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ChiCoBionts: Chitinases from the Octocoral Microbiome

ChiCoBionts: Chitinases from the Octocoral Microbiome | iBB | Scoop.it

ChiCoBionts, a new FCT-funded research project, exploits the octocoral microbiome in the search for novel chitinases of relevance to global biogeochemical cycling, food waste management, and the smart production of added-value molecules. The project starts in January 2022, is funded with 50,000 euros, and aims to discover, express, and characterise novel chitinases and chitinolytic microbes with the potential to outperform current commercial enzymes and to foster the development of blue biotechnology for chitin waste. The ChiCoBionts team joins iBB scientists from BSRG and BERG, including Tina Keller-Costa (PI), Ângela Taipa (Co-PI), Carla de Carvalho and Rodrigo Costa, in addition to ITQB researcher Nuno Borges and collaborators from the University of Brussels, Belgium.

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Insights into the Cultured Bacterial Fraction of Corals

Insights into the Cultured Bacterial Fraction of Corals | iBB | Scoop.it

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 Combining published and unpublished data, a new article featuring iBB researchers Tina Keller-Costa and Rodrigo Costa among the authors provides a comprehensive overview of the diversity and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.

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Chitin Degradation and Use Across Marine Microbiomes

Chitin Degradation and Use Across Marine Microbiomes | iBB | Scoop.it

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.

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The Microbial Rare Biosphere and Ecosystem Functioning

The Microbial Rare Biosphere and Ecosystem Functioning | iBB | Scoop.it

It is now known that a significant fraction of the total microbial diversity in nature exists at low abundance, which has given rise to an increasing number of studies on the so-called rare biosphere. With the fast-paced improvement of novel molecular technologies, surveys on the dynamics of the rare biosphere across the three domains of life (Bacteria, Archaea, Eukarya) and several environments are now possible. Importantly, this research field is transitioning from a taxonomy-driven to a functionally driven analysis, whereby the roles of rare microorganisms in boosting ecosystem functioning are addressed. In this context, a team formed by Prof. Rodrigo Costa (iBB-BSRG), Prof. Catarina Magalhães (CIIMAR-ECOBIOTEC), and PhD candidate Francisco Pascoal (Porto University), delineate the state of the art in our current knowledge of the microbial Rare Biosphere, highlighting the role of viruses in the regulation of low abundance microbial populations. The review article, published in FEMS Microbiology Ecology, also examines current concepts and methods employed in the study of the rare biosphere, integrating emerging knowledge of low abundance microorganisms into a larger ecological theory framework.

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Webinar on the Marine Sponge Microbiome by Rodrigo Costa

Webinar on the Marine Sponge Microbiome by Rodrigo Costa | iBB | Scoop.it

Rodrigo Costa from iBB-BSRG has been invited by FEMS Microbiology Ecology to speak at the Journal’s upcoming webinar on the “marine sponge microbiome”. Dr. Costa will be giving a talk entitled “Distinct adaptive features in alphaproteobacterial symbionts of marine sponges” on Thursday the 9th of July 2020, at 3pm Lisbon time. The study presented by Dr. Costa results from a collaboration with Prof. Ute Hentschel’s team at GEOMAR/University of Kiel (Germany). The webinar will bring together renowned scientist in the field of marine symbioses and metagenomics and will address the roles of symbiotic microorganisms in nutrient cycling and natural product biosynthesis in the oceans.

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Diverse Natural Product Biosynthesis Capacities in the Marine Bacterial Genus Aquimarina

Diverse Natural Product Biosynthesis Capacities in the Marine Bacterial Genus Aquimarina | iBB | Scoop.it

Aquimarina is a recently described bacterial genus of increasing research interest due to its high metabolic versatility and emerging role in the cycling of organic matter in marine ecosystems. Using comprehensive functional and comparative genomics, Sandra Godinho Silva, Tina Keller-Costa and Rodrigo Costa from BSRG-iBB revealed a previously underestimated number of gene clusters involved in the biosynthesis of natural products across several Aquimarina species, suggesting they are a promising target for the discovery of new bioactive compounds. The study, published in Environmental Microbiology, results from an extensive analysis of all the 26 Aquimarina genomes available to-date and uncovers 928 secondary metabolite biosynthetic gene clusters (BGCs) present in these genomes. Polyketide synthases, terpene synthases and non‐ribosomal peptide synthetases ranked as the most frequent BGCs encoding drug‐like candidates.

