iBB

The marine bacterial genus Aquimarina (Flavobacteriaceae, Bacteroidota) receives increased attention due to its versatile natural product biosynthesis capacity and antimicrobial activities. iBB and DBE researchers Joana Couceiro,Matilde Marques, Sandra Silva, Tina Keller-Costa and Rodrigo Costa identified two novel Aquimarina species, Aquimarina aquimarini Aq135T and Aquimarina spinulae Aq349T, isolated from marine sponges in Portugal, and describe them in the International Journal of Systematic and Evolutionary Microbiology. Aq135T is known for its production of a unique set of peptide antibiotics, aquimarins, while Aq349T is known to produce the trans-AT polyketide cuniculene. In their polyphasic approach, the researchers used phylogenetic, phylogenomic, phenotypic, and biochemical analyses to determine the novel species statuses of both strains. The bacteria are available in BSRG-iBB’s culture collection associated with the ‘Portuguese Blue Biobank’ of the Blue Bioeconomy Pact and can be purchased at three internationally recognized culture collections - DSMZ, ATCC, and UCCCB.

Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Bacteria of the family Endozoicomonadaceae are prominent symbionts of sessile marine animals, particularly corals, contributing to nutrient cycling in their hosts. A new comparative genomics study, published in ISME Communications, found a widespread occurrence of chitinases, and other genes involved in chitin degradation in cultured and uncultured Endozoicomonadaceae lineages associated with diverse marine animals. The presence of multiple, distinct chitinases on the genomes of several Endozoicomonadaceae species hints at functional variation to secure effective chitin processing in diverse micro-habitats and changing environmental conditions. This study concludes that Endozoicomonadaceae symbionts likely play important roles in chitin turnover in filter- and suspension-feeding animals and in benthic, marine ecosystems at large. The work was developed by MSc students Daniela Silva and Filipa Pedrosa in the framework of the ChiCoBionts project led by iBB/DBE researcher Tina Keller-Costa with valuable contributions from professors Ângela Taipa and Rodrigo Costa.

Sandra Silva defended her PhD thesis in Biotechnology and Biosciences at Instituto Superior Técnico, receiving the highest mentioning “Distinction and Honour”.  Her thesis entitled “Secondary metabolite biosynthesis by Aquimarina species: emerging properties and bioactivities from the rare marine biosphere” was developed under the supervision of Rodrigo Costa and Tina Keller-Costa from iBB and DBE. During the past four years, Sandra combined genomics, experimental microbiology, metabolomics, and analytical chemistry to explore marine host-associated bacteria as a source of novel natural products with antimicrobial activities.

The Blue Bioeconomy Pact led by Inovamar is one of the mobilizing agendas for corporate innovation recently funded by the European Union NextGenerationEU through the Portuguese Recovery and Resilience Plan (PRR). It consists of a consortium of 83 national entities including 53 companies of all dimensions, from large multinational corporations to small-medium enterprises and start-ups, and 30 R&D institutions. The project aims to develop the sustainable use of marine resources, creating 52 new products, processes and services across multiple sectors such as aquaculture, fisheries, food and feed, textiles, biomaterials and human health. The consortium will invest a total amount of 133 M€, of which 94 M€ are financed by the Recovery and Resilience Plan.

Instituto Superior Técnico is involved in four of the nine PBA work packages with 1.5 M€ of funding: WP1 – “Biomaterials”, WP4 – “Food”, WP5 – “Algae”, and WP9 – “The Portuguese Blue Biobank”. The project at IST is coordinated by Prof Rodrigo Costa from iBB and DBE and counts on expert contributions by Dr Teresa Cesário from iBB (WP1), Dr Tina Keller-Costa and Prof Isabel Sá-Correia from iBB (WP5 and WP9) and Prof Ana Clara Marques from CERENA and DEQ (WP4).

