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Vitorino IR, Pinto E, Martín J, Mackenzie TA, Ramos MC, Sánchez P, de la Cruz M, Vicente F, Vasconcelos V, Reyes F, Lage OM. Uncovering the biotechnological capacity of marine and brackish water Planctomycetota. Antonie Van Leeuwenhoek 2024; 117:26. [PMID: 38261060 PMCID: PMC10805854 DOI: 10.1007/s10482-023-01923-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024]
Abstract
An appealing strategy for finding novel bioactive molecules in Nature consists in exploring underrepresented and -studied microorganisms. Here, we investigated the antimicrobial and tumoral anti-proliferative bioactivities of twenty-three marine and estuarine bacteria of the fascinating phylum Planctomycetota. This was achieved through extraction of compounds produced by the Planctomycetota cultured in oligotrophic medium followed by an antimicrobial screening against ten relevant human pathogens including Gram-positive and Gram-negative bacteria, and fungi. Cytotoxic effects of the extracts were also evaluated against five tumoral cell lines. Moderate to potent activities were obtained against Enterococcus faecalis, methicillin-sensitive and methicillin-resistant Staphylococcus aureus and vancomycin-sensitive and vancomycin-resistant Enterococcus faecium. Anti-fungal effects were observed against Trichophyton rubrum, Candida albicans and Aspergillus fumigatus. The highest cytotoxic effects were observed against human breast, pancreas and melanoma tumoral cell lines. Novipirellula caenicola and Rhodopirellula spp. strains displayed the widest spectrum of bioactivities while Rubinisphaera margarita ICM_H10T affected all Gram-positive bacteria tested. LC-HRMS analysis of the extracts did not reveal the presence of any known bioactive natural product, suggesting that the observed activities are most likely caused by novel molecules, that need identification. In summary, we expanded the scope of planctomycetal species investigated for bioactivities and demonstrated that various strains are promising sources of novel bioactive compounds, which reenforces the potential biotechnological prospects offered by Planctomycetota.
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Affiliation(s)
- Inês R Vitorino
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal.
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal.
| | - Eugénia Pinto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Jesús Martín
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Thomas A Mackenzie
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Maria C Ramos
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Pilar Sánchez
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Vítor Vasconcelos
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
| | - Fernando Reyes
- Fundación MEDINA, PTS Health Sciences Technology Park, Avenida del Conocimiento 34, 18016, Granada, Spain
| | - Olga M Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre S/N, 4169-007, Porto, Portugal
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, 4450-208, Matosinhos, Portugal
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Dos Santos JDN, Pinto E, Martín J, Vicente F, Reyes F, Lage OM. Unveiling the bioactive potential of Actinomycetota from the Tagus River estuary. Int Microbiol 2024:10.1007/s10123-024-00483-0. [PMID: 38236380 DOI: 10.1007/s10123-024-00483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 01/19/2024]
Abstract
The increase in global travel and the incorrect and excessive use of antibiotics has led to an unprecedented rise in antibiotic resistance in bacterial and fungal populations. To overcome these problems, novel bioactive natural products must be discovered, which may be found in underexplored environments, such as estuarine habitats. In the present work, estuarine actinomycetotal strains were isolated with conventional and iChip techniques from the Tagus estuary in Alcochete, Portugal, and analysed for different antimicrobial bioactivities. Extracts were produced from the isolated cultures and tested for bioactivity against Staphylococcus aureus ATCC 29213, Escherichia coli ATCC 25922, Aspergillus fumigatus ATCC 240305, Candida albicans ATCC 10231 and Trichophyton rubrum FF5. Furthermore, bioactive extracts were subjected to dereplication by high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS) to putatively identify their chemical components. In total, 105 isolates belonging to 3 genera were obtained. One which was isolated, MTZ3.1 T, represents a described novel taxon for which the name Streptomyces meridianus was proposed. Regarding the bioactivity testing, extracts from 12 strains proved to be active against S. aureus, 2 against E. coli, 4 against A. fumigatus, 3 against C. albicans and 10 against T. rubrum. Dereplication of bioactive extracts showed the presence of 28 known bioactive molecules, 35 hits have one or more possible matches in the DNP and 18 undescribed ones. These results showed that the isolated bacteria might be the source of new bioactive natural products.
