Amplicon sequencing of partial regions of the ribosomal RNA loci (rDNA) is widely used to profile microbial communities. However, the rDNA is dynamic and can exhibit substantial interspecific and intraspecific variation in copy number in prokaryotes and, especially, in microbial eukaryotes. As change in rDNA copy number is a common response to environmental change, rDNA copy number is not necessarily a property of a species. Variation in rDNA copy number, especially the capacity for large intraspecific changes driven by external cues, complicates analyses of rDNA amplicon sequence data. We highlight the need to (i) interpret amplicon sequence data in light of possible interspecific and intraspecific variation, and (ii) examine the potential plasticity in rDNA copy number as an important ecological factor to better understand how microbial communities are structured in heterogeneous environments.

核糖体RNA基因座（rDNA）的部分区域的扩增子测序被广泛用于分析微生物群落。但是，rDNA是动态的，在原核生物中，尤其是在微生物真核生物中，其拷贝数可能表现出种间和种内差异。由于rDNA拷贝数的变化是对环境变化的普遍反应，因此rDNA拷贝数不一定是物种的特性。rDNA拷贝数的变化，尤其是外部线索驱动的种内较大变化的能力，使rDNA扩增子序列数据的分析变得复杂。我们强调需要（i）根据种间和种内可能的变异来解释扩增子序列数据，