Genomes of Two Brazilian Estuarine Cyanobacteria Reveal Fatty Acid Production Secrets

Two cyanobacteria strains isolated from the Patos Lagoon estuary in Southern Brazil have had their genomes sequenced and characterized in detail, revealing how their fatty acid output shifts dramatically with temperature and light. The strains, Aphanothece microscopica RSMan92 and A. stagnina RSMan2012, are the first representatives of their respective species to appear in the RefSeq genome database, expanding a previously sparse genomic record for the genus Aphanothece that included only three entries as of September 2025. The study, published in Current Genetics, combined whole-genome sequencing, phylogenomics, and metabolite profiling to paint an unusually complete picture of two organisms whose biotechnological promise had long outpaced their genomic documentation.

The assembled genome of A. microscopica RSMan92 spans 3.69 megabases distributed across 701 contigs and encodes 3,279 protein-coding sequences, while A. stagnina RSMan2012 carries a slightly smaller genome of 3.28 megabases in 153 contigs with 3,567 protein-coding sequences. GC content was closely matched between the two, at 66.96 percent for RSMan92 and 67.45 percent for RSMan2012. Both genome assemblies have been deposited in public repositories under GenBank accession numbers JBKKKY000000000.2 and JBKOUC000000000.1, with associated BioProject and BioSample records, making the data freely available for future comparative work on a genus that remains genomically underexplored worldwide.

Phylogenomic analysis built from 100 conserved single-copy protein families, aligned with MUSCLE and analyzed with RAxML, placed both strains within a highly supported clade with 100 percent bootstrap support, grouping closely with Cyanobium usitatum str. Tous and a secondary clade containing Cyanobium gracile PCC 6307 and A. cf. minutissima CCALA 015. This robust clustering supports the classification of both strains within Aphanothece sensu stricto. Yet the broader tree told a more complicated story: A. sacrum FPU1 and A. hegewaldii CCALA 016 clustered separately at notable phylogenetic distance with only moderate bootstrap support, a pattern consistent with the long-suspected polyphyly of the genus. The authors argue that some lineages currently labeled Aphanothece may eventually warrant reassignment to new or existing genera, and that integrative approaches combining genomics, morphology, ultrastructure, and ecology will be needed to untangle the group’s taxonomy.

Functional annotation revealed conserved gene repertoires in both strains. RAST-based subsystem classification showed similar proportions across 25 functional categories, with the largest gene counts in amino acids and derivatives, protein metabolism, and cofactors, vitamins, prosthetic groups, and pigments. COG-based comparison across Aphanothece genomes indicated conservation of genes involved in cell cycle control, defense mechanisms, energy production, inorganic ion transport, and secondary metabolite biosynthesis. Roughly a quarter of coding sequences in each genome fell into the category for unknown functions, a figure consistent with averages reported for other cyanobacteria, and about 15 percent of genes could not be assigned to any COG category at all, reflecting the substantial annotation gaps and genetic novelty that persist even in well-sampled microbial lineages.

The stress-response and lipid-biosynthesis machinery of both strains was cataloged in detail. Typical heat shock proteins such as groS, groL, dnaK, and htpG, along with cold shock-related genes deaD, gyrA, and infA, were identified in both genomes, indicating capacity for thermal stress adaptation. The DNA SOS response components lexA and recA were also present, and multiple fab genes supporting fatty acid chain initiation, elongation, and modification were mapped onto the KEGG fatty acid biosynthesis pathway. One difference stood out: only A. microscopica RSMan92 harbors the DesV gene, an intact open reading frame encoding a delta-5-desaturase involved in polyunsaturated fatty acid synthesis. AntiSMASH analysis additionally uncovered terpene biosynthetic gene clusters in both strains, though these showed low similarity to known references, signaling latent biosynthetic potential rather than confirmed products.

To test how environment shapes metabolism, the researchers grew the strains under nine combinations of temperature (12, 20, and 28 degrees Celsius) and light intensity (60, 120, and 180 micromoles per square meter per second), values chosen to reflect the environmental variability of the estuarine ecosystem from which the strains were isolated. Biomass was harvested on day 24, corresponding to late exponential growth phase, and analyzed by gas chromatography coupled with electron ionization mass spectrometry. The results showed that both strains synthesized saturated and monounsaturated fatty acids across conditions, but only RSMan92 produced polyunsaturated fatty acids, including linoleic acid derivatives, under variable cultivation conditions, a striking divergence given the two genomes’ otherwise similar lipid-related gene content.

