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.

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. A BSRG-iBB review paper, just published in the Journal of Fungi (Special Issue: Yeasts for a Sustainable Circular Bio-Based Economy), provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are also provided. This publication has as first-author the PhD student Marta N. Mota of the IST PhD programme in Biotechnology and Biosciences and as corresponding author her thesis supervisor, Professor Isabel Sá-Correia. Paula Múgica, from BIOREF—Collaborative Laboratory for Biorefineries, also contributed to the publication during her stay at BSRG-iBB for scientific training and collaboration in the execution of the Move2LowC project.

Helichrysum italicum is a halophyte shrub with bright yellow flowers with a strong curry-like aroma that have been used in the production of cosmetics and pharmaceuticals, for seasoning and flavoring of food, and as natural food preservatives. In a study  recently published in Food Research International, researchers of Universidade Nova de Lisboa, Polytechnic of Leiria, University of Coimbra, University of Lincoln, the Quadram Institute, and Carla C.C.R. de Carvalho (BERG-iBB), characterize the composition, bioactive compounds, and nutritive value of H. italicum flowers. The flowers were found to be a good source of minerals, omega-6 and omega-3 PUFAs, polyphenols, carotenoids, curcuminoids and other bioactive compounds with relevant antibacterial, antifungal and antioxidant properties.

Photo details: Helichrysum italicum, Bj.schoenmakers, CC0, via Wikimedia Commons.

DNA-origami biomanufacturing relies in many cases on the use of asymmetric PCR (aPCR) to generate 500-3500 base, single-stranded DNA (ssDNA) scaffolds that are then purified by agarose gel extraction, a technique that is laborious, not scalable and presents low recovery yields. In a paper just published in Separation and Purification Technology, Ana Rita Santos and Miguel Prazeres from BERG-iBB, in collaboration with Pedro Paulo from CQE, present alternative methods based on anion-exchange or multimodal chromatography that yield purified scaffolds from aPCR mixtures. The recovered scaffolds were further used to assemble DNA-origami nanostructures. The work indicates that chromatography could play an important role in scaling-up the purification of ssDNA scaffolds for the biomanufacturing DNA-origami nanostructures.

Carla CCR de Carvalho (iBB-BERG) presented the work entitled “Marine bioprocesses with bacteria from the Portuguese coast” at the “One Sustainable Ocean”, a side event of the UN Ocean conference (UNOC) held in Lisbon. The UN Ocean Conference, co-hosted by the Governments of Kenya and Portugal, aimed at starting a new chapter of global ocean action.

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.

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.

On May 30th, Dr. Margarida Palma from BSRG-iBB participated in the scientific literacy program @cientista regressa à escola to share science with the students from her primary school, at Centro Educativo de Algodôr, Mértola. The activities planned included bread fermentation, microscopic observation of yeasts from bread dough and the balloon experiment where yeasts fermenting sugar or wheat flour can inflate balloons. The educational program @cientista regressa à escola aims to bring scientists to their primary schools to promote scientific culture and literacy, especially in regions that do not have easy access to science outreach activities, contributing to curricular enrichment in sciences, and bringing science and society closer together.

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.

The ocean is an excellent source for new biocatalysts due to the tremendous genetic diversity of marine microorganisms, and it may contribute to the development of sustainable industrial processes. In a recent paper published in Microorganisms, Carlos J.C. Rodrigues and Carla C.C.R. de Carvalho (iBB-BERG) used a marine bacterium for the conversion of benzaldehyde to benzyl alcohol, which is an important chemical employed as a precursor for producing esters for cosmetics and other industries. A stirred reactor, using a fed-batch approach, enabled a 1.5-fold increase in benzyl alcohol productivity when compared with batch mode. However, product accumulation in the reactor hindered the conversion. The use of a continuous flow reactor packed with immobilized cells enabled a 9.5-fold increase in productivity when compared with the fed-batch stirred reactor system.

Understanding the behavior of human pathogens is both a challenge and a need, if we are to address infectious diseases with the best possible tools. Genome-scale metabolic models are a way to meet this task, which was just used for the second most prevalent Candida species in Europe, Candida parapsilosis. The construction and validation of a global stoichiometric model describing the whole metabolic network in this human pathogen, as well as its exploitation in drug target discovery, stemming from a collaboration between researchers from BSRG/iBB (Miguel Cacho Teixeira), ITQB-NOVA (Isabel Rocha) and CEB-UMinho (Óscar Dias), was just published in Genes.

Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses. The cell wall is among the players whose biochemical and biophysical properties can be finely tuned as yeast cells encounter different stresses throughout the course of industrial bioprocesses. A new review article from BSRG-iBB provides a critical opinion and a comprehensive view on the current knowledge on the involvement of the cell wall in the adaptive response and tolerance of yeasts to multiple stresses of biotechnological relevance. A few successful attempts to improve stress tolerance through the manipulation of cell wall biosynthetic pathway are also described and the available information for some non-conventional yeast species included. The review article is co-authored by the PhD student of the IST PhD programme in Biotechnology and Biosciences Ricardo Ribeiro and the thesis supervisor, Prof. Isabel Sá-Correia. It was was published in the journal Frontiers in Microbiology (section: Microbial Physiology and Metabolism).