Marine microbiomes are prolific sources of bioactive compounds of pharmaceutical value. A new study, published in Marine Drugs, inspected two culture collections comprising 919 host-associated marine bacteria belonging to 55 genera and several unclassified lineages. The study identified numerous isolates with a potentially rich secondary metabolism and inhibitory activities towards human-pathogenic bacteria and fungi. These culture collections, available at iBB-IST and Aveiro University, are a valuable resource of understudied marine bacteria that hold promise for a future, sustainable production of novel drug leads. The work was developed within the SymbioReactor project (DGPM | Fundo Azul program), first-authored by MSc João Almeida and coordinated by Dr Tina Keller-Costa and Prof Rodrigo Costa. The study also involved PhD student Matilde Marques, Dr Dalila Mil-Homens, Prof Miguel Teixeira and Prof Arsénio Fialho from iBB as well collaborators from Aveiro University and Biocant.

To shed light on the metabolic capacities of the bacterial symbionts of octocorals (Octocoallia, Cnidaria), iBB researchers examined 66 metagenome-assembled genomes (MAGs) from the microbial metagenomes of octocorals and seawater. The work recovered MAGs from dominant, so-far unculturable Endozoicomonadaceae and other symbionts, and identified a thus far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the ocean. Other symbionts had genes for the assimilation of chitin oligosaccharides and for chitin deacetylation, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. The study also observed sharp differences in secondary metabolite production potential between symbiotic lineages, and suggested that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. The article, published in the journal Microbiome, was led by iBB researchers Tina Keller-Costa and Rodrigo Costa and counted on contributions of EPFL MSc student Lydia Kozma, iBB PhD student Sandra Silva and collaborators from UALG-CCMAR, UFZ Leipzig and DOE JGI.

Bacterial pathogens belonging to the Vibrio genus such as Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus are some of the most common and widespread disease-causing agents in the aquaculture industry, inducing severe losses in fish and shellfish production worldwide. In a Review Article published in Frontiers in Microbiology, iBB researchers Gracinda Sanches Fernandes, Isabel-Sá Correia and Rodrigo Costa performed a meta-analysis of vibriosis outbreaks reported for the economically valuable, model aquaculture fish gilthead seabream (Sparus aurata) in the Mediterranean zone. The study reveals the acquisition of multiple antibiotic resistance traits among pathogenic Vibrio species during the past 25 years. An increase in human infections caused by Vibrio pathogens of fish – either via seafood ingestion or wound colonization - has been documented in the recent literature, and it is believed to result from the synergistic interaction between the expansion of intensive fish farming across coastal ecosystems and global warming. Finally, the authors critically examine the potential, and review cases of success, of alternative methods to antibiotics use to suppress vibrio pathogens in aquaculture, including vaccines, phage therapy and probiotics supplementation. Diverse bacterial symbionts of fish suppress vibrio pathogens in experimental trials, suggesting that the natural fish microbiome may be a reservoir of biological control agents of interest in applied biotechnology.

The marine bacterial genus Aquimarina is a promising source of novel natural products. A new study published in Marine Drugs demonstrated widespread ability of Aquimarina species to inhibit growth of human-pathogenic microbes such as Candida glabrata and methicillin-resistant Staphylococcus aureus, as well as Vibrio and other marine bacteria relevant to aquaculture. Metabolomics and genomics analyses of Aquimarina strains indicated the presence of novel polyketides and peptides, including cyclic depsipeptide-related compounds. The study further showed that Aquimarina species possess low-abundance distributions across marine biotopes worldwide. It emphasizes the relevance of this member of the microbial rare biosphere as a promising source of novel natural products, supporting future efforts to isolate new bioactive compounds from Aquimarina. The work was developed within the SymbioReactor project (DGPM | Fundo Azul program) led by Prof Rodrigo Costa and Dr Tina Keller-Costa and was first-authored by PhD student Sandra Silva. It also includes former MSc student Patrícia Paula, Dr Dalila Mil-Homens, Prof Miguel Teixeira and Prof Arsénio Fialho from BSRG-iBB as coauthors.

