Quantification of aquatic sediment prokaryotes—A multiple-steps optimization testing sands from pristine and contaminated aquifers

The total number of prokaryotic cells in aquatic sediments is a crucial measure tightly linked to energetic constraints, microbial productivity, and ecosystem status. While counting cells in water samples is routine, reliable procedures for the determination of prokaryotic cells associated to aquatic sediments are especially needed. A protocol for the direct quantification of prokaryotic cell abundance in aquatic sediments was developed and tested with sandy material from pristine and contaminated aquifers. Individual steps required in sample preparation, including preservation, cell dislodgement, density gradient centrifugation providing sample purification, and staining, were critically evaluated and optimized. Quantification of cells is conducted by flow cytometry promoting a high-throughput sample processing. Although tested for only two different types of aquifer sediments, researchers may easily adapt the protocol for their individual samples and purposes, thus conducting a brief efficiency re-evaluation of individual steps highlighted in this study.