Phylogenetic and functional characterization of the microbiome of Sargassum seaweed waste

References

• Ai, N., Jiang, Y., Omar, S., Wang, J., Xia, L., & Ren, J. (2022). Rapid measurement of cellulose, hemicellulose, and lignin content in Sargassum horneri by near-infrared spectroscopy and characteristic variables selection methods. Molecules, 27, 335. doi:10.3390/molecules27020335
   PubMed Web of Science ®Google Scholar
• Aires, T., Muyzer, G., Serrão, E. A., & Engelen, A. H. (2019). Seaweed loads cause stronger bacterial community shifts in coastal lagoon sediments than nutrient loads. Frontiers in Microbiology, 9, 3283. doi:10.3389/fmicb.2018.03283
   PubMedGoogle Scholar
• Akyol, Ç., Ince, O., & Ince, B. (2019). Crop-based composting of lignocellulosic digestates: Focus on bacterial and fungal diversity. Bioresources Technology, 288, 121549. doi:10.1016/j.biortech.2019.121549
   PubMed Web of Science ®Google Scholar
• Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature Methods, 13, 581–583. doi:10.1038/nmeth.3869
   PubMed Web of Science ®Google Scholar
• Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D. … Knight, R. (2010). QIIME allows analysis of high-throughput community sequencing data. Nature Methods, 7, 335–336. doi:10.1038/nmeth.f.303
   PubMed Web of Science ®Google Scholar
• Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A. and Knight, R. (2011). Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the USA, 108, 4516–4522.
   Google Scholar
• Carrillo-Domínguez, S., Rodríguez-Martínez, R. E., Díaz-Martínez, M., Magaña-Gallegos, E., & Cuchillo-Hilario, M. (2023). Potential application of pelagic Sargassum spp. in animal feeding. Journal of Applied Phycology, 35, 433–444. doi:10.1007/s10811-022-02877-x
   Web of Science ®Google Scholar
• Chávez, V., Uribe-Martínez, A., Cuevas, E., Rodríguez-Martínez, R. E., van Tussenbroek, B. I., Francisco, V., & Masia, L. (2020). Massive influx of pelagic Sargassum spp. on the coasts of the Mexican Caribbean 2014–2020: Challenges and opportunities. Water, 12, 2908. doi:10.3390/w12102908
   Web of Science ®Google Scholar
• Cheng, D., Jiang, C., Xu, J., Liu, Z., & Mao, X. (2020). Characteristics and applications of alginate lyases: A review. International Journal of Biological Macromolecules, 164, 1304–1320. doi:10.1016/j.ijbiomac.2020.07.199
   PubMed Web of Science ®Google Scholar
• Chen, D. M., Taylor, A. F. S., Burke, R. M., & Cairney, J. W. G. (2001). Identification of genes for lignin peroxidases and manganese peroxidases in ectomycorrhizal fungi. The New Phytologist, 152, 151–158. doi:10.1046/j.0028-646x.2001.00232.x
   PubMed Web of Science ®Google Scholar
• Chen, J., Zang, Y., Yang, Z., Qu, T., Sun, T. … Tang, X. (2022). Composition and functional diversity of epiphytic bacterial and fungal communities on marine macrophytes in an intertidal zone. Frontiers in Microbiology, 13, 3389. doi:10.3389/fmicb.2022.839465
   Web of Science ®Google Scholar
• Cleary, D. F. R., & Huang, Y. M. (2020). A comparison of the prokaryotic communities associated with seven seaweed species, sediment, and seawater from the Penghu archipelago, Taiwan. Marine Biology Research, 16, 744–761. doi:10.1080/17451000.2020.1859119
   Web of Science ®Google Scholar
• Davis, D., Simister, R., Campbell, S., Marston, M., Bose, S., McQueen-Mason, S. J., & Gallimore, W. A. (2021). Biomass composition of the golden tide pelagic seaweeds Sargassum fluitans and S. natans (morphotypes I and VIII) to inform valorisation pathways. The Science of the Total Environment, 762, 143134. doi:10.1016/j.scitotenv.2020.143134
   PubMed Web of Science ®Google Scholar
• Davis, T. A., Volesky, B., & Mucci, A. (2003). A review of the biochemistry of heavy metal biosorption by brown algae. Water Research, 37, 4311–4330. doi:10.1016/S0043-1354(03)00293-8
   PubMed Web of Science ®Google Scholar
• Del Río, P. G., Domínguez, E., Domínguez, V. D., Romaní, A., Domingues, L., & Garrote, G. (2019). Third generation bioethanol from invasive macroalgae Sargassum muticum using autohydrolysis pretreatment as first step of a biorefinery. Renewable Energy, 141, 728–735. doi:10.1016/j.renene.2019.03.083
