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- From lignocellulosic residues to protein sources: insights into biomass pre-treatments and conversionPublication . Vera dos Anjos, Isabela; Coelho, Natacha; Duarte, Hugo; Proença, Diogo Neves; Duarte, Maria F.; Jorge de Barros, Raúl José; Raposo, Sara; Gonçalves, Sandra; Romano, Anabela; Medronho, BrunoWith the global population steadily rising, the demand for sustainable protein sources has become increasingly urgent. Traditional animal- and plant-based proteins face challenges related to scalability, resource efficiency, and environmental impact. In this context, single-cell protein has emerged as a promising alternative. Derived from microorganisms such as algae, bacteria, fungi, and yeast, single-cell protein offers a high nutritional profileincluding all essential amino acids and vitamins—while enabling rapid production, minimal land and water requirements, and no generation of greenhouse gas emissions. A particularly compelling advantage of single-cell protein is its ability to be produced from agro-industrial waste, converting low-cost residues into valuable nutritional resources and contributing to environmental sustainability. Among these waste streams, lignocellulosic biomass from agricultural and forestry residues stands out as a renewable, biodegradable, and abundant feedstock. This review explores the potential of lignocellulosic waste as a substrate for single-cell protein production, emphasizing both its environmental advantages and nutritional value. It highlights the single-cell protein role as a sustainable and scalable alternative to conventional protein sources. The review also identifies key scientific, economic, and regulatory challenges, and recognizes the importance of targeted investments, particularly in policy development, public awareness, and technological innovation, to enable the broader adoption and acceptance of single-cell protein -based products.
- Potential protective role of amphibian skin bacteria against water mold saprolegnia spp.Publication . Costa, Sara; Proença, Diogo Neves; Alves, Artur; Morais, Paula V.; Lopes, IsabelAmphibian populations have experienced a severe decline over the past 40 years, driven primarily by environmental pollution, habitat destruction, climate change, and disease. This work reports, for the first time, saprolegniosis in Pelophylax perezi egg masses and saprolegniosis in amphibians in Portugal. After isolation and phylogenetic analysis, the pathogen was identified as Saprolegnia australis. Following this, the present work intended to screen a collection of P. perezi skin bacteria for the existence of bacterial strains with inhibitory action against the newly identified S. australis SC1 and two other species, Saprolegnia diclina SAP 1010 UE and Saprolegnia australis SAP 1581 UE. The results showed that various bacterial species could inhibit the growth of these three species of oomycetes. Bacteria with the most significant antagonistic action against Saprolegnia spp. predominantly belonged to the genus Bacillus, followed by Serratia, Pseudomonas, and Aeromonas. Despite variations in bacterial diversity among frog populations, the present study also demonstrated the presence of bacteria on frogs’ skin that were capable of inhibiting Saprolegnia spp., as evidenced by in vitro challenge assays. These findings highlight the protective function of bacteria present in amphibian skin. The observed bacterial diversity may contribute to the metabolic redundancy of the frog skin microbiome, helping to maintain its functional capacity despite shifts in the community composition. Additionally, the study found that, when providing a more advantageous environment for pathogen growth—in this case a peptone–glucose (PG) medium instead of R2A—the percentage of bacteria with moderate-to-strong antagonistic activity dropped by 13% to 4%. In conclusion, the presence of bacteria capable of inhibiting Saprolegnia spp. in adult individuals and across different environmental conditions may contribute to lowering the susceptibility of frog adults towards Saprolegnia spp., compared with that in the early stages of development, like the tadpole or egg stages.
- From Lignocellulosic residues to protein sources: insights into biomass pre-treatments and conversionPublication . Vera dos Anjos, Isabela; Coelho, Natacha; Duarte, Hugo; Proença, Diogo Neves; Duarte, Maria F.; Jorge de Barros, Raúl José; Raposo, Sara; Gonçalves, Sandra; Romano, Anabela; Medronho, BrunoWith the global population steadily rising, the demand for sustainable protein sources has become increasingly urgent. Traditional animal- and plant-based proteins face challenges related to scalability, resource efficiency, and environmental impact. In this context, single-cell protein has emerged as a promising alternative. Derived from microorganisms such as algae, bacteria, fungi, and yeast, single-cell protein offers a high nutritional profileincluding all essential amino acids and vitamins—while enabling rapid production, minimal land and water requirements, and no generation of greenhouse gas emissions. A particularly compelling advantage of single-cell protein is its ability to be produced from agro-industrial waste, converting low-cost residues into valuable nutritional resources and contributing to environmental sustainability. Among these waste streams, lignocellulosic biomass from agricultural and forestry residues stands out as a renewable, biodegradable, and abundant feedstock. This review explores the potential of lignocellulosic waste as a substrate for single-cell protein production, emphasizing both its environmental advantages and nutritional value. It highlights the single-cell protein role as a sustainable and scalable alternative to conventional protein sources. The review also identifies key scientific, economic, and regulatory challenges, and recognizes the importance of targeted investments, particularly in policy development, public awareness, and technological innovation, to enable the broader adoption and acceptance of single-cell protein -based products.
