Sample Preservation Solution Increases Nucleic Acid Yield and Environmental RNA Quality in Sediments Across an Estuarine Salinity Gradient

Abstract

Environmental nucleic acid-based assessments are powerful tools for understanding microbial ecology, and environmental degradation in aquatic environments. This approach is particularly useful in guiding restoration in estuaries, some of the most degraded ecosystems in the world. The recent popularity of this approach has been accompanied by a parallel increase in the diversity of applied methods. A range of best practice methods exist across the field that can be employed and are selected based on environmental considerations such as physicochemical gradients, maximizing yield, and quality of nucleic acids sampled across sites within a study area. A consistent approach to intra-study nucleic acid sampling also ensures accurate comparison between those sites. This study evaluates environmental nucleic acid (eNA) sampling methods across salinity gradients in aquatic ecosystems, focusing on the impact of preservation techniques on environmental DNA (eDNA) yield and environmental RNA (eRNA) yield and quality. Fieldwork was conducted at three sites within the Coorong estuary system in South Australia, representing low salinity, marine, and hypersaline conditions. Snap freezing and LifeGuard preservation solution treatments were applied in situ to compare their effects on nucleic acid yields and eRNA integrity. Snap freezing enhanced eDNA yield in low salinity sediments but negatively impacted eRNA integrity in marine and hypersaline conditions. Conversely, treatment with preservation solution consistently improved both eDNA and eRNA recovery across all salinity levels, which makes this approach a good candidate for preserving eNA molecules across environmental gradients. The study underscores the necessity of tailoring sample preservation methods to specific environmental conditions for accurate eNA-based microbial community assessments in coastal ecosystems. These findings contribute to the development of robust eNA sampling protocols for benthic communities under varying salinity conditions.