Sequencing World Soil DNA with Archived Soil Samples

Soil is the interface between the earth crust and the atmosphere, and strongly interacts with aboveground life and water on Earth’s surface. Soil hosts a quarter of our planet’s biodiversity: one gram of soil, or a teaspoon, contains one billion bacterial cells. This corresponds to about ten thousand different bacterial genomes, up to one million individual fungi, about one million cells of protists, and several hundred of nematodes. Beside micro-organisms and micro-fauna, different species of meso- and macro-/mega-fauna live in the soil, such as arthropods, earthworms and mammals. Soil biodiversity is recognized as a crucial factor in soil functioning and as a provider of several ecosystem services. It drives life aboveground through complex food webs, and serves to reach the ambitious UN biodiversity, climate and food security goals (several of the SDGs).

ISRIC maintains a global collection of reference soil samples from some 1000 profiles collected from all over the world over the past 60 years as a reference for research. The collection is truly unique, and is fully described and analyzed for physical and chemical parameters but lacks analysis for biological parameters. This project will yield new insights of soil microbial community distribution pattern and microbial functional characteristics at a global scale, and will serve as a reference for future study. A total number of 4658 samples will be analyzed for soil DNA from about 63 countries and sampled in different moments in time between 1952 and 2016.

• To extract and sequence DNA from the ISRIC’s archived reference soil samples. 

• To build a microbial reference of the world soils. 

• To assess microbial communities (bacterial abundance, bacterial community composition, fungal abundance, fungal community composition) in the world dominant soils.

• Selection of typical soil samples for DNA extraction pre-testing and quality check 

• Separation of archived soil samples 

• Soil DNA extraction 

• Soil DNA sequencing (including library construction) 

• Bioinformatic analysis for microbial community abundance, composition and correlate with corresponding environments

• To establish a world soil microbial reference database for the layered soil microbials of the main soil types and profiles  

• To characterise soil microbial community structure (prokaryotic abundance, prokaryotic community composition, fungal abundance, fungal community composition) and spatial distribution of the soil microorganisms 

• To analyse soil microbial community type, relationships between soil structural, soil chemical and physical properties and functional metrics at multiple scales 

• To analyse soil microbial functional flora: species, interaction/influence relationship between distribution of functional flora groups and genes and the environment; soil beneficial microorganisms, participating in C, N cycle, P-dissolving, K-solubilizing bacteria or N-fixing bacteria etc.; methane oxidation, methanogenesis etc.

The project is coordinated by ISRIC–World Soil Information and project partners include:

• ISRIC–World Soil Information, The Netherlands 

• University of Chinese Academy of Sciences, Beijing, P.R. of China 

• Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, P.R. of China 

• The Netherlands Institute of Ecology, the Royal Netherlands Academy of Arts & Sciences, Wageningen, The Netherlands

The project is co-funded by University of Chinese Academy of Sciences, Agricultural Genomics Institute at Shenzhen and ISRIC-World Soil Information.