Lake bacterium’s genome points the way to greener bioplastic production

A bacterium fished out of the shoreline soil of India’s largest brackish water lagoon has been shown to carry the genetic toolkit for making biodegradable plastic, and a statistical overhaul of its growth conditions has more than doubled how much polymer it can produce. The microbe, Streptomyces cavourensis strain BG2AG, was isolated from Chilika Lake on the coast of Odisha, India, and characterized in a study that combined whole genome sequencing with Taguchi experimental design, a statistical method for testing many culture variables at once. Under unoptimized conditions the strain produced 0.30 plus or minus 0.03 grams of polyhydroxyalkanoate, or PHA, per liter of culture, with the polymer making up roughly 42 percent of the cell dry weight. After optimization, yield rose to 0.724 plus or minus 0.04 grams per liter, a 1.4-fold increase in PHA content compared with the starting conditions.

PHAs are polyesters that many bacteria synthesize inside their cells when nutrients such as nitrogen or phosphorus run short but carbon remains plentiful. The polymers act as intracellular carbon storage granules that the cell can draw on when external food sources disappear. Because PHAs are biodegradable and biocompatible, and their mechanical properties can resemble those of conventional plastics, they are considered candidates for industrial, environmental and biomedical applications.

Chilika Lake offered a promising hunting ground. The lagoon’s estuarine microbes, particularly actinobacteria, may have evolved versatile metabolic pathways that help them withstand fluctuating salinity, pollution and nutrient limitation. Those adaptive traits can include efficient carbon utilization and intracellular carbon storage through PHA biosynthesis. The authors had previously shown that BG2AG could produce extractable PHA films, and genome-based pathway analysis in that earlier work identified annotated genes involved in PHA biosynthesis. The Streptomyces group, better known for antibiotic production, remains relatively underexplored for PHA, even though gram-positive bacteria can yield better quality polymer than gram-negative ones, whose lipopolysaccharides can interfere with extraction.

To characterize the strain fully, the team sequenced its genome on an Illumina NovaSeq 6000 platform, generating paired-end reads that were quality filtered and assembled with the SPAdes assembler. The result was a 7.56 megabase genome spread over 17 scaffolds, with a GC content of 72.18 percent, typical of the GC-rich genomes of Streptomyces species. The largest scaffold measured about 7.05 million base pairs, and assembly metrics such as an N50 of 7,045,463 base pairs and an L50 of 1 indicated a highly contiguous assembly. Quality control was stringent: of 38,482,000 reads analyzed, 94.2 percent mapped back to the assembled genome, and the genome showed 99.91 percent coverage at both 5-fold and 10-fold sequencing depth. A BUSCO completeness check found 123 complete orthologs, or 99.2 percent, including 119 single-copy and 4 duplicated genes, with only 1 fragmented and none missing.

Annotation painted a picture of a metabolically versatile organism. The RAST server identified 6,737 coding sequences, 56 transfer RNA genes and 2 ribosomal RNA genes. Functional annotation using the KEGG database assigned 2,995 genes overall, with 719 linked to metabolic pathways, 333 to secondary metabolite biosynthesis and 11 to fatty acid degradation. The antiSMASH pipeline detected 32 biosynthetic gene clusters, including nonribosomal peptide synthetase, polyketide synthase, siderophore, ectoine, melanin, terpene and metallophore-associated clusters. The presence of ectoine clusters with 100 percent similarity, along with desferrioxamine B and griseobactin clusters, suggested strong osmotic and oxidative stress tolerance. The authors propose, as a hypothesis, that such stress-related clusters may indirectly facilitate PHA biosynthesis by reinforcing stress tolerance and metabolic flexibility during carbon-rich, nutrient-limited growth phases, since fatty acid degradation genes support conversion of fatty acids into acetyl-CoA, the key precursor for polymer formation.

Phylogenetic analysis settled the strain’s identity. Its 16S ribosomal RNA sequence showed 99.97 percent similarity to Streptomyces cavourensis NBRC 13026, the type strain, and 99.38 percent to Streptomyces bacillaris NBRC 13487. A comparative whole genome analysis using the Type Strain Genome Server compared BG2AG with its four nearest relatives, and OrthoVenn3 clustering showed that the strain contains only one unique orthologous cluster while sharing 4,695 genes with the related organisms. A CARD-based screen for antibiotic resistance genes detected rifamycin- and tetracycline-associated resistance determinants, which the authors note provides biosafety information relevant to any future environmental or industrial deployment, since transferable resistance elements would require further risk assessment before large-scale use.

