hardoim, Cristiane; Cardinale, Massimiliano; Cucio, Ana C. B.; Esteves, Ana; Berg, Gabriele; Xavier, Joana R.; Cox, C. J.; Costa, RodrigoComplex and distinct bacterial communities inhabit marine sponges and are believed to be essential to host survival, but our present-day inability to domesticate sponge symbionts in the laboratory hinders our access to the full metabolic breadth of these microbial consortia. We address bacterial cultivation bias in marine sponges using a procedure that enables direct comparison between cultivated and uncultivated symbiont community structures. Bacterial community profiling of the sympatric keratose species Sarcotragus spinosulus and lrcinia variabilis (Dictyoceratida, Irciniidae) was performed by polymerase chain reaction-denaturing gradient gel electrophoresis and 454-pyrosequecing of 16S rRNA gene fragments. Whereas cultivation-independent methods revealed species-specific bacterial community structures in these hosts, cultivation-dependent methods resulted in equivalent community assemblages from both species. Between 15 and 18 bacterial phyla were found in S. spinosulus and I. variabilis using cultivation-independent methods. However, Alphaproteobacteria and Gammaproteobacteria dominated the cultivation-dependent bacterial community. While cultivation-independent methods revealed about 200 and 220 operational taxonomic units (OTUs, 97% gene similarity) in S. spinosulus and I. variabilis, respectively, only 33 and 39 OTUs were found in these species via culturing. Nevertheless, around 50% of all cultured OTUs escaped detection by cultivation-independent methods, indicating that standard cultivation makes otherwise host-specific bacterial communities similar by selectively enriching for rarer and generalist symbionts. This study sheds new light on the diversity spectrum encompassed by cultivated and uncultivated sponge-associated bacteria. Moreover, it highlights the need to develop alternative culturing technologies to capture the dominant sponge symbiont fraction that currently remains recalcitrant to laboratory manipulation.
- Diversity of the candidate phylum Poribacteria in the marine sponge Aplysina fulvaPublication . Hardoim, Cristiane; Cox, C. J.; Peixoto, R. S.; Rosado, A. S.; da Silva Costa, Rodrigo; Van Elsas, J. D.Poribacterial clone libraries constructed for Aplysina fulva sponge specimens were analysed with respect to diversity and phylogeny. Results imply the coexistence of several, prevalently “intraspecific” poribacterial genotypes in a single sponge host, and suggest quantitative analysis as a desirable approach in studies of the diversity and distribution of poribacterial cohorts in marine sponges.
- Microbial communities and bioactive compounds in marine sponges of the family Irciniidae-a reviewPublication . Hardoim, Cristiane C. P.; Costa, RodrigoMarine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.
- Microbiome diversity and composition in the phylogenetically related marine sponges S. spinosulus and I. variabilisPublication . Hardoim, Cristiane Cassiolato Pires; Costa, Rodrigo; Cox, Cymon J.; Canario, Adelino V. M.In this Thesis the theory of a uniform prokaryotic community associated with marine sponges was challenged. To this end, an in-depth inspection of the abundance, diversity, and composition of prokaryotic communities in the phylogenetically related marine sponges S. spinosulus and I. variabilis was undertaken. The within-habitat, between-habitat and temporal dynamics of these communities were disclosed. Further, an innovative approach to measure bacterial cultivation bias in the characterization of these communities was employed. Using state-of-the-art imaging technologies, both sponge species were classified as high microbe abundance sponges and bacterial cells were shown to be mainly associated with sponge cells and to neglect the sponge skeleton. PCR-DGGE fingerprinting was initially used and revealed that, within the same habitat, distinct bacterial communities were associated with S. spinosulus and I. variabilis. This was latter confirmed by 454 pyrosequencing of the same communities. Further, when two different cultivation-independent methods were applied to profile the bacterial communities associated with these hosts, a similar structure was obtained for S. spinosulus specimens, whereas the same was not true for I. variabilis. Using a common cultivation-dependent method, an alike bacterial community was detected in both sponge species, as opposed to the species-specific profiles obtained via cultivation-independent methods. Unexpectedly, around half of the OTUs recovered with the cultivation-dependent method was exclusive to this procedure. When between-habitat comparisons were made, replicates from the same sponge species were more similar to one another than replicates of different species independently of the sampling sites. Furthermore, the bacterial community associated with S. spinosulus displayed a state of dynamic stability over three consecutive years, whereby about half of the observed S. spinosulus could be detected in all sampling years. Remarkably, the archaeal community associated with S. spinosulus was dominated by one single OTU affiliated with Nitrosopumilus sp., a known ammonia-oxidizer. Overall, the prokaryotic community associated with S. spinosulus and I. variabilis was species-specific, and these communities were also maintained across biogeographical and temporal gradients, however the environmental also played a role.