A transatlantic endeavour involving researchers from BSRG-iBB, CQE (IST) and Université Laval and INRS (Canada) provided the first comprehensive assessment of prokaryotic communities in the late winter ice and its underlying water along a natural salinity gradient in Hudson Bay, a cryo-environment marking the transition between Subarctic and Arctic biomes. The study, published in Science of Total Environment, was led by Prof. Rodrigo Costa, first-authored by MIT-Portugal PhD student Lígia Coelho and co-authored by PhD student Joana Couceiro, Dr Tina Keller-Costa and Profs. Zita Martins and João Canário. The team found sharp shifts in community structure between the ice and underlying water samples at sampling sites with higher salinity, and high abundance of culturable, pigment-producing bacteria in ice. The study suggests that salinity, photosynthesis and dissolved organic matter are main drivers of prokaryotic community structure in the winter ice of Hudson Bay, the ecosystem with the fastest sea ice loss in the Canadian North.

Marine invertebrates together with a plethora of symbiotic and free-living algae, fungi and prokaryotes are amidst the most prolific producers of bioactive compounds in coral reefs and marine environments at large. Their natural products often show astounding structural novelty and complexity, facilitating chemically mediated behaviours and interspecies interactions from competition to cooperation. There is great potential for a minimally invasive and economically reliable exploitation of bioactive secondary metabolites from the highly diverse and chemically complex reef communities. iBB researchers Tina Keller-Costa and Rodrigo Costa (BSRG) are guest editing a special issue on Coral Reef Ecology, Conservation and Inspiration for Marine Drugs Development in the Journal Marine Drugs and cordially invite the scientific community to contribute original research or review articles on the role of natural products in coral reef ecology and conservation, organismal interactions and biotechnology.

Octocorals are marine invertebrates abundant in the Portuguese coast, which host complex microbiomes. Yet the functional relationship between host health and its symbiotic consortium has still to be determined. A new study from an international team led by iBB researchers Tina Keller-Costa and Rodrigo Costa employed comparative metagenomics to uncover the functional and phylogenetic features of the microbiomes of healthy tissue from three octocoral species from the Portuguese coast. The authors also explored how the octocoral microbiome shifts to a pathobiome state in one of the coral species. The study reveals that the octocoral microbiome is distinct from those of the environmental surroundings (that is, seawater and sediments), is host genus (but not species) specific, and undergoes complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defence arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. The authors argue that these features collectively contribute to the stabilization of host-microbe symbiosis in octocorals and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. The article was published in the journal Microbiome.

Microbiome research has grown considerably in the past few years, producing large amounts of data to address current and future societal challenges. ELIXIR, the European Infrastructure for Biological Data, and BioData.pt, the Portuguese node of Elixir, are assembling a national microbiome community to address these challenges and promote data findability, accessibility, interoperability, and reuse, as well as knowledge exchange, among Portuguese and European researchers. In this context, the 1st Microbiome Summit took place last February 4th 2021, and counted on contributions from several BSRG-iBB members, including doctorate researchers Nuno Borges and Tina Keller-Costa, PhD students Sandra Godinho Silva, Rúben Silva and Gracinda Sanches-Fernandes who all prepared short videos about their latest research, and Prof. Rodrigo Costa, who gave an invited talk entitled “The microbiome of marine sponges: diversity, function and biotechnology”.

A new article, published in mSystems, delved into the secondary metabolite biosynthesis potential of Flavobacteriaceae to find highly intertwined phylogenetic-secondary metabolism relationships within this family. The authors examined 2,680 genomes to suggest that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone and widely distributed bacterial taxon. These features likely underpin the broad host range and opportunistic-to-pathogenic behaviour encompassed by species in this family. This study breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads. Particularly, it highlights a versatile secondary metabolism among species belonging to the genera Aquimarina and Kordia, which should be explored in future natural product research endeavours. The study was first-authored by former iBB/DBE PhD student Sandra Silva and coordinated by professor Rodrigo Costa, counting on expert contributions from iBB/DBE scientist Tina Keller-Costa, and Ulisses Nunes da Rocha and Masun Homsi from the Helmholtz Centre for Environmental Research, Leipzig, Germany.

