Ecology Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
Genetic Unit, University of León, Campus de Vegazana S/N, 24071 León, Spain.
Sci Total Environ. 2021 Sep 10;786:147410. doi: 10.1016/j.scitotenv.2021.147410. Epub 2021 Apr 30.
Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their assemblages provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow community-environment relationships in diatoms. Nevertheless, we found no significant relationship between compositional variation and geographical distances. Overall, our work shows the complementary nature of both approaches and highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.
硅藻是淡水生态系统中的重要生物，因为它们是初级生产者，因此，分析它们的组合可以提供有关生态系统功能的相关信息。硅藻的传统鉴定方法基于形态特征，这既耗时又需要训练有素的专家。然而，DNA 条形码提供了一种替代方法，可以克服形态学方法的一些局限性。在这里，我们评估这两种方法是否可以在不同的分类学分辨率下，使用来自 22 个地中海池塘的综合数据集，来研究附生硅藻元群落的模式和机制（包括环境过滤和扩散限制）。我们使用 rbcL 条形码基因片段与高通量测序相结合来推断硅藻群落组成。通过普罗克鲁斯旋转分析和普罗克鲁斯随机化检验评估两种方法之间的整体对应程度，而使用 BIOENV、Mantel 检验和基于距离的冗余分析的综合组合来研究局部环境变量和地理距离的作用。我们的结果表明，两种方法在硅藻元群落组成变化方面的对应程度相对较差。我们推测，参考数据库的不完整性和生物信息学处理是分子方法最有可能产生的偏差，而有限的计数努力和隐种的存在可能是形态学方法的主要偏差。另一方面，两种方法检测到的硅藻群落组成变化与环境模板密切相关，这可能与硅藻中狭窄的群落-环境关系有关。然而，我们没有发现组成变化与地理距离之间存在显著关系。总的来说，我们的工作表明了这两种方法的互补性，并强调了 DNA metabarcoding 在解决淡水群落生态学的经验研究问题中的重要性，尤其是一旦参考数据库包含了出现的分类群的大多数基因型，并克服了生物信息学偏差。
