Integrating metagenomics and high-throughput screening for bioprospecting marine producers of polyhydroxyalkanoates

• Published in: Letters in applied microbiology Vol. 78; no. 8
• Main Authors: Zhong, Naicai, Chen, Yuan, Pan, Wenfeng, Meng, Hailin, Liang, Kun, Lu, Jun, Jiang, Yanlin, Zhong, Chenyou, Yang, Muzhi, Zhai, Yinglei, Zhong, Jinyi
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.08.2025
• Subjects: Aquatic habitats; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Biodegradability; Biodegradation; Biopolymers; Bioprospecting; Bioprospecting - methods; Biosynthesis; Brackish water; Cell culture; Culture media; Deep sea; Fermentation; Fluorescence; Gas chromatography; Geologic Sediments - microbiology; Halomonas - classification; Halomonas - genetics; Halomonas - isolation & purification; Halomonas - metabolism; High-throughput screening; High-Throughput Screening Assays - methods; Marine environment; Metagenomics; Metagenomics - methods; Microorganisms; Polyhydroxyalkanoates; Polyhydroxyalkanoates - biosynthesis; Screening; Seawater - microbiology; Sediments; Strains (organisms); marine microorganism; polyhydroxyalkanoates (PHA); fluorescence; metagenomics; high-throughput screening
• ISSN: 1472-765X; 0266-8254; 1472-765X
• DOI: 10.1093/lambio/ovaf096

With the escalating global demand for eco-friendly materials, polyhydroxyalkanoates (PHAs) have emerged as promising biodegradable alternatives to conventional plastics. This study is based on the systematic investigation of microbial community distribution and functional composition associated with PHA biosynthesis across diverse marine environments through metagenomic analysis. Leveraging environmental characteristics and PHA synthesis potential, we developed targeted culture media. We successfully isolated 102 PHA-producing bacterial strains from various marine habitats, including brackish water interfaces and deep-sea sediments. Gas chromatography quantification revealed a significant correlation (R² = 0.67) between Nile red fluorescence intensity and PHA content in metagenomically-predicted strains, effectively addressing false-positive issues in fluorescence-based screening. We subsequently established a high-throughput screening platform combining microplate technology with fluorometric quantification, identifying 10 elite strains for fermentation optimization and PHA characterization. Notably, strain R1-4-2 (identified as Halomonas olivaria) demonstrated exceptional performance with 2.59 g l−1 cell dry weight (CDW) and 52.89% PHA content (1.52 g l−1 CDW), representing both a novel microbial resource for sustainable PHA production and a potential chassis for synthetic biology applications. These findings provide critical scientific insights and technical frameworks for advancing industrial-scale production of biodegradable biopolymers.