   Web of Science ®Google Scholar
• Dong, S., Yang, J., Zhang, X.-Y., Shi, M., Song, X.-Y., Chen, X.-L., & Zhang, Y.-Z. (2012). Cultivable alginate lyase-excreting bacteria associated with the arctic brown alga Laminaria. Marine Drugs, 10, 2481. doi:10.3390/md10112481
   PubMed Web of Science ®Google Scholar
• Drula, E., Garron, M. L., Dogan, S., Lombard, V., Henrissat, B., & Terrapon, N. (2022). The carbohydrate-active enzyme database: Functions and literature. Nucleic Acids Research, 50, D571–D577. doi:10.1093/nar/gkab1045
   PubMed Web of Science ®Google Scholar
• Fernando, P. S. I., Kim, K.-N., Kim, D., & Jeon, Y.-J. (2019). Algal polysaccharides: Potential bioactive substances for cosmeceutical applications. Critical Reviews in Biotechnology, 39, 99–113. doi:10.1080/07388551.2018.1503995
   Web of Science ®Google Scholar
• Gaynor, M., & Mankin, A. S. (2003). Macrolide antibiotics: Binding site, mechanism of action, resistance. Current Topics in Medicinal chemistry, 3, 949. doi:10.2174/1568026033452159
   PubMed Web of Science ®Google Scholar
• Gliszczynska-Swiglo, A. (2007). Folates as antioxidants. Food Chemistry, 101, 1480–1483. doi:10.1016/j.foodchem.2006.04.022
   Web of Science ®Google Scholar
• Gower, J., & King, S. (2019). Seaweed, seaweed everywhere. Science, 365, 27. doi:10.1126/science.aay0989
   PubMed Web of Science ®Google Scholar
• Hervé, V., Lambourdière, J., René-Trouillefou, M., Devault, D. A., & Lopez, P. J. (2021). Sargassum differentially shapes the microbiota composition and diversity at coastal tide sites and inland storage sites on Caribbean islands. Frontiers in Microbiology, 12, 701155. doi:10.3389/fmicb.2021.701155
   PubMedGoogle Scholar
• Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M. (2016). KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research, 44, D457–D462. doi:10.1093/nar/gkv1070
   PubMed Web of Science ®Google Scholar
• Keatinge-Clay, A. T., Maltby, D. A., Medzihradszky, K. F., Khosla, C., & Stroud, R. M. (2004). An antibiotic factory caught in action. Nature Structural & Molecular Biology, 11, 888–893. doi:10.1038/nsmb808
   PubMed Web of Science ®Google Scholar
• Kostas, E. T., Adams, J. M. M., Ruiz, H. A., Duran-Jimenez, G., & Lye, G. J. (2021). Macroalgal biorefinery concepts for the circular bioeconomy: A review on biotechnological developments and future perspectives. Renewable Sustainable Energy Reviews, 151, 111553. doi:10.1016/j.rser.2021.111553
   Web of Science ®Google Scholar
• Laeliocattleya, R. A., Suloi, Y. A. F., Gayatri, P. P., Putri, N. A., & Anggraeni, Y. C. (2020). Fucoidan content from brown seaweed (Sargassum filipendula) and its potential as radical scavenger. Journal of Physics: Conference Series, 1430, 012023.
   Google Scholar
• Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D. … Huttenhower, C. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology, 31, 814–821. doi:10.1038/nbt.2676
   PubMed Web of Science ®Google Scholar
• Langin, K. (2018). Seaweed masses assault Caribbean islands. Science, 360, 1157–1158. doi:10.1126/science.360.6394.1157
   PubMed Web of Science ®Google Scholar
• Leong, Y. K., & Chang, J. S. (2022). Integrated role of algae in the closed-loop circular economy of anaerobic digestion. Bioresources and Technology, 360, 127618. doi:10.1016/j.biortech.2022.127618
   PubMed Web of Science ®Google Scholar
• Lombo, F., Menendez, N., Salas, J. A., & Mendez, C. (2006). The aureolic acid family of antitumor compounds: Structure, mode of action, biosynthesis, and novel derivatives. Applied Microbiology and Biotechnology, 73, 1–14. doi:10.1007/s00253-006-0511-6
   PubMed Web of Science ®Google Scholar
• Martin, M., Barbeyron, T., Martin, R., Portetelle, D., Michel, G., & Vandenbol, M. (2015). The cultivable surface microbiota of the brown alga Ascophyllum nodosum is enriched in macroalgal-polysaccharide-degrading bacteria. Frontiers in Microbiology, 6, 1487. doi:10.3389/fmicb.2015.01487
   PubMed Web of Science ®Google Scholar