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Grant Awarded to iBB for the Sustainable Production of Bioactive Metabolites from the Sea

Grant Awarded to iBB for the Sustainable Production of Bioactive Metabolites from the Sea | iBB | Scoop.it

A new research project “SymbioReactor - Sustainable production of bioactive metabolites from microbial symbionts of marine sponges and corals” was recently awarded 178k EUR funding by the Fundo Azul programme from the Ministry of the Sea (Blue Biotechnology call 5/2017). SymbioReactor aims to uncover the antibacterial, antifungal and antitumor properties of an existing culture collection at BSRG-iBB comprising a yet uncharted panel of 1,000 bacterial symbionts from marine sponges and corals. The project’s overarching goal resides in the exploration of marine symbiotic communities to develop customized, effective tools that lead to the sustainable production of pharmacologically applicable metabolites from the seas. The project is headed by Rodrigo Costa and Tina Keller-Costa from BSRG-iBB and involves two public research institutions (University of Aveiro and Centro de Neurociências e Biologia Celular), an industrial partner (Biotrend) and an international consultant (Max Planck Institute for Chemical Ecology). It also counts with the support of the Centro Ciência Viva do Algarve and the Straw Patrol initiative for scientific dissemination.

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BAGECO 15: Ecosystem Drivers in a Changing Planet

BAGECO 15: Ecosystem Drivers in a Changing Planet | iBB | Scoop.it

The 15th Symposium on Bacterial Genetics and Ecology, dedicated to the topic "Ecosystem drivers in a changing planet", will be held in Lisbon on 26–30 May 2019. The event brings together leading experts in the fields of applied and environmental microbiology, metagenomics, bacterial evolution and related areas. BAGECO 15 will provide a forum to discuss the roles played by microorganisms in the functioning of natural and man-made ecosystems, and as sources of inspiring metabolites and materials of use in a future circular economy. The 5-day symposium is chaired by Rodrigo Costa from BSRG-iBB. Click on title to learn more.

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Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth

Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth | iBB | Scoop.it

Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. Microorganisms associated with octocorals possess a widespread yet uncharted capacity to synthetize a broad range of these natural products. In this review article published in Marine Drugs, Inês Raimundo, Sandra Silva, Rodrigo Costa and Tina Keller-Costa from BSRG-iBB uncover a wide diversity of bioactive natural products, particularly alkaloids, cyclopeptides, terpenoids and polyketides, reported to date for octocoral-derived microbes, with remarkable antibacterial, antifungal, antiviral, antifouling and anticancer activities. Beyond providing an overview of these bioactive compounds, the authors reveal hundreds of putative secondary metabolite biosynthetic gene clusters across 15 genomes of bacteria isolated from octocorals in Portugal, highlighting their potential as sources of novel metabolites suitable for bioprospection studies. They finish by discussing how to harness this biotechnological potential using multidisciplinary laboratory experimentation. This review provides the scientific community with an integrated view of the current status of secondary metabolite biosynthesis by octocoral-associated microbes and the methodological challenges that are to be met in order to achieve a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties from the blue economy sector.

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Impact of Microbiome Healing on Fish Larviculture

Impact of Microbiome Healing on Fish Larviculture | iBB | Scoop.it

The project "MicroControl: Exploiting the healing capacity of nature´s microbiomes for improved fish larviculture" has been recommended for funding by FCT (2017 Call for SR&TD Project Grants). The goal of MicroControl is to develop multi-species cocktails of beneficial fish symbionts to prevent bacterial disease incidence during fish larval rearing, a stage at which fish individuals are highly susceptible to acute outbreaks that pronouncedly impact land-based rearing of hundreds of economically important species. The team will conduct larval rearing trials under “microbiome therapy” to address the effectiveness of the approach in gilthead seabream (Sparus aurata), the third most cultivated fish species worldwide. The project, which falls within the scientific area of Biological Sciences, is headed by Rodrigo Costa from BSRG-iBB and involves a collaboration with Instituto Português do Mar e da Atmosfera.

 

Photo details: Gilthead seabream (Sparus aurata) larva, from Sara I.C. Castanho, “The potential of Asparagopsis armata to control the bacterial load associated to live feed to improve Seabream (Sparus aurata) larvae performance”, MSc Thesis., Algarve University, Portugal, June 2014.

