Growth rates are central to understanding microbial interactions and community dynamics. Metagenomic growth estimators have been developed, specifically codon usage bias (CUB) for maximum growth rates and “peak-to-trough ratio” (PTR) for in situ rates. Both were originally tested with pure cultures, but natural populations are more heterogeneous, especially in individual cell histories pertinent to PTR. To test these methods, we compared predictors with observed growth rates of freshly collected marine prokaryotes in unamended seawater. We prefiltered and diluted samples to remove grazers and greatly reduce virus infection, so net growth approximated gross growth. We sampled over 44 h for abundances and metagenomes, generating 101 metagenome-assembled genomes (MAGs), including Actinobacteria, Verrucomicrobia, SAR406, MGII archaea, etc. We tracked each MAG population by cell-abundance-normalized read recruitment, finding growth rates of 0 to 5.99 per day, the first reported rates for several groups, and used these rates as benchmarks. PTR, calculated by three methods, rarely correlated to growth (r ~−0.26–0.08), except for rapidly growing γ-Proteobacteria (r ~0.63–0.92), while CUB correlated moderately well to observed maximum growth rates (r = 0.57). This suggests that current PTR approaches poorly predict actual growth of most marine bacterial populations, but maximum growth rates can be approximated from genomic characteristics.

增长率是了解微生物相互作用和群落动态的核心。已经开发了宏基因组生长估计器，特别是用于最大生长速率的密码子使用偏差 (CUB) 和用于原位速率的“峰谷比”(PTR)。两者最初都是用纯培养物进行测试的，但自然种群更具异质性，尤其是在与 PTR 相关的单个细胞历史中。为了测试这些方法，我们将预测因子与在未经修正的海水中观察到的新鲜收集的海洋原核生物的增长率进行了比较。我们预过滤和稀释样品以去除食草动物并大大减少病毒感染，因此净增长接近总增长。我们对丰度和宏基因组进行了超过 44 小时的采样，生成了 101 个宏基因组组装基因组 (MAG)，包括放线菌、疣微菌、SAR406、MGII 古细菌等。我们通过细胞丰度标准化读取招募跟踪每个 MAG 群体，发现每天的增长率为 0 到 5.99，这是几个组的首次报告率，并将这些速率用作基准。PTR，通过三种方法计算，很少与增长相关（r ~-0.26–0.08)，除了快速生长的γ-变形菌 ( r ~0.63–0.92)，而 CUB 与观察到的最大增长率 ( r  = 0.57) 的相关性中等。这表明当前的 PTR 方法无法预测大多数海洋细菌种群的实际生长，但最大增长率可以从基因组特征中近似得出。