iBB

Microbial life present in the marine environment has to be able to adapt to rapidly changing and often extreme conditions. In a recently published paper, Ricardo F.S. Pereira and Carla C.C.R. de Carvalho form iBB and colleagues from CQE and ISEL, used genomic, lipidomic and biochemical approaches to characterise a Serratia rubidaea, isolated from a sample taken at a shallow water hydrothermal vent, and its red product. Several state-of-the-art techniques, such as DSC, FTIR, NMR, and Ultra-High Resolution Qq-Time-of-Flight mass spectrometry, were used to characterize the structure of the red pigment which was found to be prodigiosin.

A new study from iBB, carried out within the scope of the Mobilizer Project Move2LowC, was published in the Journal of Fungi. The work describes the development, by adaptive laboratory evolution (ALE), of an evolved strain of the oleaginous yeast Rhodotorula toruloides more tolerant to the four major inhibitors present in lignocellulosic hydrolysates (LCH) (acetic acid, formic acid, hydroxymethylfurfural, and furfural). This outcome represents an advantage for the exploitation of promising lignocellulosic biomass feedstocks in bioprocesses envisaging the transition to a sustainable bio-based economy. In fact, the presence of toxic compounds in LCH is among the main barriers affecting the efficiency of lignocellulose-based fermentation processes, in particular hindering the production of intracellular lipids by oleaginous yeasts. These microbial oils are promising sustainable alternatives to vegetable oils for biodiesel production. The more protective role of the evolved strain cellular envelope (cell wall and plasma membrane) was demonstrated and the improved performance of this multi-tolerant strain for lipid production from a synthetic lignocellulosic hydrolysate medium, supplemented with those inhibitors, was confirmed. The work was led by Isabel Sá-Correia and the two first co-authors are the MSc student in Microbiology Mónica A. Fernandes, and the PhD student in Biotechnology and Biosciences Marta N. Mota. Dr. Nuno T. Faria has contributed with the lipid profile characterization.

Carla C. C. R. de Carvalho, Kilian Neves and Sebastião Tavares participated in the annual meeting of project Yum Algae, funded by programme Blue Growth of EEA Grants. The Yum Algae researchers from Instituto Superior Técnico, Instituto Superior de Agronomia, NORCE Norwegian Research Centre, and Pagarete Solutions, met at NORCE facilities in Bergen, Norway. The results presented are very promising to improve the sensory quality of microalgae ingredients in foods such as bread and cheese. Future actions were planned for the scale up of the process.

Carla CCR de Carvalho and the Ph.D. student Ricardo FS Pereira presented their work during the FEMS2023 congress in Hamburg, Germany. The congress organized by Federation of European Microbiological Societies is the largest event in the field of microbiology in Europe. Carla de Carvalho presented the talk entitled “Development of efficient bioprocesses using isolated marine bacteria” in the Industrial Microbiology and Bioeconomy session. Ricardo Pereira did a flash presentation entitled “Marine bioprocess development: targeting the production of prodigiosin” during the Biotechnology & Synthetic Microbiology session.

Pathologies such as psoriasis and rheumatoid arthritis have an inflammatory base triggered, in part, by an impairment of antioxidant defense systems which leads to overaccumulation of oxidative species (ROS). In a recently published paper, entitled “Up-Regulation of the Nrf2/HO-1 Antioxidant Pathway in Macrophages by an Extract from a New Halophilic Archaea Isolated in Odiel Saltworks”, researchers of the Universidad de Sevilla, Universidad de Huelva and Carla C. C. R. de Carvalho (iBB), show that an extract of Haloarcula sp. OS, containing bacterioruberin and significant amounts of fatty acids, exhibits high antioxidant activity. The study shows, for the first time, that the extract reduces LPS-induced oxidative stress and acute inflammation in THP-1 macrophages by attenuating both ROS levels and the production of the pro-inflammatory cytokines TNF-a and IL-6. The mechanism involves the activation of the Nrf-2/HO-1signaling pathway, and supports the use of the extract as a therapeutic agent in the treatment of oxidative stress-related inflammatory diseases.

