Impact of Anaerobic Cold Storage on Subseafloor Microbial Communities

Abstract Sediment cores recovered from the deep sea often cannot be sampled for microbiological analysis immediately due to the need for core splitting and processing for subsequent onboard measurements and core storage. Consequently, sections are often stored at 4°C under anaerobic conditions for extended periods. However, the impact of the temporal storage on microbiological analysis remains uncertain. In this study, using paired sediment samples from the Japan Trench collected during International Ocean Discovery Program (IODP) Expedition 386, we performed comparative analysis of microbial community composition between samples immediately frozen after core recovery onboard and samples stored anaerobically for 9–11 months onshore. Although the overall community structure was broadly preserved, we observed substantial increases in some opportunistic taxa (e.g., Shewanella, Psychrobacter, and Firmicutes) and a marked decrease in archaeal abundance and diversity. Nevertheless, more than 95% of amplicon sequence variants (ASVs) were retained, and key subseafloor bacterial lineages such as Atribacterota and Chloroflexi showed no significant change in abundance. These results indicate that although long‐term cold storage can introduce identifiable preservation‐related biases, DNA‐based analyses of archived cores can still provide meaningful insights into subseafloor microbial communities when interpreted with appropriate caution.