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Here, we introduce and validate a framework that adjudicates conflicting AGS estimates by testing which estimate yields a gap between scaled functional diversity and scaled taxonomic diversity that is consistent with the expected positive association between genome size and gene functional breadth. Across independent environmental gradients, metagenomic AGS estimates align with this framework and expectations from metagenome\u2010assembled genome (MAG) dynamics and gene co\u2010occurrence network module sizes, whereas 16S rRNA metabarcoding\u2010based AGS estimates deviate, particularly in extreme environments with sparse reference coverage. Applying this validated framework, we reveal a U\u2010shaped relationship between soil pH and AGS across a broad pH range, unifying prior findings of decreasing AGS from acidic to neutral soils with a newly observed increase along an alkaline gradient. Applying the same framework to a saline\u2010gradient dataset, we further suggest that conclusions of a recent study regarding eco\u2010evolutionary trade\u2010offs under salt stress may stem from method biases. This work identifies a potentially pervasive conflict in AGS estimation, provides a framework to resolve it, and clarifies and expands relationships between AGS and the environment.<\/jats:p>","DOI":"10.1002\/advs.77591","type":"journal-article","created":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T18:00:31Z","timestamp":1790532031000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Functional\u2013Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients"],"prefix":"10.1002","author":[{"given":"Huanhuan","family":"Zhu","sequence":"first","affiliation":[{"name":"State Key Laboratory of Microbial Diversity and Innovative Utilization Institute of Microbiology Chinese Academy of Sciences  Beijing China"},{"name":"College of Life Sciences University of Chinese Academy of Sciences  Beijing 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