Trubovitz Sarah, Sandin Miguel M, Caron David A
Department of Biological Sciences, University of Southern California, Los Angeles, California, United States of America.
Ocean Sciences Department, University of California-Santa Cruz, Santa Cruz, California, United States of America.
PLoS One. 2025 Jun 20;20(6):e0326053. doi: 10.1371/journal.pone.0326053. eCollection 2025.
Rapidly improving DNA sequencing technology has revolutionized our ability to efficiently survey the biodiversity of microbial life. We are now equipped to investigate protistan richness and community dynamics on scales that would not have been imaginable with traditional observational methods. However, for most taxa the relationship between DNA sequences and morphologically-defined species is poorly understood, and morphology has remained the cornerstone of taxonomy for centuries. To better utilize the wealth of sequence data being collected, we must understand how it relates to entities such as individuals, populations, and species. Here we use a combined microscopy and sequencing approach to unveil the striking intragenomic and intraspecies genetic variation in one group of ecologically-important marine protists, the polycystine Radiolaria. Long-read 18S rRNA gene amplicon data from 173 isolated and morphologically-identified radiolarians showed that the vast majority (90%) yielded multiple sequence variants per specimen. Furthermore, every morphospecies analyzed displayed a range of different genetic signatures. Intraspecies genetic variability was expressed as specimens having different assemblages of ASVs, different dominant ASVs, or having no ASVs in common with other specimens of the same morphospecies. By integrating morphological and molecular information, we begin to parse the genetic richness of Radiolaria in ocean environments, as well as illuminate relationships between taxa, and their poorly-known life stages. Our findings emphasize the need to account for protists' taxon-specific sequence variability, particularly their intragenomic and intraspecies genetic variation, in interpreting metabarcoding diversity survey data.
快速发展的DNA测序技术彻底改变了我们有效调查微生物生命多样性的能力。现在，我们有能力在传统观测方法无法想象的尺度上研究原生生物的丰富度和群落动态。然而，对于大多数分类群来说，DNA序列与形态学定义的物种之间的关系还知之甚少，而形态学在几个世纪以来一直是分类学的基石。为了更好地利用所收集的丰富序列数据，我们必须了解它与个体、种群和物种等实体之间的关系。在这里，我们使用显微镜和测序相结合的方法，揭示了一类具有重要生态意义的海洋原生生物——多囊放射虫中惊人的基因组内和种内遗传变异。来自173个分离并经形态学鉴定的放射虫的长读长18S rRNA基因扩增子数据显示，绝大多数（90%）标本每个都产生了多个序列变体。此外，分析的每个形态物种都显示出一系列不同的遗传特征。种内遗传变异性表现为标本具有不同的ASV组合、不同的优势ASV，或者与同一形态物种的其他标本没有共同的ASV。通过整合形态学和分子信息，我们开始剖析海洋环境中放射虫的遗传丰富度，并阐明分类群之间的关系以及它们鲜为人知的生命阶段。我们的研究结果强调，在解释宏条形码多样性调查数据时，需要考虑原生生物特定分类群的序列变异性，特别是它们的基因组内和种内遗传变异。
