Salter Ian
Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC) Observatoire Océanologique, Banyuls/mer, France.
Faroe Marine Research Institute, Torshavn, Faroe Islands.
PLoS One. 2018 Feb 23;13(2):e0192409. doi: 10.1371/journal.pone.0192409. eCollection 2018.
Environmental DNA (eDNA) can be defined as the DNA pool recovered from an environmental sample that includes both extracellular and intracellular DNA. There has been a significant increase in the number of recent studies that have demonstrated the possibility to detect macroorganisms using eDNA. Despite the enormous potential of eDNA to serve as a biomonitoring and conservation tool in aquatic systems, there remain some important limitations concerning its application. One significant factor is the variable persistence of eDNA over natural environmental gradients, which imposes a critical constraint on the temporal and spatial scales of species detection. In the present study, a radiotracer bioassay approach was used to quantify the kinetic parameters of dissolved eDNA (d-eDNA), a component of extracellular DNA, over an annual cycle in the coastal Northwest Mediterranean. Significant seasonal variability in the biological uptake and turnover of d-eDNA was observed, the latter ranging from several hours to over one month. Maximum uptake rates of d-eDNA occurred in summer during a period of intense phosphate limitation (turnover <5 hrs). Corresponding increases in bacterial production and uptake of adenosine triphosphate (ATP) demonstrated the microbial utilization of d-eDNA as an organic phosphorus substrate. Higher temperatures during summer may amplify this effect through a general enhancement of microbial metabolism. A partial least squares regression (PLSR) model was able to reproduce the seasonal cycle in d-eDNA persistence and explained 60% of the variance in the observations. Rapid phosphate turnover and low concentrations of bioavailable phosphate, both indicative of phosphate limitation, were the most important parameters in the model. Abiotic factors such as pH, salinity and oxygen exerted minimal influence. The present study demonstrates significant seasonal variability in the persistence of d-eDNA in a natural marine environment that can be linked to the metabolic response of microbial communities to nutrient limitation. Future studies should consider the effect of natural environmental gradients on the seasonal persistence of eDNA, which will be of particular relevance for time-series biomonitoring programs.
环境DNA（eDNA）可定义为从环境样本中回收的DNA库，其中包括细胞外DNA和细胞内DNA。最近有大量研究表明，利用eDNA检测大型生物具有可能性。尽管eDNA在水生系统中作为生物监测和保护工具具有巨大潜力，但其应用仍存在一些重要局限性。一个重要因素是eDNA在自然环境梯度中的持久性变化，这对物种检测的时间和空间尺度构成了关键限制。在本研究中，采用放射性示踪生物测定法来量化溶解态eDNA（d-eDNA，细胞外DNA的一个组成部分）在西北地中海沿岸一年周期内的动力学参数。观察到d-eDNA的生物摄取和周转存在显著的季节性变化，周转时间从数小时到一个多月不等。d-eDNA的最大摄取率出现在夏季，此时正处于强烈的磷酸盐限制期（周转时间<5小时）。细菌产量和三磷酸腺苷（ATP）摄取量的相应增加表明，微生物将d-eDNA作为有机磷底物加以利用。夏季较高的温度可能通过普遍增强微生物代谢来放大这种效应。偏最小二乘回归（PLSR）模型能够重现d-eDNA持久性的季节性周期，并解释了观测值中60%的方差。快速的磷酸盐周转和低浓度的生物可利用磷酸盐，这两者均表明存在磷酸盐限制，是该模型中最重要的参数。pH值、盐度和氧气等非生物因素的影响极小。本研究表明，在自然海洋环境中，d-eDNA的持久性存在显著的季节性变化，这可能与微生物群落对营养限制的代谢反应有关。未来的研究应考虑自然环境梯度对eDNA季节性持久性的影响，这对于时间序列生物监测计划尤为重要。
