The impact of rearing environment on C. elegans: Phenotypic, transcriptomic and intergenerational responses to 3D enriched habitats
Environmental context profoundly influences organismal biology, yet laboratory studies often rely on simplified conditions that may not fully capture natural phenotypic repertoire. This exploratory study investigated how rearing environment affects various aspects of Caenorhabditis elegans biology by comparing worms cultured in three-dimensional decellularized fruit tissue scaffolds with those raised on standard two-dimensional agar plates. While fat content and feeding rate remained stable across conditions, other life history traits demonstrated varying degrees of plasticity in response to environmental context. We observed that scaffold-grown worms exhibited reduced body size, altered reproductive strategies, and mild enhancements in stress resistance, burrowing ability, swimming kinematics and exploratory behavior. RNA sequencing revealed distinct transcriptional profiles between scaffold-grown and agar-grown worms, with most changes arising within one generation. Some traits showed evidence of intergenerational inheritance. Our findings highlight the sensitivity of C. elegans biology to rearing conditions and underscore the importance of considering environmental context in interpreting laboratory results. This work sets the foundation for future research into the mechanisms underlying environmental adaptation and phenotypic plasticity in model organisms. Overall design: RNA-seq profiling of WT yound adult C. elegans grown under 2 different rearing habitats (traditional agar habitat or 3D decellularized fruit tissue scaffold) with ancestors (>10 prior generations) also grown on either of these 2 habitats (2x2 factorial design): (1) worms with an agar ancestry and raised on agar (agar:agar); (2) worms with an agar ancestry, but raised on scaffold (agar:scaffold); (3) worms with a scaffold ancestry, but raised on agar (scaffold:agar); and (4) worms with a scaffold ancestry and raised on scaffold (scaffold:scaffold). 3 sequencing replicates per condition. Each sample was pooled from worms collected from at least 3 different plates, on at least 3 different days.