气候变化领域集成服务门户(CCPortal): Genomic fingerprints of the world's soil ecosystems

CCPortal

DOI	10.1128/msystems.01112-23
	Genomic fingerprints of the world's soil ecosystems
	Graham, Emily B.; Garayburu-Caruso, Vanessa A.; Wu, Ruonan; Zheng, Jianqiu; Mcclure, Ryan; Jones, Gerrad D.
发表日期	2024
ISSN	2379-5077
英文摘要	Despite the explosion of soil metagenomic data, we lack a synthesized understanding of patterns in the distribution and functions of soil microorganisms. These patterns are critical to predictions of soil microbiome responses to climate change and resulting feedbacks that regulate greenhouse gas release from soils. To address this gap, we assay 1,512 manually curated soil metagenomes using complementary annotation databases, read-based taxonomy, and machine learning to extract multidimensional genomic fingerprints of global soil microbiomes. Our objective is to uncover novel biogeographical patterns of soil microbiomes across environmental factors and ecological biomes with high molecular resolution. We reveal shifts in the potential for (i) microbial nutrient acquisition across pH gradients; (ii) stress-, transport-, and redox-based processes across changes in soil bulk density; and (iii) greenhouse gas emissions across biomes. We also use an unsupervised approach to reveal a collection of soils with distinct genomic signatures, characterized by coordinated changes in soil organic carbon, nitrogen, and cation exchange capacity and in bulk density and clay content that may ultimately reflect soil environments with high microbial activity. Genomic fingerprints for these soils highlight the importance of resource scavenging, plant-microbe interactions, fungi, and heterotrophic metabolisms. Across all analyses, we observed phylogenetic coherence in soil microbiomes-more closely related microorganisms tended to move congruently in response to soil factors. Collectively, the genomic fingerprints uncovered here present a basis for global patterns in the microbial mechanisms underlying soil biogeochemistry and help beget tractable microbial reaction networks for incorporation into process-based models of soil carbon and nutrient cycling. IMPORTANCE We address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate. We address a critical gap in our understanding of soil microorganisms and their functions, which have a profound impact on our environment. We analyzed 1,512 global soils with advanced analytics to create detailed genetic profiles (fingerprints) of soil microbiomes. Our work reveals novel patterns in how microorganisms are distributed across different soil environments. For instance, we discovered shifts in microbial potential to acquire nutrients in relation to soil acidity, as well as changes in stress responses and potential greenhouse gas emissions linked to soil structure. We also identified soils with putative high activity that had unique genomic characteristics surrounding resource acquisition, plant-microbe interactions, and fungal activity. Finally, we observed that closely related microorganisms tend to respond in similar ways to changes in their surroundings. Our work is a significant step toward comprehending the intricate world of soil microorganisms and its role in the global climate.
英文关键词	soil microbiology; metagenomics; metaanalysis; machine learning; carbon cycling; nitrogen cycling; biogeochemistry; biogeography; soil microbiome; functional potential
语种	英语
WOS研究方向	Microbiology
WOS类目	Microbiology
WOS记录号	WOS:001216398000001
来源期刊	MSYSTEMS
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/306759
作者单位	United States Department of Energy (DOE); Pacific Northwest National Laboratory; Washington State University; Oregon State University
推荐引用方式 GB/T 7714	Graham, Emily B.,Garayburu-Caruso, Vanessa A.,Wu, Ruonan,et al. Genomic fingerprints of the world's soil ecosystems[J],2024.
APA	Graham, Emily B.,Garayburu-Caruso, Vanessa A.,Wu, Ruonan,Zheng, Jianqiu,Mcclure, Ryan,&Jones, Gerrad D..(2024).Genomic fingerprints of the world's soil ecosystems.MSYSTEMS.
MLA	Graham, Emily B.,et al."Genomic fingerprints of the world's soil ecosystems".MSYSTEMS (2024).