Bei Qicheng, Williams Nathan L R, Furtado Laura E, Blasi Daria Di, Williams Jelani, Brotas Vanda, Tarran Glen, Rees Andrew P, Bowler Chris, Fuhrman Jed A
Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, United States.
Faculdade de Ciências, Marine and Environmental Science Centre (MARE)/Aquatic Research Network (ARNET), Universidade de Lisboa, 1749-016, Lisbon, Portugal.
ISME Commun. 2025 Jul 30;5(1):ycaf131. doi: 10.1093/ismeco/ycaf131. eCollection 2025 Jan.
High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50°N to 40°S during the 29 Atlantic Meridional Transect. Using the single-copy gene, we estimated an average bacterial abundance of 1.0 × 10 haploid genome equivalents per liter. Leveraging a recent report that the gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope = 1.03, Pearson's = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson's = 0.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography.
高通量测序为海洋和其他生态系统中的微生物多样性提供了前所未有的见解。然而，大多数基于测序的研究仅报告相对（组成）丰度而非绝对丰度，限制了它们在生态建模和生物地球化学分析中的应用。在这里，我们提出了一种宏基因组学方案，该方案纳入基因组内标，以量化未分级海水中原核生物和真核浮游植物的绝对丰度，它们共同构成了海洋食物网的基础。我们将此方法应用于在29次大西洋子午断面调查期间采集的50°N至40°S的表层海水。使用单拷贝基因，我们估计每升平均细菌丰度为1.0×10个单倍体基因组当量。利用最近一份报告称该基因在浮游植物中通常为单拷贝，我们还对真核浮游植物进行了量化。宏基因组学估计与蓝细菌（斜率 = 1.03，皮尔逊相关系数 = 0.89）和真核浮游植物（斜率 = 0.72，皮尔逊相关系数 = 0.84）的流式细胞术数据密切吻合。与流式细胞术相比，对纳米和微微真核生物的分类分辨率有了很大提高。硅藻、甲藻和的估计值明显高于显微镜计数，这可能反映了显微镜计数不足以及潜在的倍性变化。这些发现突出了宏基因组学绝对定量的价值，并为微生物海洋学的定量评估提供了一个强大的框架。