The metabolite profiles clustered primarily by temperature rather than light. In RSMan92, methyl 9-cis, 11-trans-octadecadienoate and gamolenic acid showed high relative abundance at 28 degrees Celsius, while 9,12-octadecadienoic acid methyl ester and methyl c-linolenate were more abundant at lower temperatures. In RSMan2012, monounsaturated compounds such as trans-13-octadecenoic acid methyl ester and methyl myristoleate were more abundant at lower temperatures and slightly higher irradiances, whereas other esters declined under the same conditions. Both strains shared derivatives of palmitic and oleic acids, consistent with the fab gene pathways identified genomically. The authors caution that these differences likely arise not from gene presence alone but from differential gene expression, regulation, enzyme specificity, and environmental cues, and they note that transcriptomic and proteomic follow-up will be needed to resolve the expression-function discrepancies.

The strains themselves carry a research history that predates this genomic work. Both were originally isolated from the Patos Lagoon estuary in Rio Grande do Sul and maintained in the Aidar & Kutner Microorganism Collection at the University of São Paulo. Previous studies had reported that RSMan92 exhibits high carbon fixation capacity, that the strains can help remove organic matter from wastewater, and that they produce pigments with antioxidant activity. RSMan92 can also grow heterotrophically in the dark on glucose, lactose, or sucrose, whereas RSMan2012 has been reported only as autotrophic. Both are non-toxic and tolerate high salinity, traits that the new study suggests may further modulate gene expression and lipid biosynthesis under fluctuating estuarine conditions.

The broader context is one of persistent genomic blind spots. More than 400 cyanobacterial genera have been described, and the group’s members are prolific producers of bioactive metabolites spanning peptides, lipids, terpenes, polysaccharides, and alkaloids, yet the genomes of most producing strains remain unavailable. In Brazil, where 30 cyanobacterial genera have been described based on 16S rDNA analysis, documentation has historically relied on classical morphology, and estuarine ecosystems in particular remain underexplored. Against that backdrop, the new Aphanothece genomes, together with their environmentally modulated fatty acid profiles and terpene gene clusters, offer a template for how genomics and metabolomics can be combined to evaluate native strains. The authors position the work as a step toward unlocking the bioprospecting potential of Brazilian cyanobacteria for applications ranging from biodiesel feedstocks, where oleic and palmitoleic acids are valued for oxidative stability, to nutraceutical and pharmaceutical formulations built on saturated and polyunsaturated fatty acids.

For now, the practical takeaways remain at the screening stage. The GC/EI-MS analysis was explicitly framed as a preliminary, qualitative profiling method, and the terpene clusters await exploration under alternative cultivation conditions or through heterologous expression. What the study firmly establishes is that two morphologically modest estuarine cyanobacteria, long studied for their growth and pigment traits, carry genomes rich in lipid metabolism genes whose metabolic outputs diverge in ways their gene inventories alone would not predict. That gap between genomic similarity and metabolic divergence is precisely where the authors say future work, integrating transcriptomics, proteomics, and targeted metabolite quantification, should focus next.

Subject of Research: Polyphasic genomic and metabolomic characterization of two Aphanothece cyanobacteria strains from Southern Brazil, focusing on fatty acid biosynthesis under varying temperature and light conditions.

Article Title: Polyphasic characterization and genomic insights of the cyanobacteria Aphanothece microscopica and A. stagnina from Southern Brazil with emphasis on fatty acid biosynthesis

Article References: Delgado, R. T., Becker, B., Pushkareva, E., Schäfer, M., & Mendes, C. R. B. (2025). Polyphasic characterization and genomic insights of the cyanobacteria Aphanothece microscopica and A. stagnina from Southern Brazil with emphasis on fatty acid biosynthesis. Current Genetics, 71(1), Article 22. https://doi.org/10.1007/s00294-025-01328-7

Image Credits: AI Generated

DOI: 10.1007/s00294-025-01328-7

Keywords: cyanobacteria, Aphanothece, genomics, fatty acid biosynthesis, Patos Lagoon, phylogenomics, polyunsaturated fatty acids, terpene gene clusters, biotechnology, estuarine microbiology, GC-MS, Brazil