Acidity promotes degradation of multi-species environmental DNA in lotic mesocosms
Discover the research led by Prof. Matthew Seymour and his team, exploring multispecies environmental DNA (eDNA) dynamics in river ecosystems. Prof. Seymour investigates eDNA degradation over time and in varying environments across upland stream mesocosms. The findings highlight rapid eDNA decay, especially in acidic conditions, aiding predictive models for biodiversity dynamics in dynamic river ecosystems.
Introduction
To enhance biodiversity assessments, traditional methods are being supplemented with molecular environmental DNA (eDNA) techniques. However, there's still limited understanding of the factors influencing eDNA persistence. This study fills this gap by assessing lotic eDNA persistence in replicated field streams, revealing rapid degradation, particularly in acidic environments, and shedding light on eDNA dynamics in lotic systems.
Results
Environmental Variation
The experimental sites featured mesocosms designed for lotic comparisons across Welsh uplands and UK land uses. Each site had four circulating mesocosms with three channels drawing water from nearby streams. pH ranged from 6.73 to 5.35, temperatures from 14.47 °C to 16.16 °C, and total dissolved nitrogen varied from 0.14 mg/L to 0.49 mg/L. Selected taxa for eDNA analysis included Daphnia magna, Ephemera danica, and Anguilla anguilla. Environmental variation is shown through boxplots of pH, temperature, and total dissolved nitrogen across sites, illustrating dynamics within the mesocosms.
Quantitative PCR
Successful eDNA amplification occurred from time points 0 to 43 h, peaking at time 0 and declining to near 0 at hour 43. Sucrose had no significant effect on DNA quantification. Significant negative effects of time and positive effects of pH on water-derived eDNA were found. Biofilm eDNA was detected for E. danica but not for D. magna and A. anguilla, with faster decay rates at acidic sites. Overall, biofilm-derived eDNA declined significantly over time and was higher at higher pH levels.
Discussion
In flowing waters, eDNA persistence varies with acidity affecting decay dynamics while nutrient load and temperature show no significant effects. LoticeDNA persisted up to 43 hours, highlighting the influence of environmental conditions on decay dynamics. These findings stress the importance of considering environmental variation and spatio-temporal dynamics in eDNA-based biodiversity assessments, particularly in rapidly degrading lotic systems. Further investigation is needed on eDNA accumulation in biofilm, especially in nutrient-rich environments. Overall, this underscores the necessity for comprehensive ecological assessments considering environmental dynamics across diverse river catchments.
Methods
Experimental Setup
We used four experimental stream mesocosms near the Llyn Brianne Reservoir in upland Wales, each with three circulating channels (20 m×20 cm×20 cm) and a flow rate of ~2 m/s. They represented moorland and conifer forest catchments with circumneutral (pH 6.8 to 7.2) and acidic (pH 5.3 to 5.8) waters. These mesocosms mirror the acid–base gradient of the upper Tywi catchment and environmental diversity across upland Wales and Britain.