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“The Wonders of the Marine Bacterial World” by iBB

“The Wonders of the Marine Bacterial World” by iBB | iBB | Scoop.it

Lisbon is celebrating 20 years of the Expo Event ("Expo98"). On the 22nd of May iBB members Prof. Rodrigo Costa, Dr. Tina Keller Costa, B.Sc. Inês Raimundo, M.Sc. Rúben Silva and undergrad student Carlos Clara will be participating in an exposition showing diverse subjects around ocean sciences (“O Mar de Alto a Baixo”). The team will focus on "the wonders of the marine bacterial world". They will show specimens of marine invertebrates, such as sponges and corals, which deeply interact with marine bacteria. Bioluminescence-, biofilm- and antibiotic-producing bacterial cultures will be exhibited to the wide audience.

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Special Issue: Coral Reef Ecology, Conservation, and Inspiration for Marine Drugs Development

Special Issue: Coral Reef Ecology, Conservation, and Inspiration for Marine Drugs Development | iBB | Scoop.it

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.

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New Metagenomic Insights Into the Octocoral Microbiome

New Metagenomic Insights Into the Octocoral Microbiome | iBB | Scoop.it

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.

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BSRG-iBB Researchers Participate in the 1st Microbiome PT Summit

BSRG-iBB Researchers Participate in the 1st Microbiome PT Summit | iBB | Scoop.it

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”.

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Probiotics in Fish Aquaculture

Probiotics in Fish Aquaculture | iBB | Scoop.it

Aquaculture is the fastest-growing sector in food production worldwide. BSRG-iBB researchers Nuno Borges, Tina Keller-Costa, PhD candidate Gracinda Sanches-Fernandes and Prof. Rodrigo Costa, together with colleagues from the University of Aveiro, have recently published a review in Annual Review of Animal Biosciences examining molecular studies of bacterial diversity, function, and host immunity modulation at early stages of fish development, where microbial infections cause important economic losses. The authors uncover host colonization and virulence factors from a synthetic assemblage of fish pathogens using comparative genomics and address the use of probiotics and paraprobiotics as disease-prevention strategies in fish larval and juvenile rearing. They also propose guidelines for future microbiome research of presumed relevance to fish larviculture.

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Biotechnology and the Rare Biosphere

Biotechnology and the Rare Biosphere | iBB | Scoop.it

The structure of natural microbial communities is, to a large extent, shaped by a highly diverse pool of low abundance species, usually referred to as the “rare biosphere”. Particularly, low abundance prokaryotes form a vast genetic and metabolic reservoir currently believed to play key roles in ecosystem functioning and recovery from anthropic impacts. However, harnessing the metabolism of such prokaryotes is limited due to their low numbers and recalcitrance to lab cultivation. While some are capable of concerting active metabolism and near-zero growth states, others can quickly grow while degrading xenobiotics. Thus, divergent metabolic strategies can be found in the rare biosphere that may be advantageous in multiple bioprocesses. A team of researchers led by Rodrigo Costa from iBB-BSRG, featuring Francisco Pascoal (Microbiology MSc graduate) as first author, reviews our current knowledge of the ecophysiology of low abundance prokaryotes. The authors discuss how educated exploitation of the rare biosphere can aid the development of future biotechnology-based processes, products, and services, with emphasis on the Bioremediation sector. The study was published in Frontiers in Microbiology, section Microbiotechnology.

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Automated Structure Prediction and Chemical Elucidation of Novel Bacterial Polyketides

Automated Structure Prediction and Chemical Elucidation of Novel Bacterial Polyketides | iBB | Scoop.it

Bacterial trans-acyltransferase polyketide synthases (trans-AT PKSs) are complex enzymes encoding the biosynthesis of a large diversity of polyketides, which are secondary metabolites usually possessing antitumoral and antibacterial bioactivities. Trans-AT PKSs are often found in difficult-to-cultivate and understudied microorganisms, making the assessment of their biosynthetic components and genome-guided natural product identification challenging. In a multidisciplinary effort involving researchers from ETH Zürich, Jena University, Institut Pasteur, and BSRG-iBB, a bio- and chemoinformatics web application (TransATor) was created to enable de novo structural prediction of trans-AT PKS-derived polyketides from sequence data, and tested as a structure elucidation-aid in the description of new polyketides from unusual bacterial sources. The results were communicated in Nature Chemical Biology.

 

Photo details: Aquimarina cultures, the source of the novel polyketide cuniculene. Credits: Patrícia Paula.