The perspective article entitled "Harnessing the microbiome to prevent biodiversity loss", an international collaboration uniting renowned scientists active in the fields of symbiosis and microbial ecology and evolution, was included in a collection of articles from nature’s portfolio that address challenges for achieving United Nations’ Sustainable Development Goals. The perspective, led by Raquel Peixoto at King Abdullah University of Science and Technology (KAUST), counted on expert contributions by Rodrigo Costa and Tina Keller-Costa on microbiome manipulation strategies in aquaculture and coral reef ecosystems. The initiative was launched by a round table headed by the Beneficial Microorganisms for Marine Organisms (BMMO) network during the 15th Symposium on Bacterial Genetics and Ecology (BAGECO15, Lisbon 2019) chaired by Rodrigo Costa.

PhD students Joao Couceiro, João Almeida, Matilde Marques, and Laurence Meunier presented posters about their marine microbiome and symbiosis research at BAGECO2023.  

DBE Faculty member and IBB researcher Rodrigo Costa, part of the scientific committee of BAGECO, chaired a full day of sessions on Host-Microbe Interactions and gave the talk entitled "Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon".

It was an excellent opportunity to network and connect with fellow scientists, foster new collaborations, and build lasting friendships.

Ruben Silva defended his PhD thesis in Biotechnology and Biosciences at Instituto Superior Técnico on July 06th 2023.  His thesis entitled “Uncovering the chitin degradation potential of the microbiomes of marine sponges and octocorals” was developed under the supervision of Prof Rodrigo Costa and Dr Tina Keller-Costa from iBB and Dr Cymon Cox from the Centre of Marine Sciences (CCMAR) in Faro. During the past years, Ruben studied chitin degradation pathways in culturable and unculturable bacterial symbionts of marine sponges and corals using metagenomics, genomics, and bioassays.  

A new study provides insights into the prokaryotic communities and heavy metal distribution in different body parts of the marine sponge Chondrosia reniformis, a model organism relevant for marine conservation and biotechnology. The study was published in Zoology and results from an international collaboration between researchers from iBB-IST and the Università Politecnica delle Marche in Italy.  The work was led by Italian PhD student Camilla Roveta and Prof. Rodrigo Costa from BSRG-iBB/DBE and included MIT Portugal PhD student Joana F. Couceiro from BSRG-iBB. Fifteen prokaryotic phyla were detected in association with this sponge. Three lineages of ammonium-oxidizing organisms co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as key metabolic pathway within the C. reniformis microbiome. Mercury levels varied according to the body site of the sponge, with higher levels accumulating in internal sites (choanosome). Minor levels of Hg could be detected in the microbial fractions extracted from the sponge host, suggesting that the sponge-associated microbiome may participate in Hg adsorption and removal processes in benthic ecosystems. This study paves the way for scientists to deepen the possible application of marine sponges not only as bioindicators of environmental health, but also as bioremediation tools of metal polluted environments.

Metagenomics is an expanding field within microbiology and related disciplines. The number of metagenomes deposited in public databases is exponentially rising, but data mining and interpretation can be challenging due to mis-annotated metadata entries. The new Marine Metagenome Metadata Database (MarineMetagenomeDB) helps researchers to identify marine metagenomes of interest for re-analysis and meta-analysis and is a valuable resource for non-bioinformaticians to find marine metagenome samples with curated metadata. The study, published in Environmental Microbiome, was led by Dr Ulisses Nunes da Rocha and team from the Helmholtz Centre for Environmental Research (Germany), and counted on specialist guidance in marine metadata standardization from iBB/DBE PhD-student Sandra Silva and researchers Tina Keller-Costa and Rodrigo Costa. The user-friendly web app is publicly available at here.

In a perspective article published in Nature Microbiology, experts in the field of symbiosis and microbiome research address the current, acute loss of plant and animal diversity that poses serious threats to the functioning of terrestrial and marine ecosystems, human health, and the development of a sustainable bio-based economy. The potential, and examples of success, of microbiome-based interventions such as probiotics administration and microbiome transplants in improving the health and resilience of a broad range of host organisms towards climate change stressors and the emergence of novel diseases is debated, and a perspective is provided on how such interventions may contribute to the conservation and maintenance of services of man-made and natural ecosystems. The perspective, led by Prof. Raquel Peixoto at King Abdullah University of Science and Technology (KAUST), counted on expert contributions by iBB-BSRG researchers Dr. Rodrigo Costa and Dr. Tina Keller-Costa on microbiome manipulation strategies in aquaculture and coral reef ecosystems. The initiative was launched by a round table headed by the Beneficial Microorganisms for Marine Organisms (BMMO) network during the 15th Symposium on Bacterial Genetics and Ecology (BAGECO15, Lisbon 2019) chaired by Prof. Rodrigo Costa.

