Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.

全球土壤微生物被认为主要由有机碳源维持。某些细菌也消耗无机能源，例如微量气体，但它们被认为是稀有的群落成员，除了一些贫营养土壤。在这里，我们结合宏基因组、生物地球化学和建模方法来确定土壤微生物群落如何满足能源和碳需求。对 40 个宏基因组和 757 个衍生基因组的分析表明，超过 70% 的土壤细菌类群编码酶以消耗无机能源。来自 19 个门的细菌编码酶，利用微量气体氢气和一氧化碳作为有氧呼吸的补充电子供体。此外，我们确定了第四门（Gemmatimonadota）可能具有需氧甲烷氧化的能力。与宏基因组分析一致，来自不同栖息地的土壤剖面内的群落会迅速氧化氢气、一氧化碳，并在较小程度上氧化低于大气浓度的甲烷。热力学模型表明，这三种气体氧化产生的能量足以满足能够消耗它们的细菌细胞的维持需求。多种细菌还编码酶以使用微量气体作为电子供体来支持碳固定。总而言之，这些研究结果表明，痕量气体氧化在土壤生态系统中具有主要的选择优势，其中优选的有机底物的可用性限制了微生物的生长。无机能源可以维持大多数土壤细菌的观察也对理解不断变化的世界中的大气化学和微生物生物多样性具有广泛的意义。