Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary.
Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary.
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DOI：
10.1371/journal.pone.0175186
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发表时间：
2017
期刊：
影响因子：
3.7
通讯作者：
Charlop-Powers Z
中科院分区：
文献类型：
--
作者：
Stoeckle MY;Soboleva L;Charlop-Powers Z
普查海洋动物种群的困难阻碍了有效的海洋管理。分析水中生物体脱落的DNA痕迹可能有助于评估。在这里，我们测试了水生环境DNA（eDNA）作为鱼类存在的指标，在较低的哈德逊河口。通过汇编1988年至2015年期间进行的12次传统调查，编制了一份本地海洋鱼类及其相对丰度的清单。为了提高eDNA鉴定的成功率，对代表18种海洋鱼类的31个标本进行了两个线粒体基因区域的测序，将12S eDNA靶序列的覆盖率提高到80%。从2016年1月开始，我们在两个对比鲜明的河口位置收集了76个一升的海岸线地表水样本。用脊椎动物特异性12S引物扩增eDNA。生物信息学分析扩增的DNA，使用GenBank的参考文库和我们新生成的12S序列，检测到大多数（81%）本地丰富或常见的物种和相对较少（23%）不常见的类群，并对应于传统调查确定的季节性存在和栖息地偏好。大约2%的鱼类读数是当地沃茨中罕见或不存在的常见食用物种，与废水输入一致。尽管哈德逊河流入，但很少检测到淡水物种。这些结果支持进一步的探索，并建议eDNA将有助于以相对较低的成本精细尺度的海洋鱼类种群的地理和时间映射。
The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental DNA (eDNA) as an indicator of fish presence in the lower Hudson River estuary. A checklist of local marine fish and their relative abundance was prepared by compiling 12 traditional surveys conducted between 1988–2015. To improve eDNA identification success, 31 specimens representing 18 marine fish species were sequenced for two mitochondrial gene regions, boosting coverage of the 12S eDNA target sequence to 80% of local taxa. We collected 76 one-liter shoreline surface water samples at two contrasting estuary locations over six months beginning in January 2016. eDNA was amplified with vertebrate-specific 12S primers. Bioinformatic analysis of amplified DNA, using a reference library of GenBank and our newly generated 12S sequences, detected most (81%) locally abundant or common species and relatively few (23%) uncommon taxa, and corresponded to seasonal presence and habitat preference as determined by traditional surveys. Approximately 2% of fish reads were commonly consumed species that are rare or absent in local waters, consistent with wastewater input. Freshwater species were rarely detected despite Hudson River inflow. These results support further exploration and suggest eDNA will facilitate fine-scale geographic and temporal mapping of marine fish populations at relatively low cost.