Abstract
The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.
Highlights
Shrimp farming in tropical and subtropical coastal areas is a growing activity due to market demand for high-quality protein intake [1]
Based on already known metabolic pathways, 13 natural product biosynthetic gene clusters were predicted in the genome of CENA596: two containing NRPSs, two containing polyketide synthases (PKSs), three containing hybrid NRPS and PKS (NRPS/PKS), two terpene metabolic gene clusters, two encoding ribosomally synthesized and post-translationally modified peptides (RIPPs), and two gene clusters not classified in any specific type
The use of 120 conserved proteins has been recently proposed as a standard method for bacterial taxonomy and we introduced it to investigate the currently available Nodularia genomes and metagenome-assembled genome (MAG) [111]
Summary
Shrimp farming in tropical and subtropical coastal areas is a growing activity due to market demand for high-quality protein intake [1]. Shrimp farming is developed in constructed ponds near estuaries and lagoons along the coastline. Coastal waters are a common water source for shrimp ponds on most farms, either used directly or pumped via coastal lagoons [5]. Water nutrient over-enrichment in the ponds due to fertilizer use, shrimp excretions, and unconsumed aquafeeds lead to cyanobacterial blooms [6,7,8,9]. A brackish water planktonic heterocytous cyanobacterium, has been responsible for major blooms along ocean coastlines, estuaries, brackish water basins, and saline lakes of the European, Australian/Oceania, and African continents [10,11,12,13,14,15,16,17,18,19]
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