Epidemiology of Highly Pathogenic Microorganisms, Robert Koch-Institute, Berlin, Germany.
Coopera ONGD, Logroño, Spain.
Mol Ecol Resour. 2018 May;18(3):502-510. doi: 10.1111/1755-0998.12754. Epub 2018 Feb 8.
Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate-derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA. To test whether urban wild mammals can be detected using fly iDNA, we performed DNA metabarcoding of pools of flies captured in Berlin, Germany, using three combinations of blocking primers. Our results show that domestic animal sequences are, as expected, very dominant in urban environments. Nevertheless, wild mammal sequences can often be retrieved, although they usually only represent a minor fraction of the sequence reads. Fly iDNA metabarcoding is therefore a viable approach for quick scans of urban wildlife diversity. Interestingly, our study also shows that blocking primers can interact with each other in ways that affect the outcome of metabarcoding. We conclude that the use of complex combinations of blocking primers, although potentially powerful, should be carefully planned when designing experiments.
城市地区的野生动物检测极具挑战性。传统的监测技术，如直接观察，面临着城市野生动物极其难以捉摸的局限性。最近的研究表明，无脊椎动物衍生 DNA（iDNA）可用于评估热带雨林中的野生动物多样性。在大多数城市中无处不在且非常丰富的苍蝇，也可用于检测城市地区的野生动物。然而，在城市生态系统中，大量的家养哺乳动物 DNA 可能完全掩盖了野生哺乳动物 DNA 的存在。为了测试是否可以使用蝇 iDNA 检测城市野生动物，我们使用三种组合的阻断引物对在德国柏林捕获的蝇进行了 DNA 宏条形码分析。我们的结果表明，在城市环境中，如预期的那样，家畜序列非常占主导地位。尽管如此，通常可以检索到野生动物序列，尽管它们通常只占序列读取的一小部分。因此，蝇 iDNA 宏条形码分析是快速扫描城市野生动物多样性的可行方法。有趣的是，我们的研究还表明，阻断引物可以相互作用，从而影响宏条形码分析的结果。我们得出结论，尽管使用复杂的阻断引物组合可能具有强大的功能，但在设计实验时应谨慎计划。