• Mei, X., Wu, C., Zhao, J., Yan, T., & Jiang, P. (2019). Community structure of bacteria associated with drifting Sargassum horneri, the causative species of golden tide in the Yellow Sea. Frontiers in Microbiology, 10, 1192. doi:10.3389/fmicb.2019.01192
   PubMed Web of Science ®Google Scholar
• Merle, H., Resière, D., Mesnard, C., Pierre, M., Jean-Charles, A., Béral, L., & Nevière, R. (2021). Case report: Two cases of keratoconjunctivitis tied to Sargassum algae emanations. American Journal of Tropical Medicine and Hygiene, 104, 403–405. doi:10.4269/ajtmh.20-0636
   PubMed Web of Science ®Google Scholar
• Milledge, J. J., Nielsen, B. V., & Bailey, D. (2016). High-value products from macroalgae: The potential uses of the invasive brown seaweed, Sargassum muticum. Reviews in Environmental Science and Biotechnology, 15, 67–88. doi:10.1007/s11157-015-9381-7
   Web of Science ®Google Scholar
• Miranda, J. L. L., Celis, L. B., Estévez, M., Chávez, V., van Tussenbroek, B. I., Uribe-Martínez, A., & Cauich-Kantun, C. (2021). Commercial potential of pelagic Sargassum spp. in Mexico. Frontiers in Marine Science, 8, 768470. doi:10.3389/fmars.2021.768470
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2017). Kinetic and thermodynamic properties of alginate lyase and cellulase co-produced by Exiguobacterium species Alg-S5. International Journal of Biological Macromolecules, 98, 103–110. doi:10.1016/j.ijbiomac.2017.01.091
   PubMed Web of Science ®Google Scholar
• Mohapatra, B. R. (2018). Biocatalytic efficacy of immobilized cells of Chryseobacterium sp. Alg-SU10 for simultaneous hydrolysis of urethane and urea. Biocatalysis and Biotransformation, 36, 307–315. doi:10.1080/10242422.2018.1445228
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2020). Biocatalytic characteristics of chitosan nanoparticle-immobilized alginate lyase extracted from a novel Arthrobacter species AD-10. Biocatalysis and Agricultural Biotechnology, 23, 101458. doi:10.1016/j.bcab.2019.101458
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2021a). Characterization of β-mannanase extracted from a novel Streptomyces species Alg-S25 immobilized on chitosan nanoparticles. Biotechnology & Biotechnological Equipment, 35, 150–161. doi:10.1080/13102818.2020.1858158
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2021b). Comparative kinetic analysis of alginate lyase and mannanase co-produced via solid-state fermentation of cow dung supplemented with seaweed wastes by a novel Streptomyces sp. Alg-S23. Biomass Conversion and Biorefinery, 11, 2013–2025. doi:10.1007/s13399-020-00658-5
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2021c). Solid-state fermentation conditions optimization, homology modelling and molecular docking of β-mannanase of a novel Streptomyces species LB66 isolated from Sargassum seaweed waste. Biocatalysis and Biotransformation, 41, 187–197. doi:10.1080/10242422.2021.2010719
   Web of Science ®Google Scholar
• Mohapatra, B. R. (2022). Fermentation medium optimization, molecular modelling and docking analysis of the alginate lyase of a novel Pseudomonas sp. LB56 isolated from seaweed waste. Biotechnology & Biotechnological Equipment, 36, 281–291. doi:10.1080/13102818.2022.2071635
   Web of Science ®Google Scholar
• Mohapatra, B. R., Schambeau, L., Pannell, L. K., & Kiene, R. P. (2017). Comparative proteomics of temperate and polar Phaeocystis species. Nova Hedwigia, 105, 15–27. doi:10.1127/nova_hedwigia/2016/0393
   Web of Science ®Google Scholar
• Morand, P., & Merceron, M. (2005). Macroalgal population and sustainability. Journal of Coastal Research, 2005, 1009–1020. doi:10.2112/04-700A.1
   Google Scholar
• Nilsson, R. H., Larsson, K.-H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S. … Abarenkov, K. (2018). The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research, 47, D259–D264. doi:10.1093/nar/gky1022
   Web of Science ®Google Scholar
• Oh, R. M., Bollati, E., Maithani, P., Huang, D., & Wainwright, B. J. (2021). The microbiome of the reef macroalga Sargassum ilicifolium in Singapore. Microorganisms, 9, 898. doi:10.3390/microorganisms9050898
   PubMed Web of Science ®Google Scholar