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.

Dr Tina Keller-Costa, BSRG-iBB researcher, and Matilde Marques, MIT Portugal PhD student in Biotechnology and Biosciences, attended the International Coral Reef Symposium (ICRS), held from 03 to 08 July 2022 in Bremen, Germany. Tina gave a talk on her latest metagenomics studies on the octocoral microbiome while Matilde presented a poster on viruses and bacteriophage communities of octocorals and seawater. The event was hosted by the University of Bremen and counted with 1050 in-person and over 270 virtual participants. To enable a science-to-policy dialogue the symposium also welcomed leading German and international politicians, as well Prince Albert II of Monaco and H.H. Princess Mashael Saud AlShalan from Saudi Arabia, who advocated for ocean conservation and sustainability. It was the first time in its 50-years history that ICRS was brought to Europe and the first carbon neutral ICRS.

The Norwegian Minister of Fisheries and Ocean Policy Bjørnar Selnes Skjæran, the Minister of International Development Anne Beathe Tvinnereim, and the Embassador in Lisbon Tove Bruvik Westberg, visited the Instituto Superior de Agronomia as promotor of projects funded by EEA grants. Anabela Raymundo and Cristiana Nunes (LEAF-ISA), Carla de Carvalho (iBB-IST) and António Pagarete (Pagarete Microalgae Solutions) presented the collaborations they have had with Norwegian research groups including the project Yum Algae. This projects aims at finding enzymes to improve the sensory quality of microalgae ingredients in foods and during the visit several products, such as bread, cheese and ice cream containing microalgae, were tasted. The visit also included members of the “Unidade Nacional de Gestão” of EEA Grants and of “Direção Geral de Política do Mar”.

Miguel Cacho Teixeira’s was recognized in this year’s edition of the ULisboa/CGD scientific prizes. Miguel received an honorable mention for his work in the category "Biology, Biological Engineering, Biochemistry and Biotechnology". His work is focused on understanding fungal infections caused by pathogenic yeasts of the Candida genus, on a genome-wide perspective, and on using this information to improve therapeutic options. The award ceremony took place on the 28th of June.

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.

L-asparaginases have an acknowledge role in food and pharmaceutical industries. Accordingly, efforts to produce highly efficient, selective and stable L-asparaginases are currently underway. One of the strategies used to fulfill this goal involves the production of recombinant. In a recent paper published in Marine Biotechnology, Pedro Fernandes (iBB-BERG) and colleagues from the University of Hormozgan and Tarbiat Modares University in Iran report the production of a novel marine recombinant L‑asparaginase and provide its biochemical and structural characterization. The results obtained suggest the potential of the thermostable recombinant enzyme obtained for practical applications in food and pharmaceutical areas.

Lupanine is used as a building block in the synthesis of sparteine, a chiral selector in drug synthesis. This alkaloid is found in wastewaters derived from the debittering process that makes lupin beans edible. In a recently published work, carried out by researchers of the Faculty of Sciences and Faculty of Pharmacy from the University of Lisbon, and Teresa Esteves, Frederico Ferreira, Flávio Ferreira and Ana Mota from BERG-iBB, a computational chemistry approach was taken to design molecularly imprinted polymers (MIPs) selecting itaconic acid, a biobased building block, as a functional monomer that can provide higher affinities for lupanine. In this work, lupanine was concentrated from lupin bean wastewater by nanofiltration, extracted with ethyl acetate, and purified using the synthesized MIP, which was able to selectively recognize lupanine and improve its purity to 88%, with 82% recovery of the alkaloid, showing the potential application of this strategy to render the industrial process more sustainable.

Understanding the mechano–biological coupling mechanisms of biomaterials for tissue engineering is of major importance to assure proper scaffold performance in situ. Therefore, it is of paramount importance to establish correlations between biomaterials, their processing conditions, and their mechanical behaviour, as well as their biological performance. In a collaborative work between CDRSP-Politécnico de Leiria and SCERG-iBB  (João C. Silva and Frederico Ferreira), it was possible to infer a correlation between the addition of different concentrations of graphene nanoparticles (GPN) in three-dimensional poly(ε-caprolactone) (PCL)-based scaffolds, their extrusion-based processing parameters, and the lamellar crystal orientation observed in the different scaffolds through small-angle X-ray scattering experiments. Moreover, in vitro cell culture studies performed at SCERG-iBB demonstrated the suitability and potential of these novel 3D PCL/GPN scaffolds for tissue engineering applications. The results of this study were just published in Polymers.