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Affiliation(s)
- José Diogo Neves Dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, S/N, 4169-007, Porto, Portugal.
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal.
| | - Eugénia Pinto
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
- Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Jesús Martín
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Francisca Vicente
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Fernando Reyes
- Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Fundación MEDINA, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de La Salud, 18016, Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, S/N, 4169-007, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros Do Porto de Leixões, University of Porto, Avenida General Norton de Matos, S/N, 4450-208, Matosinhos, Portugal
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Santos JDND, Klimek D, Calusinska M, Lobo-da-Cunha A, Catita J, Gonçalves H, González I, Reyes F, Lage OM. Streptomyces meridianus sp. nov. isolated from brackish water of the Tagus estuary in Alcochete, Portugal. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486346 DOI: 10.1099/ijsem.0.005987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
An isolation effort focused on sporogenous Actinomycetota from the Tagus estuary in Alcochete, Portugal, yielded a novel actinomycetal strain, designated MTZ3.1T, which was subjected to a polyphasic taxonomic study. MTZ3.1T is characterised by morphology typical of members of the genus Streptomyces, with light beige coloured substrate mycelium, which does not release pigments to the culture medium and with helicoidal aerial hyphae that differentiate into spores with a light-grey colour. The phylogeny of MTZ3.1T, based on the full 16S rRNA gene sequence, indicated that its closest relatives were Streptomyces alkaliterrae OF1T (98.48 %), Streptomyces chumphonensis KK1-2T (98.41 %), Streptomyces albofaciens JCM 4342T (98.34 %), Streoptomyces paromomycinus NBRC 15454T (98.34 %) and Streptomyces chrestomyceticus NRBC 13444T (98.34 %). Moreover, average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridisation (dDDH) are below the species cutoff values (ANI 67.70 and 68.35 %, AAI 77.06 and 76.71 % and dDDH 22.10 and 21.50 % for S. alkaliterrae OF1T and S. chumphonensis KK1-2T, respectively). Whole genome sequencing revealed that MTZ3.1T has a genome of 5 644 485 bp with a DNA G+C content of 71.29 mol% and 5044 coding sequences. Physiologically, MTZ3.1T is strictly aerobic, able to grow at 15-37 °C, optimally at 25 °C and between pH5 and 8 and showed high salinity tolerance, growing with 0-10 %(w/v) NaCl. Major cellular fatty acids are C15 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0. Furthermore, it was able to utilise a variety of nitrogen and carbon sources. Antimicrobial screening indicated that MTZ3.1T has potent anti-Staphylococcus aureus activity. On the basis of the polyphasic data, MTZ3.1T is proposed to represent a novel species, Streptomyces meridianus sp. nov. (= CECT 30416T = DSM 114037T=LMG 32463T).
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Affiliation(s)
- José Diogo Neves Dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n° 4169-007 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Porto, Portugal
| | - Dominika Klimek
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 4365 Esch-Belval Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), Belvaux, Luxembourg
| | - Alexandre Lobo-da-Cunha
- Department of Microscopy, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - José Catita
- Paralab, SA, Valbom, Portugal
- FP-I3ID, FP-BHS, Faculdade de Ciências da Saúde, Universidade Fernando Pessoa, Rua Carlos da Maia 296, 4200-150 Porto, Portugal
| | | | - Ignacio González
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud1, 8016 Granada, Spain
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud1, 8016 Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n° 4169-007 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Porto, Portugal
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Vitorino IR, Klimek D, Calusinska M, Lobo-da-Cunha A, Vasconcelos V, Lage OM. Stieleria sedimenti sp. nov., a Novel Member of the Family Pirellulaceae with Antimicrobial Activity Isolated in Portugal from Brackish Sediments. Microorganisms 2022; 10:2151. [PMID: 36363743 PMCID: PMC9692418 DOI: 10.3390/microorganisms10112151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 09/23/2023] Open
Abstract