• Oviatt, C. A., Huizenga, K., Rogers, C. S., & Miller, W. J. (2019). What nutrient sources support anomalous growth and the recent Sargassum mass stranding on Caribbean beaches? A review. Marine Pollution Bulletin, 145, 517–525. doi:10.1016/j.marpolbul.2019.06.049
   PubMed Web of Science ®Google Scholar
• Park, S. R., Han, A. R., Ban, Y. H., Yoo, Y. J., Kim, E. J., & Yoon, Y. J. (2010). Genetic engineering of macrolide biosynthesis: Past advances, current state, and future prospects. Applied Microbiology and Biotechnology, 85, 1227–1239. doi:10.1007/s00253-009-2326-8
   PubMed Web of Science ®Google Scholar
• Patyshakuliyeva, A., Falkoski, D. L., Wiebenga, A., Timmermans, K., & de Vries, R. P. (2019). Macroalgae derived fungi have high abilities to degrade algal polymers. Microorganisms, 8, 52. doi:10.3390/microorganisms8010052
   PubMed Web of Science ®Google Scholar
• Resiere, D., Valentino, R., Nevière, R., Banydeen, R., Gueye, P., Florentin, J., Cabié, A., Lebrun, T., Mégarbane, B., Guerrier, G., & Mehdaoui, H. (2018). Sargassum seaweed on Caribbean islands: An international public health concern. The Lancet, 392, 2691. doi:10.1016/S0140-6736(18)32777-6
   Web of Science ®Google Scholar
• Rodríguez-Martínez, R. E., Roy, P. D., Torrescano-Valle, N., Cabanillas-Terán, N., Carrillo-Domínguez, S. … van Tussenbroek, B. I. (2020). Element concentrations in pelagic Sargassum along the Mexican Caribbean coast in 2018-2019. Peer J, 8, e8667. 2020 Feb 26. doi:10.7717/peerj.8667
   PubMed Web of Science ®Google Scholar
• Schneider, G. (2005). Enzymes in the biosynthesis of aromatic polyketide antibiotics. Current Opinions in Structural Biology, 15, 629–636. doi:10.1016/j.sbi.2005.10.002
   PubMed Web of Science ®Google Scholar
• Serebryakova, A., Aires, T., Viard, F., Serrao, E. A., Engelen, A. H., & Melcher, U. (2018). Summer shifts of bacterial communities associated with the invasive brown seaweed Sargassum muticum are location and tissue dependent. PLoS One, 13, e0206734. doi:10.1371/journal.pone.0206734
   PubMed Web of Science ®Google Scholar
• Shen, B., Liu, W., & Nonaka, K. (2003). Enediyne natural products: Biosynthesis and prospects towards engineering novel antitumor agents. Current Medicinal Chemistry, 10, 2317–2325. doi:10.2174/0929867033456701
   PubMed Web of Science ®Google Scholar
• Smetacek, V., & Zingone, A. (2013). Green and golden seaweed tides on the rise. Nature, 504, 84–88. doi:10.1038/nature12860
   PubMed Web of Science ®Google Scholar
• Thakur, N., Salama, E.-S., Sharma, M., Sharma, P., Sharma, D., & Li, X. (2022). Efficient utilization and management of seaweed biomass for biogas production. Materials Today Sustainability, 18, 100120. doi:10.1016/j.mtsust.2022.100120
   Google Scholar
• Torralba, M. G., Franks, J. S., Gomez, A., Yooseph, S., Nelson, K. E., & Grimes, D. J. (2017). Effect of Macondo prospect 252 oil on microbiota associated with pelagic Sargassum in the northern Gulf of Mexico. Microbial Ecology, 73, 91–100. doi:10.1007/s00248-016-0857-y
   PubMed Web of Science ®Google Scholar
• Van Lanen, S. G., & Shen, B. (2008). Biosynthesis of enediyne antitumor antibiotics. Current Topics in Medicinal Chemistry, 8, 448–459. doi:10.2174/156802608783955656
   PubMed Web of Science ®Google Scholar
• Wainwright, B. J., Bauman, A. G., Zahn, G. L., Todd, P. A., & Huang, D. (2019). Characterization of fungal biodiversity and communities associated with the reef macroalga Sargassum ilicifolium reveals fungal community differentiation according to geographic locality and algal structure. Marine Biodiversity, 49, 2601–2608. doi:10.1007/s12526-019-00992-6
   Web of Science ®Google Scholar
• Wang, M., Hu, C., Barnes, B. B., Mitchum, G., Lapointe, B., & Montoya, J. P. (2019). The great Atlantic Sargassum belt. Science, 365, 83–87. doi:10.1126/science.aaw7912
   PubMed Web of Science ®Google Scholar
• Wolfe, B. E., Kuo, M., & Pringle, A. (2012). Amanita thiersii is a saprotrophic fungus expanding its range in the United States. Mycologia, 104, 22–33. doi:10.3852/11-056
   PubMed Web of Science ®Google Scholar