Data from: Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.数百年来，生态学家们一直在探究动植物群落的多样性与功能性状如何在不同生物群区（biome）间发生变化。与之形成鲜明对比的是，尽管土壤微生物是生物地球化学循环的核心驱动引擎，亦是陆地生态系统中活生物量的主要储存库，但针对土壤微生物群落的同类探索才刚刚起步。本研究采用宏基因组测序（metagenomic sequencing）技术，对从寒冷荒漠、炎热荒漠、森林、草原以及苔原（tundra）采集的16份土壤微生物群落的组成与功能属性展开了对比分析。无植被覆盖的寒冷荒漠土壤中的微生物群落，其功能多样性（即蛋白编码基因类别多样性）、系统发育多样性与分类多样性水平通常均为最低。在所有土壤样本中，功能β多样性与分类β多样性及系统发育β多样性均呈显著相关；无论采用何种多样性衡量指标，荒漠微生物群落均与非荒漠群落存在显著差异。荒漠微生物群落中，与渗透调节（osmoregulation）和休眠相关的基因相对丰度更高，而与养分循环、植物源有机化合物分解代谢相关的基因相对丰度则更低。荒漠土壤中的抗生素抗性基因（antibiotic resistance genes）相对丰度始终较非荒漠土壤低三倍，这表明塑造荒漠微生物群落的主导因素是非生物环境条件，而非种间竞争相互作用。作为迄今为止针对土壤分类多样性、系统发育多样性与功能多样性的最全面调研，本研究证实，宏基因组研究方法可用于构建预测性认知，揭示微生物多样性与功能如何随陆地生物群区发生变化。