The phylum Planctomycetota is known for having uncommon biological features. Recently, biotechnological applications of its members have started to be explored, namely in the genus Stieleria. Here, we formally describe a novel Stieleriaisolate designated as strain ICT_E10.1T, obtained from sediments collected in the Tagus estuary (Portugal). Strain ICT_E10.1T is pink-pigmented, spherical to ovoid in shape, and 1.7 µm ± 0.3 × 1.4 µm ± 0.3 in size. Cells cluster strongly in aggregates or small chains, divide by budding, and have prominent fimbriae. Strain ICT_E10.1T is heterotrophic and aerobic. Growth occurs from 20 to 30 °C, from 0.5 to 3% (w/v) NaCl, and from pH 6.5 to 11.0. The analysis of the 16S rRNA gene sequence placed strain ICT_E10.1T into the genus Stieleria with Stieleria neptunia Enr13T as the closest validly described relative. The genome size is 9,813,311 bp and the DNA G+C content is 58.8 mol%. Morphological, physiological, and genomic analyses support the separation of this strain into a novel species, for which we propose the name Stieleria sedimenti represented by strain ICT_E10.1T as the type of strain (=CECT 30514T= DSM 113784T). Furthermore, this isolate showed biotechnological potential by displaying relevant biosynthetic gene clusters and potent activity against Staphylococcus aureus.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Dominika Klimek
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
- The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, 2 Avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Magdalena Calusinska
- The Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Vasconcelos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
- CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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Vitorino IR, Klimek D, Calusinska M, Lobo-da-Cunha A, Vasconcelos V, Lage OM. Rhodopirellula aestuarii sp. nov., a novel member of the genus Rhodopirellula isolated from brackish sediments collected in the Tagus River estuary, Portugal. Syst Appl Microbiol 2022; 45:126360. [PMID: 36166947 DOI: 10.1016/j.syapm.2022.126360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/31/2022] [Accepted: 09/08/2022] [Indexed: 10/31/2022]
Abstract
Bacteria within the phylum Planctomycetota are biologically relevant due to unique characteristics among prokaryotes. Members of the genus Rhodopirellula can be abundant in marine habitats, however, only six species are currently validly described. In this study, we expand the explored genus diversity by formally describing a novel species. The pink-coloured strain ICT_H3.1T was isolated from brackish sediments collected in the Tagus estuary (Portugal) and a 16S rRNA gene sequence-based analysis placed this strain into the genus Rhodopirellula (family Pirellulaceae). The closest type strain is Rhodopirellula rubra LF2T, suggested by a similarity of 98.4% of the 16S rRNA gene sequence. Strain ICT_H3.1T is heterotrophic, aerobic and able to grow under microaerobic conditions. The strain grows between 15 and 37 °C, over a range of pH 6.5 to 11.0 and from 1 to 8% (w/v) NaCl. Several nitrogen and carbon sources were utilized by the novel isolate. Cells have an elongated pear-shape with 2.0 ± 0.3 × 0.9 ± 0.2 µm in size. Cells of strain ICT_H3.1T cluster in rosettes through a holdfast structure and divide by budding. Younger cells are motile. Ultrathin cell sections show cytoplasmic membrane invaginations and polar fimbriae. The genome size is 9,072,081 base pairs with a DNA G + C content of 56.1 mol%. Genomic, physiological and morphological comparison of strain ICT_H3.1T with its relatives suggest that it belongs to a novel species within the genus Rhodopirellula. Hence, we propose the name Rhodopirellula aestuarii sp. nov., represented by ICT_H3.1T (=CECT30431T = LMG32464T) as the type strain of this novel species. 16S rRNA gene accession number: GenBank = OK001858. Genome accession number: The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JAMQBK000000000. The version described in this paper is version JAMQBK010000000.
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Affiliation(s)
- Inês Rosado Vitorino
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal.
| | - Dominika Klimek
- Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg; The Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Luxemburg
| | - Magdalena Calusinska
- Luxembourg Institute of Science and Technology (LIST), 41 rue du Brill, L-4422 Belvaux, Luxemburg
| | - Alexandre Lobo-da-Cunha
- Laboratório de Biologia Celular, Instituto de Ciências Biomédicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Vítor Vasconcelos
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Olga Maria Lage
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; CIIMAR/CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
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