- Phylogenomics as baseline for taxonomy description: Amphibiibacter pelophylacis gen. nov., sp. nov., a novel taxon of the family Sphaerotilaceae, class Betaproteobacteria, isolated from the skin microbiota of Pelophylax perezi from different populationsPublication . Costa, Sara; Proença, Diogo Neves; Lopes, Isabel; Morais, Paula V.Bacterial strain SL12-8T was characterized and isolated from the skin microbiota of Pelophylax perezi, the Perez’s frog. Strain SL12-8T stained Gram-negative and formed rod-shaped cells that grew optimally at 25 °C and pH 7.0–7.5. The G+C content of the DNA was 66.2 mol%. Ubiquinone 8 was the respiratory quinone identified in the studied strain and the most closely related taxon. The major fatty acids were summed in feature 3 and summed in feature 8 and C16:0, representing 84% of the total fatty acids. Phylogenetic analyses based on the 16S rRNA gene sequence placed strain SL12-8T within the order Burkholderiales in a distinct lineage. The 16S rRNA gene sequence similarities of strain SL12-8T to that of Rubrivivax albus, Scleromatobacter humisilvae, Piscinibacter aquaticus, Azohydromonas caseinilytica and Aquincola agrisoli were 94.41, 94.08, 93.72, 93.72 and 93.64%, respectively. The draft genome sequence of strain SL12-8T comprises 3,115,197 bases with a 313-fold mapped genome coverage. The assembled genome consists of 53 large contigs with more than 500 bp, and the genome encodes 2,814 putative coding sequences. The analysis of the available genomes from the closest genera showed 124 core genes that reveal a novel genus-level clade including the strain SL12-8T . Analysis of the SL12-8T genome revealed the presence of the beta-lactone and terpene biosynthetic gene clusters. The phylogenomic, phylogenetic, phenotypic and chemotaxonomic data showed that strain SL12-8T (=UCCCB 131T =CECT 30762T ) represents the type of a novel species and genus, for which we propose the name Amphibiibacter pelophylacis gen. nov., sp. nov.
- Flavobacterium magnesitis sp. nov. and Flavobacterium zubiriense sp. nov. two novel Flavobacterium species isolated from alkaline magnesite residuesPublication . Matos, Leonor; Maccarrio, Lorrie; Chung, Ana Paula; Proença, Diogo Neves; Sørensen, Søren; Morais, Paula V; Francisco, RomeuThree bacterial strains, designated FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5, were isolated from distinct magnesite residues in Spain. Phylogenetic and phylogenomic analysis places them within the genus . Strains FBOR7N2.3 and FZUR7N2.5 share 100% of similarity in the 16S rRNA gene sequence, and both are most closely related to AR-3-4 with which they share 97.5% of 16S rRNA gene similarity. Strain FZUC8N2.13 forms a distinct lineage most closely related to IMCC36792 with 97.7% 16S rRNA gene similarity. The closest phylogenomic neighbours of these three strains are DSM 1076, '' BBQ-18 and PK15. The average nucleotide identity and digital DNA-DNA hybridization values between the three strains and closest members of the genus are below the threshold values of 95% and 70%, respectively. Strains FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5 stain Gram-negative, are rod-shaped and form yellow colonies. Optimum growth occurs at 25 °C and pH 7. The genomic G+C contents are 33.4 mol% for strain FZUC8N2.13 and 33.2 mol% for strains FBOR7N2.3 and FZUR7N2.5. The major isoprenoid quinone is menaquinone 6. The major fatty acids are summed feature 3 (C ω7c and/or C ω6c) (22.6-31.1%), iso-C (13.6-16.2 %) and anteiso-C (8.7-10.5%). The polar lipids consist of two aminolipids, two aminophospholipids and one glycolipid. The phylogenetic, phylogenomic, phenotypic and chemotaxonomic data indicate that FZUC8N2.13, FBOR7N2.3 and FZUR7N2.5 are distinct from the described species of and should be classified as novel species, for which we propose the names for strain FZUC8N2.13 (=UCCCB 179=CECT 30977) and for strains FBOR7N2.3 (=UCCCB 178=CECT 30976) and FZUR7N2.5 (=UCCCB 216=CECT 31036).
- Plant growth-promoting bacteria as biological control agents for sustainable agriculture: targeting root-knot nematodesPublication . Mata, Adriana S.; Cruz, Carlos; Gaspar, João Rodrigues; Abrantes, Isabel; Conceição, Isabel Luci; Morais, Paula V.; Proença, Diogo NevesThe increasing frequency of extreme weather events affects ecosystems and threatens food production. The reduction of chemical pesticides, together with other ecological approaches, is crucial to more sustainable agriculture. Plantparasitic nematodes (PPN), especially root-knot nematodes (RKN), Meloidogyne spp., are responsible for extensive damage to a wide range of economically important crops, leading to yield losses and reduced quality of the products. This study aims to show the potential of native potato-growing soil bacterial strains as biological control agents in a more sustainable agriculture perspective. After screening thirty bacterial strains, a bacterial consortium, composed of B. amyloliquefaciens UC_2.4, P. capeferrum UC_21.3 A.1, and P. capeferrum UC_21.30 A.1, was defined and investigated in more detail due to their potential for plant growth-promoting bacteria (PGPB), fungicidal, and nematicidal activities. The genomes of the strains were sequenced and analyzed for PGPB traits, and phenotypic assays were also performed. The nematicidal activity of these strains towards PPN and the model organism Caenorhabditis elegans was assessed. Their potential as PGPB and for controlling PPN on soil was evaluated in pot assays with tomato plants cv. Coração de Boi, by using bacterial strains alone and as a consortium. Here, the bacterial consortium showed some PGPB traits verified by genome mining and phenotypic assays in vitro and pot assays with plants. It was able to act as nematicidal agents with 100% efficacy towards PPN but not against C. elegans, indicating a highly targeted action mechanism, which might be attributed to the surfactin, fengycin, and lipopeptides, not affecting other nontarget organisms that play essential roles in soil health. The bacterial consortium reduced the infectivity of PPN in plants by threefold. This bacterial consortium was established for the first time and has the potential to serve as a new tool for managing RKN in a more sustainable agricultural environment.