The Algal-Phage Symbiont Symphony: Decoding the Luteimonas padinae Resistome and Engineering Phage ‘Conductors’ for Precision Microbiome Orchestration

Abstract

The complex interplay between marine bacteria and their viral predators represents a critical, yet underexplored, dimension of algal microbiome regulation. This study investigates the tripartite relationship between the epiphytic bacterium Luteimonas padinae, its infecting bacteriophages, and their shared Padina spp. algal host, with the dual objectives of (1) characterizing the L. padinae resistome and phage defense mechanisms, and (2) developing engineered phage ‘conductors’ for targeted microbiome manipulation. We first isolated and genomically characterized L. padinae strains from Padina algal surfaces, revealing a diverse arsenal of antibiotic resistance genes and CRISPR-Cas systems indicative of extensive phage exposure. Concurrently, we discovered and sequenced three novel lytic phages with distinct infection strategies against L. padinae, including one podophage encoding a previously uncharacterized alginate lyase. Building upon these findings, we employed a synthetic biology approach to create phage variants with enhanced host range and biofilm penetration capabilities through rational tail fiber modification and CRISPR-Cas payload integration. Microcosm experiments demonstrated that precisely timed phage cocktails could reduce L. padinae load by 89% without disrupting beneficial microbiome members, while multi-omics analysis revealed phage-induced shifts in algal exometabolite profiles. Our results establish L. padinae-phage as a model system for marine microbiome editing and provide a blueprint for phage-based algal probiotic development. The demonstrated ability to ‘conduct’ microbiome composition through engineered phages opens new avenues for sustainable aquaculture and marine carbon cycle management.