This project aims to calculate single-ASVs-based growth rates from amplicon metabarcoding data overtime in manipulation experiments.

This data has been deposited in ENA under the accession number PRJEB60085.

Marine prokaryotes play crucial roles in ocean biogeochemical cycles, being their contribution strongly influenced by their growth rates. Hence, elucidating the variability and phylogenetic imprint of marine prokaryotes' growth rates are crucial for better determining the role of individual taxa in biogeochemical cycles. Here, we estimated prokaryotic growth rates at high phylogenetic resolution in manipulation experiments using water from the northwestern Mediterranean Sea. Experiments were run in the four seasons with different treatments that reduced growth limiting factors: predators, nutrient availability, viruses, and light. Single-amplicon sequence variants (ASVs)-based growth rates were calculated from changes in estimated absolute abundances using total prokaryotic abundance and the proportion of each individual ASV. The trends obtained for growth rates in the different experiments were consistent with other estimates based on total cell-counts, CARD-FISH subcommunity cell-counts or metagenomic-OTUs. Our calculations unveil a broad range of growth rates [0.3-10 d-1] with significant variability even within closely related ASVs. Likewise, the impact of growth limiting factors changed over the year for individual ASVs. High numbers of responsive ASVs were shared between winter and spring seasons, as well as throughout the year in the treatments with reduced nutrient limitation and viral pressure. The most responsive ASVs were rare in the in situ communities, comprising a large pool of taxa with the potential to rapidly respond to environmental changes. Essentially, our results highlight the lack of phylogenetic coherence in the range of growth rates observed, and differential responses to the various limiting factors, even for closely related taxa.

We thank Carolina Marín-Vindas, Cèlia Marrasé, Montse Sala, Vanessa Balagué and all the participants in the experiments. We also thank Mireia Burnat and Helena Catena who participated in DNA extraction and David Kirchman who commented on an earlier draft. This research was supported by grants REMEI (CTM2015-70340-R) and MIAU (RTI2018-101025-B-100) funded by the Spanish Ministry of Science and Innovation. We acknowledge the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2019-000928-S). Adrià Auladell and Ona Deulofeu-Capo were supported by Spanish FPI grants.