Sandra Godinho Silva, PhD candidate in Biotechnology and Biosciences, presented a talk entitled 'Big data meets natural products discovery: mining thousands of bacterial genomes to identify novel sources of drug leads' at the FEMS Conference on Microbiology 2022, held from 30 June to 2 July 2022 in Belgrade, Serbia. Her presentation explored the results of a large-scale comparative genomics approach to study natural product biosynthesis potential across 2680 bacterial genomes representing 1158 species and 175 genera of the metabolically-versatile order Flavobacteriales (phylum Bacteroidetes). Sandra was awarded a FEMS Research and Training Grant (GO-2019-511) to conduct her studies in the framework of an international collaboration on high-throughput genome mining led by Prof. Rodrigo Costa (BSRG-iBB, Portugal) and Dr. Ulisses N. da Rocha (Microbial Data Science Group, Helmholtz Centre for Environmental Research - UFZ , Leipzig, Germany). The results will be compiled in Sandra’s PhD thesis, under the supervision of Prof. Rodrigo Costa and Dr. Tina Keller Costa (BSRG-iBB). Sandra also had the opportunity to co-chair an oral poster session with Prof. Bauke Oudega on 'FEMS Supported Projects & Miscellaneous', and her participation in the FEMS 2022 Conference was supported by a FEMS Congress Attendance Grant.

A joint collaborative effort coordinated by Prof Jörn Piel from the ETH Zürich (Switzerland) led to the identification of new antibiotic compounds from Aquimarina sp. strain Aq135 which was cultivated from the marine sponge Ircinia variabilis in the laboratory of Prof Rodrigo Costa from BSRG-iBB. Activity-guided isolation identified novel antibacterial peptides, named aquimarins, featuring a new scaffold with an unusual C-terminal amino group and chlorine moieties. Structure–activity relationship studies with these compounds showed that the synthetically more laborious chlorinations are not required for antibacterial activity but enhance cytotoxicity. In contrast, variants lacking the C-terminal amine were virtually inactive, suggesting diamines similar to the terminal aquimarin residue as candidate building blocks for new peptidomimetic antibiotics. The study was published in Angewandte Chemie.

Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Combining published and unpublished data, a new article featuring iBB researchers Tina Keller-Costa and Rodrigo Costa among the authors provides a comprehensive overview of the diversity and function of culturable bacteria isolated from tropical, temperate, and cold-water corals. The study, published in the journal mSystems, compiles a total of 3,055 coral-associated isolates described in 52 reports from various laboratories around the world. The work presents a comparative genomic analysis of 74 strains and identifies signatures of potentially beneficial bacterium-coral symbioses among them. Such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and can potentially be applied in novel reef restoration and rehabilitation efforts. This genome and culture collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope that many scientists across the globe will ask for access to these resources for future studies.

Little is known about the structure and diversity of chitin-degrading microbial communities across marine niches. Researchers from BSRG-iBB, including PhD student Rúben Silva and former students Inês Raimundo (now a PhD student at KAUST) and Laurence Meunier (now a PhD student at University of Brussels), and led by Rodrigo Costa and Tina Keller-Costa have shed light on chitin processing within the microbiomes of marine sponges, octocorals, sediments, and seawater. The study, published in Microbiome, integrates cultivation-dependent and -independent approaches to unveil chitin degradation pathways across diverse marine bacteria. Functional metagenomics revealed that the marine sponge microbiome is rich in polysaccharide deacetylases, suggesting the ability of this consortium to convert chitin into its more biotechnologically versatile form - chitosan. The findings further suggest that chitin is processed via multiple mechanisms across marine micro-niches, favoring the hypothesis that inter-species microbial cross-feeding facilitates the co-existence of chitin users within the microbiomes of filter-feeding marine invertebrates. The study also reports on new chitinolytic enzymes from the genus Aquimarina that may find use in the blue biotechnology sector.