replying to E. D. Osburn et al. Nature Microbiology https://doi.org/10.1038/s41564-024-01687-w (2024)

In a recent paper, we used soil metagenomes from global biomes to assess life history strategies across soil bacterial communities¹. We compiled 102 traits in a multi-table coinertia analysis to characterize the life history strategies of soil bacteria. Although we only used annotated reads for the calculation of most traits, full metagenomes were used to quantify bacterial average genome size (AGS) and ribosomal RNA operon copy numbers. In response, Osburn and co-workers² pointed out a potential bias in our method for estimating bacterial AGS. We acknowledge that estimating bacterial AGS for an environment as complex and unexplored as soil is non-trivial. Although we agree that our approach has a bias towards bacterial AGS overestimation, we show that the alternative calculation proposed by Osburn et al.² appears to have an even stronger underestimation bias. Still, neither approach led to a different conclusion for our proposed life history strategies, demonstrating the robustness of our results.

回复ED Osburn 等人。自然微生物学https://doi.org/10.1038/s41564-024-01687-w (2024)

在最近的一篇论文中，我们使用全球生物群落的土壤宏基因组来评估土壤细菌群落的生活史策略¹。我们通过多表共惯性分析编制了 102 个性状，以表征土壤细菌的生活史策略。尽管我们仅使用带注释的读数来计算大多数性状，但完整的宏基因组用于量化细菌平均基因组大小 (AGS) 和核糖体 RNA 操纵子拷贝数。作为回应，Osburn 和同事²指出我们估计细菌 AGS 的方法存在潜在偏差。我们承认，估算像土壤这样复杂且未经探索的环境中的细菌 AGS 并非易事。尽管我们同意我们的方法对细菌 AGS 高估存在偏见，但我们表明 Osburn 等人提出的替代计算。²似乎有更强的低估偏差。尽管如此，这两种方法都没有为我们提出的生活史策略得出不同的结论，这证明了我们结果的稳健性。