Enzymes may be the right catalysts for efficient and clean processes, contributing to energy savings and negligible by-products and waste. Following the success of the Special Issue on “Biocatalysis, Enzyme and Process Engineering” in Processes (MDPI), the editors Pedro Fernandes and Carla C. C. R. de Carvalho wrote an editorial paper discussing the different papers published on this subject.

The use of Mannosylerythritol lipids (MELs), a group of biosurfactants with excellent biochemical properties, in bioremediation in marine and terrestrial environments has been envisioned. However, knowledge regarding their ecotoxicity is limited, and the current production costs are too high to make them competitive in the surfactant market. In an effort to facilitate the use of MELs for marine bioremediation purposes, the team from 2BRG/iBB studied MELs production using seawater in medium formulation as reported on “Towards Mannosylerythritol Lipids (MELs) for Bioremediation: Effects of NaCl on M. antarcticus Physiology and Biosurfactant and Lipid Production; Ecotoxicity of MELs”, published in Journal of Marine Science and Engineering. The cells were exposed to different levels of NaCl during fermentation and the effects of increased salinity on the cells and their performance were monitored. In addition, the cells were briefly exposed to osmotic shock by introducing pure NaCl into the broth to measure their physiological responses. Although the overall effect of NaCl in the medium was negative, cells produced more lipases in these stress conditions. Furthermore, the changes triggered by osmotic shock caused changes in the cell surface and affected their hydrophobicity, reducing the levels of MELs adsorbed to the cells, which in turn led to an increase in the formation of MEL-rich beads. Marine-level salinity (3.5%) was found to be sufficient to enable the production of MELs under non-sterile conditions and to inhibit the introduction of bacterial contaminants. Finally, the toxicity levels of MELs in a model marine organism and plant model were lower than those of other biosurfactants and a commercial chemical dispersant used for bioremediation.

This publication has as first-author the (now former) PhD student Petar Kekovic of the MIT-Portugal Program in Bioengineering - and as a corresponding author Frederico Ferreira and Nuno Faria.  Additionally, the co-authors and a team from Sintef – Roman Netzer, Umer Farooq and Ariadna Szczybelski submitted a patent application for formulation of a novel MEL based oils spill response agent, reference number 117583.

Marine bacteria present enzymatic activities that result from extensive evolution necessary for cell survival under the harsh and continuously changing conditions found in the marine environment. Metagenomic techniques and cultivation of not-yet-cultured bacteria, combined with high-throughput screening techniques, have allowed the identification of new biocatalysts and the development of industrial processes. In a recently published paper, Carlos J.C. Rodrigues and Carla C.C.R. de Carvalho (iBB) review the latest studies related to growth of marine bacteria under laboratorial conditions, screening techniques, and bioprocess development.

The work developed by the master’s student Catarina Jones, supervised by Teresa Esteves and Paola Sanjuan-Alberte, entitled “Novel wireless Nanobioelectronic Systems to Rewire Cancer Bioelectricity” was selected among several works developed at the University of Lisbon (UL) and presented at the 7th annual conference of RedeSAÚDE on the 14th of November. This research, which developed an effective, targeted, and non-invasive therapy for breast cancer by exploiting cancer's unique bioelectrical properties, was awarded as the Best Master Thesis in the Oncology and Precision Medicine field at UL.  This project emphasized the critical role of interdisciplinary teamwork in pioneering and achieving breakthroughs in healthcare innovation.

A heartfelt appreciation is given to RedeSAÚDE's organizers for bringing together experts from various healthcare fields, fostering an environment of innovative thinking and providing substantial incentives for biotech research and innovation.

Carla C. C. R. de Carvalho and Ricardo Pereira (2BRG-iBB) participated in the annual meeting of the EU funded project FuturEnzyme (https://www.futurenzyme.eu). The 16 partners that integrate the project met during July 6 and 7, in the house of UHAM members, the Institute of Plant Science and Microbiology (IPM, Hamburg, Germany), next to the Botanical Garden. The work carried out during the first 24M of the project was presented and discussed between partners and in the presence of members of the Advisory Board.