With the genome as a guide, the team ran a series of single-factor experiments. PHA production peaked at neutral pH, reaching 0.64 grams per liter with a PHA content of 59.25 percent at pH 7, and fell sharply under alkaline conditions, dropping to just 0.02 grams per liter at pH 11. Temperature told a similar story: the highest accumulation, 0.652 grams per liter with 59.81 percent content, occurred at 37 degrees Celsius, while only 0.02 grams per liter was recorded at 27 degrees. Among five carbon sources tested, glucose was best, yielding a cell dry weight of 1.12 grams per liter and a PHA concentration of 0.65 grams per liter, or 58.03 percent content, followed by D-fructose. Among nitrogen sources, wheat bran led with 0.623 grams per liter and 58.77 percent content, while ammonium sulphate performed worst. Incubation time mattered too: production peaked at four days, equivalent to 96 hours, with 0.653 grams per liter, then declined over longer periods, a pattern consistent with nutrient depletion and intracellular polymer degradation.

Extraction method also influenced recovery. Of three pretreatments tested, sodium dodecyl sulfate combined with sodium hypochlorite gave the best results, with a cell dry weight of 1.08 grams per liter, a PHA concentration of 0.660 grams per liter and a content of 61.11 percent. The sodium chloride and Triton X-100 based methods recovered less polymer, at 0.485 and 0.306 grams per liter respectively. The authors caution that sodium hypochlorite, while effective at lysing cells, is a strong oxidizing agent that can scission polymer chains and reduce molecular weight, potentially affecting mechanical strength and thermal stability of the product.

The final step combined the six most influential variables, each at two levels, into an L8 Taguchi orthogonal array of eight experimental runs analyzed by signal-to-noise ratios and analysis of variance. The optimum combination was glucose at 1 percent, wheat bran at 0.1 percent, pH 7, 37 degrees Celsius and 96 hours of incubation, with the SDS-hypochlorite extraction method. Analysis of variance identified pH, temperature and carbon source as the most significant factors. An approximate contribution analysis based on changes in signal-to-noise values estimated that carbon source accounted for about 52 percent of the variation in PHA yield, pH about 38 percent, temperature about 28 percent and incubation period about 11 percent, while nitrogen source and extraction method each contributed less than 6 percent. The team validated the result by growing the strain under the optimized recipe and quantifying the polymer gravimetrically.

Fourier transform infrared spectroscopy confirmed the polymer’s identity. The spectrum of material extracted from the optimized cultures showed a strong absorption band at about 1744 per centimeter, the signature of ester carbonyl groups, along with aliphatic carbon-hydrogen stretches near 2923 and 2853 per centimeter, carbon-hydrogen bending between 1648 and 1457, and carbon-oxygen-carbon stretching of ester linkages at about 1032 per centimeter, collectively confirming the polyester nature of the biopolymer. Intracellular accumulation was also verified with Sudan Black B and Nile Red staining. The authors note that the genomic data did not directly guide the selection of optimization variables but confirmed the presence of key PHA biosynthesis genes, validating the strain’s intrinsic metabolic potential. They also stress that the optimized parameters were established in shake flasks, so scale-up in controlled bioreactor systems would need to be standardized before industrial production. Future directions they outline include metabolic engineering to channel more carbon toward polymer synthesis, fed-batch or continuous cultivation for tighter nutrient control, and copolymer synthesis to tailor material properties for wider industrial and biomedical use.

Subject of Research: Genome characterization and culture optimization for polyhydroxyalkanoate production by a Streptomyces strain isolated from Chilika Lake

Article Title: Genome assisted characterization and culture condition optimization for polyhydroxyalkanoate production by Streptomyces cavourensis BG2AG isolated from Chilika Lake

Article References: Giri, S., Behera, S. S., Parwez, Z., Pradhan, S., Gouda, S. K., Panda, A. N., & Ray, L. (2026). Genome assisted characterization and culture condition optimization for polyhydroxyalkanoate production by Streptomyces cavourensis BG2AG isolated from Chilika Lake. Biotechnology for Sustainable Materials, 3(1), Article 7. https://doi.org/10.1186/s44316-026-00056-3

Image Credits: AI Generated

DOI: 10.1186/s44316-026-00056-3

Keywords: Streptomyces cavourensis, polyhydroxyalkanoates, bioplastics, Chilika Lake, whole genome sequencing, Taguchi design, biodegradable polymers, actinobacteria, biosynthetic gene clusters, FTIR, bioprocess optimization, acetyl-CoA