Joana Raquel Fernandes de Sousa

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Centre of Biological Engineering, University of Minho

Joana Raquel Fernandes de Sousa


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https://researchid.co/joanasousa
8

Scopus Publications

17

Scholar Citations

1

Scholar h-index

1

Scholar i10-index

Scopus Publications

  • A comparative evaluation of new prebiotic candidates. Part 1: Chemical and structural characterization, digestibility, and in vitro fermentation using faecal inoculum from healthy donors
    Sergio Martínez-Gómez, Joana Sousa, Ana Cordeiro, Sónia G. Barbosa, Ricardo Franco-Duarte, Ana C. Pinheiro, Ligia R. Rodrigues, Sara C. Silvério, Remedios Yáñez, José Luis Alonso
    Food Research International, 2026
  • Fodinibius alkaliphilus sp. nov., a moderately halophilic and alkaliphilic bacterium isolated from an inland saltern in central Portugal and reclassification of Aliifodinibius salipaludis as Fodinibius salipaludis sp. nov.
    Yang He, Marta Filipa Simões, Rafael R. de la Haba, Cátia Santos-Pereira, Joana Sousa, Joana S. Gomes, Sara C. Silvério, Lígia R. Rodrigues, André Antunes
    International Journal of Systematic and Evolutionary Microbiology, 2025
    A novel moderately halophilic and alkaliphilic Gram-stain-negative, strictly aerobic, bacterial strain (N2T) was isolated from an inland saltern in central Portugal. The taxonomic position of this isolate was determined based on polyphasic taxonomic and phylogenomic analysis. Phylogenetic analysis based on 16S rRNA gene sequences indicated that isolate N2T belongs to the genus Fodinibius, showing the highest similarity to Fodinibius halophilus 2W32T (98.14%). Phylogenomic analysis based on whole genomes, using the up-to-date bacterial core gene sets (92 genes), showed that strain N2T formed a distinct monophyletic lineage within the genus Fodinibius. The cells of N2T were motile rods that grew at temperatures between 30 and 40 °C (optimum at 35 °C), pH levels of 6.0–11.0 (optimum at pH 9.0) and salinities of 13–20 % (w/v) NaCl (optimum at 15% NaCl). Cells tested positive for oxidase and catalase activity. The predominant isoprenoid quinone was menaquinone-7 (MK-7), and the major fatty acids were iso-C15:0, anteiso-C15:0, C16:1 ω6c and/or 10-methyl C16:0. The polar lipids included two aminolipids, two glycolipids and seven phospholipids. The DNA G+C content was 42.0 mol%. Based on phylogenetic, phylogenomic, genomic, phenotypic and chemotaxonomic data, we propose that strain N2T (=KCTC 102228T=MCCC 1K08942T) represents a novel species within the genus Fodinibius, with the name Fodinibius alkaliphilus sp. nov. We also propose the reclassification of Alifodinibius salipaludis as Fodinibius salipaludis sp. nov.
  • Heterologous expression and structure prediction of a xylanase identified from a compost metagenomic library
    Joana Sousa, Cátia Santos-Pereira, Joana S. Gomes, Ângela M. A. Costa, Andréia O. Santos, Ricardo Franco-Duarte, João M. M. Linhares, Sérgio F. Sousa, Sara C. Silvério, Lígia R. Rodrigues
    Applied Microbiology and Biotechnology, 2024
    Xylanases are key biocatalysts in the degradation of the β‐1,4‐glycosidic linkages in the xylan backbone of hemicellulose. These enzymes are potentially applied in a wide range of bioprocessing industries under harsh conditions. Metagenomics has emerged as powerful tools for the bioprospection and discovery of interesting bioactive molecules from extreme ecosystems with unique features, such as high temperatures. In this study, an innovative combination of function-driven screening of a compost metagenomic library and automatic extraction of halo areas with in-house MATLAB functions resulted in the identification of a promising clone with xylanase activity (LP4). The LP4 clone proved to be an effective xylanase producer under submerged fermentation conditions. Sequence and phylogenetic analyses revealed that the xylanase, Xyl4, corresponded to an endo-1,4-β-xylanase belonging to glycosyl hydrolase family 10 (GH10). When xyl4 was expressed in Escherichia coli BL21(DE3), the enzyme activity increased about 2-fold compared to the LP4 clone. To get insight on the interaction of the enzyme with the substrate and establish possible strategies to improve its activity, the structure of Xyl4 was predicted, refined, and docked with xylohexaose. Our data unveiled, for the first time, the relevance of the amino acids Glu133 and Glu238 for catalysis, and a close inspection of the catalytic site suggested that the replacement of Phe316 by a bulkier Trp may improve Xyl4 activity. Our current findings contribute to enhancing the catalytic performance of Xyl4 towards industrial applications. Key points • A GH10 endo-1,4-β-xylanase (Xyl4) was isolated from a compost metagenomic library • MATLAB’s in-house functions were developed to identify the xylanase-producing clones • Computational analysis showed that Glu133 and Glu238 are crucial residues for catalysis Graphical abstract
  • Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples
    Cátia Santos-Pereira, Joana Sousa, Ângela M. A. Costa, Andréia O. Santos, Teresa Rito, Pedro Soares, Ricardo Franco-Duarte, Sara C. Silvério, Lígia R. Rodrigues
    Applied Microbiology and Biotechnology, 2023
    The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples’ microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. Key points • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
  • Metagenomics to unravel the microbial biodiversity and biotechnological potential of extreme high salinity environments
    Cátia Santos-Pereira, Joana Sousa, Sara C. Silvério, Marta Filipa Simões, André Antunes, Lígia R. Rodrigues
    Functional Metagenomics Microbial Diversity Interaction and Application in Bioremediation, 2023
  • Application of metagenomics in the field of biotechnological conversion of lignocellulosic residues
    Andréia O. Santos, Joana Sousa, Ângela M.A. Costa, Joana L. Rodrigues, Eduardo J. Gudiña, Sara C. Silvério, Lígia R. Rodrigues
    Functional Metagenomics Microbial Diversity Interaction and Application in Bioremediation, 2023
  • Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water
    Joana Sousa, Sara C. Silvério, Angela M. A. Costa, Ligia R. Rodrigues
    Catalysts, 2022
    Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
  • Improved method for the extraction of high-quality DNA from lignocellulosic compost samples for metagenomic studies
    Ângela M. A. Costa, Andréia O. Santos, Joana Sousa, Joana L. Rodrigues, Eduardo J. Gudiña, Sara C. Silvério, Ligia R. Rodrigues
    Applied Microbiology and Biotechnology, 2021
    The world economy is currently moving towards more sustainable approaches. Lignocellulosic biomass has been widely used as a substitute for fossil sources since it is considered a low-cost bio-renewable resource due to its abundance and continuous production. Compost habitats presenting high content of lignocellulosic biomass are considered a promising source of robust lignocellulose-degrading enzymes. Recently, several novel biocatalysts from different environments have been identified using metagenomic techniques. A key point of the metagenomics studies is the extraction and purification of nucleic acids. Nevertheless, the isolation of high molecular weight DNA from soil-like samples, such as compost, with the required quality for metagenomic approaches remains technically challenging, mainly due to the complex composition of the samples and the presence of contaminants like humic substances. In this work, a rapid and cost-effective protocol for metagenomic DNA extraction from compost samples composed of lignocellulosic residues and containing high content of humic substances was developed. The metagenomic DNA was considered as representative of the global environment and presented high quality (> 99% of humic acids effectively removed) and sufficient quantity (10.5-13.8 µg g-1 of compost) for downstream applications, namely functional metagenomic studies. The protocol takes about 4 h of bench work, and it can be performed using standard molecular biology equipment and reagents available in the laboratory. KEY POINTS/HIGHLIGHTS: • Metagenomic DNA was successfully extracted from compost samples rich in humic acids • The improved protocol was established by optimizing the cell lysis method and buffer • Complete removal of humic acids was achieved through the use of activated charcoal • The suitability of the DNA was proven by the construction of a metagenomic library.

RECENT SCHOLAR PUBLICATIONS

  • Improved method for the extraction of high-quality DNA from lignocellulosic compost samples for metagenomic studies
    ÂMA Costa, AO Santos, J Sousa, JL Rodrigues, EJ Gudiña, SC Silvério, ...
    Applied microbiology and biotechnology 105 (23), 8881-8893 , 2021
    2021
    Citations: 17

MOST CITED SCHOLAR PUBLICATIONS

  • Improved method for the extraction of high-quality DNA from lignocellulosic compost samples for metagenomic studies
    ÂMA Costa, AO Santos, J Sousa, JL Rodrigues, EJ Gudiña, SC Silvério, ...
    Applied microbiology and biotechnology 105 (23), 8881-8893 , 2021
    2021
    Citations: 17