In the past 22nd and 23rd of May, PhD students from the Biotechnology and Biosciences doctoral program, Luís Sousa and Ricardo Pereira, attended the First Workshop on Computational Enzyme Bioprospecting and Engineering at the Barcelona Supercomputing Center (BSC). As a part of a joint program between two European projects, Oxipro (DOI 10.3030/101000607) and FuturEnzyme (DOI 10.3030/101000327), the last where IST-ID is a working partner headed by  Carla C. C. R. de Carvalho (iBB), the attendees were able to use the leading softwares for computational protein engineering. With Galaxy, attendees were able to create and develop their own workflows for Computational Bioprospecting, HMM routines, and basic sequence similarity analysis. For Protein Engineering, the Schrodinger Suite and the AsiteDesign Galaxy were made available to perform analysis and visualization of enzyme structures, perform tasks such as system preparation, visualization, sitemap calculations, ligand docking and enzyme redesign. The workshop promoted interdisciplinary thinking and collaboration between different fields, highlighted the real-world applications of computational protein engineering, and its importance in advancing our understanding of biological systems and developing new solutions for global challenges.

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).

Biosurfactants, particularly mannosylerythritol lipids (MELs), have excellent biochemical properties and a wide range of potential applications. However, for use at an industrial level, it is necessary to develop more sustainable production processes, both in terms of the environment and economy. In this regard, the study “Production of mannosylerythritol lipids using oils from oleaginous microalgae: two sequential microorganism culture approach” led by iBB team, with Tiago Coelho, Miguel Nascimento, Nuno Faria, Frederico Fereira, together with LNEG team, Alberto Reis and Luísa Gouveia, was just published in Microorganisms journal. It reports, for the first time, the production of MELs using oils produced from microalgae. The bio-oil was extracted from Neochloris oleoabundans and evaluated for its use as a sole carbon source or as a co-substrate strategy, using D-glucose as an additional carbon source, on Moesziomyces spp. cultures to support cell growth and induce the production of MELs. Both M. antarcticus and M. aphidis were able to grow and produce MELs using algae-derived bio-oils as carbon sources and, interestingly, there were no significant differences in productivity when oils from microalgae or vegetable oils were used as carbon sources. These results provide new perspectives for the production of MELs in systems that combine different microorganisms.

Xylonic acid (XA) is on the list of the 30 platform chemicals to be produced from biomass, as identified by the US Department of Energy.

The group of researchers Maryna Bondar, Teresa Cesário and Manuela Fonseca (iBB) was the first to report the capability of a bacterial species belonging to Safety Level 1, Paraburkholderia sacchari, at the time classified as Burkholderia sacchari, to produce large amounts of XA from xylose. XA is thermally stable and biocompatible, non-toxic, water soluble and non-corrosive, with properties similar to Gluconic Acid (GA). Its use in the pharmaceutical, food and chemical industries in general has been addressed with success.

While GA is produced from glucose, XA is obtained from xylose (sugar not used for human consumption). The invention relates to a biological process for XA production using xylose or lignocellulosic hydrolysates as substrate and a bacterial strain as biocatalyst. With this bioprocess, XA concentrations between 370 g/L and 390 g/L were obtained, corresponding to volumetric productivities from 4.8 g/(L.h) to 7.1 g/(L.h). The yield of XA on xylose ranged from 89% to 100%.

Microbes are known to contaminate money. In the project CleanCoin, funded by INCM, Carla C.C.R. de Carvalho (iBB), Telmo Santos (UNIDEMI, UNL) and Maria José Caramujo (cE3c, FCUL, UL), studied the bacterial population present at the surface of coins. In a recently published white paper, the research team and collaborators from INCM, present the results and compare the number of viable bacteria in coins with those found on other objects such as bank cards and mobile phones.