Whole-genome sequencing of 9 of the 15 bacterial members of the synthetic bacterial community used in co-cultures with Prymnesium parvum under nutrient limitation for the Blueremediomics-coculture project, 2024

Microalgal-bacterial interactions strongly influence algal physiology; however, the mechanisms structuring these associations under defined nutrient limitation remain poorly understood. In this study, we investigated how nitrogen (N), phosphorus (P), and vitamin B12 limitation modulate the transcriptional responses of the haptophyte Prymnesium parvum and a defined 15-member bacterial synthetic community (SynCom). Laboratory cultures of P. parvum were maintained or co-cultured with the SynCom under three nutrient regimes: N, P, and B12 limitation. This experimental design enabled the assessment of both algal and bacterial transcriptional dynamics in response to nutrient stress and microbial interactions. To enable strain-resolved transcriptomic analyses, the genomes of all SynCom members were sequenced and assembled prior to the co-culture experiments. Six bacterial genomes were available from previous studies, whereas the remaining nine strains were sequenced in-house. Each bacterial strain was first cultured on marine agar plates and subsequently grown in marine broth for three days at 20C, 200 rpm. Cultures were then centrifuged at 10,000 g for 10 minutes, and genomic DNA was extracted from the resulting pellets using the NucleoSpin Plant II kit (Macherey-Nagel), following the manufacturers protocol. Sequencing libraries were prepared using the Nanopore Ligation Sequencing Kit V14 and sequenced individually on Flongle flow cells using a MinION device (Oxford Nanopore Technologies). Basecalling and demultiplexing were conducted using Guppy v6.4.8 (Oxford Nanopore Technologies) for all isolates, except for Marinovum algicola and Marivita cryptomonadis, for which Dorado v7.3.11 was used for basecalling and demultiplexing.