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Background Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as “banquettes”. In recent years, interest in the potential uses of these P. oceanica banquettes has increased and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, a metagenomic study was performed to investigate the microbial community associated with P. oceanica banquettes.
Results The microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Cyanobacteria. Pseudoalteromonas was the most abundant genus, followed by Alteromonas , Labrencia, and Aquimarina . The metagenome reads were binned and assembled into 23 near-complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges and hydrothermal vents, indicated that banquettes have numbers of natural products and Carbohydrate-Active Enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New condensation (C) domains in multi-enzymatic non ribosomal peptide synthetases (NRPS) solely found in P. oceanica banquettes were recovered; 90 of the 181 found lacked known homologues. Furthermore, new proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found.
Conclusions Our results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes.
Keywords
Gammaproteobacteria, Myxococcota, oceanica
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This is a list of supplementary files associated with this preprint. Click to download.
- TableS1RubioPortilloetal..pdf
Table S1. Taxonomies of each MAG inferred using the GTDB-tk database and the MIGA platform. * indicates MAGs that were classified using phylogenetic reconstructions obtained with PhyloPhlan.
- TableS2.pdf
Table S2. Main features of the published metagenomes used in this paper.
- TableS3RubioPortilloetal..xlsx
Table S3. Average sequencing depth and taxonomic assignment of each assembled contig (< 5 Kb) from the Posidonia oceanica banquettes.
- TableS4.pdf
Table S4. Classification of K and C domains using NaPDoS database in the Metagenome Assembled Genomes (MAGs) recovered from Posidonia oceanica banquettes.
- SupplementaryFiguresRubioPortilloetal..pdf
Figure S1. Phylogenetic assignment of assembled genome bins MAG19 and MAG5. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Organisms are colored based on genome size (Mb, in brackets). Figure S2. Phylogenetic assignment of assembled genome bins MAG69. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S3. Phylogenetic assignment of assembled genome bins MAG122 and MAG79. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S4. Phylogenetic assignment of assembled genome bin MAG121. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S5. Phylogenetic assignment of assembled genome bin MAG66. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S6. Phylogenetic assignment of assembled genome bin MAG114. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S7. Phylogenetic assignment of assembled genomes MAG36, 54 and 106. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S8. Krona plot created from Kaiju taxonomic classification of sequence reads from the Posidonia oceanica banquettes. Figure S9. Comparison of Posidonia oceanica contig K141-4070505 with closely related phage genomes.
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
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Subject Areas
General Microbiology
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This work is licensed under a CC BY 4.0 License. Read Full License
Background Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as “banquettes”. In recent years, interest in the potential uses of these P. oceanica banquettes has increased and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, a metagenomic study was performed to investigate the microbial community associated with P. oceanica banquettes.
Results The microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Cyanobacteria. Pseudoalteromonas was the most abundant genus, followed by Alteromonas , Labrencia, and Aquimarina . The metagenome reads were binned and assembled into 23 near-complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges and hydrothermal vents, indicated that banquettes have numbers of natural products and Carbohydrate-Active Enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New condensation (C) domains in multi-enzymatic non ribosomal peptide synthetases (NRPS) solely found in P. oceanica banquettes were recovered; 90 of the 181 found lacked known homologues. Furthermore, new proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found.
Conclusions Our results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
This is a list of supplementary files associated with this preprint. Click to download.
- TableS1RubioPortilloetal..pdf
Table S1. Taxonomies of each MAG inferred using the GTDB-tk database and the MIGA platform. * indicates MAGs that were classified using phylogenetic reconstructions obtained with PhyloPhlan.
- TableS2.pdf
Table S2. Main features of the published metagenomes used in this paper.
- TableS3RubioPortilloetal..xlsx
Table S3. Average sequencing depth and taxonomic assignment of each assembled contig (< 5 Kb) from the Posidonia oceanica banquettes.
- TableS4.pdf
Table S4. Classification of K and C domains using NaPDoS database in the Metagenome Assembled Genomes (MAGs) recovered from Posidonia oceanica banquettes.
- SupplementaryFiguresRubioPortilloetal..pdf
Figure S1. Phylogenetic assignment of assembled genome bins MAG19 and MAG5. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Organisms are colored based on genome size (Mb, in brackets). Figure S2. Phylogenetic assignment of assembled genome bins MAG69. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S3. Phylogenetic assignment of assembled genome bins MAG122 and MAG79. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S4. Phylogenetic assignment of assembled genome bin MAG121. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S5. Phylogenetic assignment of assembled genome bin MAG66. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S6. Phylogenetic assignment of assembled genome bin MAG114. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S7. Phylogenetic assignment of assembled genomes MAG36, 54 and 106. The phylogenetic tree was obtained with PhyloPhlAn using broadly conserved proteins to extract phylogenetic signal. Figure S8. Krona plot created from Kaiju taxonomic classification of sequence reads from the Posidonia oceanica banquettes. Figure S9. Comparison of Posidonia oceanica contig K141-4070505 with closely related phage genomes.
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