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Genomic Blueprints of Marine Sponge-prokaryote Symbiosis Revealed in Alphaproteobacteria

Genomic Blueprints of Marine Sponge-prokaryote Symbiosis Revealed in Alphaproteobacteria | iBB | Scoop.it

The role and relevance of low-abundance microbial populations – the so-called “rare biosphere” - in the environment is a matter of current debate in microbial ecology, with implications to our understanding of the functioning of host-microbiome interactions. Using marine sponges and their symbionts as a model system, iBB researchers and colleagues revealed that a complex consortium of low-abundant Alphaproteobacteria symbionts share diverse genomic attributes likely to improve host fitness through several mechanisms. These involve, but are not limited to, host cellular detoxification, provision of essential vitamins, nutritional exchange and chemical defense. The study, led by Rodrigo Costa from BSRG and published in Scientific Reports, suggests a role for the rare biosphere as reservoirs of host-beneficial traits and functional resilience in host-associated microbiomes.

 

Photo details: singleton (i.e., strain-specific) genes, core and pan-genomes across ten low abundance Alphaproteobacteria species cultivated from the marine sponge Spongia officinalis.

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Research Scientist Position in Applied and Environmental Microbiology

Research Scientist Position in Applied and Environmental Microbiology | iBB | Scoop.it

A position is open at iBB to hire a doctorate researcher under the scope of the FCT-funded MicroControl project. The selected candidate (PhD holder) will work on the development of multi-species bacterial inoculants to prevent diseases and promote well-being of fish larvae in aquaculture settings. The Research Scientist will apply next-generation sequencing (NGS) technologies to study the onset of the fish microbiome during successive stages of larval rearing, and to determine whether microbiome manipulation approaches are effective in suppressing the proliferation of pathogenic bacteria in fish larviculture. Most of the work will be performed at BSRG-iBB under the supervision of Prof. Rodrigo Costa, with two secondments of approximately 1 month planned for experimental work at EPPO-IPMA (Olhão, Algarve) under the supervision of Dr. Laura Ribeiro.  More information on the position and how to apply can be found here under the acronym MicroControl. The application deadline is February 6th 2019. You can read more about the MicroControl project here: https://www.scoop.it/t/ibb?q=Microcontrol 

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Metagenomic Binning Illuminates the Evolution of Unculturable, Symbiotic Bacteria

Metagenomic Binning Illuminates the Evolution of Unculturable, Symbiotic Bacteria | iBB | Scoop.it

Most microorganisms cannot be cultivated in the laboratory, what hinders our understanding of their physiology, evolution and functional roles. In collaboration with GEOMAR, University of Kiel, iBB researchers used modern nucleotide composition binning methodologies to assemble the genome of an “unculturable” bacterial symbiont from microbial metagenomes. The research led to the identification of a novel alphaproteobacterial lineage found to be intimately associated with marine sponges, termed "SERC" (sponge-enriched Rhodospirillales clade), characterized by the lack of chemotaxis and motility traits and enrichment of genes required for the utilization of organic sulfur, biosynthesis of natural products, and cell detoxification processes. The work was published in FEMS Microbiology Ecology.

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Detecting Signatures of a Sponge‐Associated Lifestyle in Bacterial Genomes

Detecting Signatures of a Sponge‐Associated Lifestyle in Bacterial Genomes | iBB | Scoop.it

In a collaborative effort led by Prof. Torsten Thomas & Group at UNSW (Australia), with participation of Prof. Rodrigo Costa from iBB, the existence of “life-style” (symbiotic vs. free-living)-specific functions among marine bacteria is deeply interrogated within the genera Aquimarina, Pseudovibrio, Ruegeria (culturable marine sponge symbionts) and Synechococcus (“yet-to-be-cultured” marine sponge symbionts). The team finds that the detection of life-style specific functions is realistic within symbionts specifically adapting to a given host than within generalist symbionts common to several hosts, which usually show several adaptive features to an existence in the free-living environment. Click on title to learne more. 

 

Photo Details: The marine sponge Sarcotragus spinosulus next to a sea anemone on rocky bottom off the Algarve coast, South Portugal. Copyright Rodrigo Costa.

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The Prokaryotic Consortium of the Gorgonian Coral Eunicella labiata

The Prokaryotic Consortium of the Gorgonian Coral Eunicella labiata | iBB | Scoop.it
Microbial communities inhabiting gorgonian corals provide hosts with nutrient provision and chemical defence. BSRG-iBB researchers led by Rodrigo Costa have found that the microbiome of the gorgonian Eunicella labiata is diverse, distinct from seawater, and rich in specific bacterial phylotypes. Furthermore, they have shown that many dominant E. labiata symbionts can be cultivated. Click on tilte to learn more about the research in FEMS Microbiology and Ecology.
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