Abstract
The discovery of biomarkers for assessing soil health requires the exploration of organisms that can explain the core functions of soil and identification of species with major roles in these functions. However, identifying specific keystone markers within the soil microbiota is challenging. Next-generation sequencing (NGS)-based molecular-biological methods have revealed information on soil biodiversity; however, whether this biodiversity is related to soil health remains unclear. In this study, we performed NGS on grassland surface soil to compare the prokaryotic and eukaryotic genetic diversity to determine the chemical soil quality and examined markers associated with soil health. Microorganisms associated with the nitrogen cycle, bioremediation, plant pathogenicity, antibiotic production, and material degradation showed potential for use as markers. To propose a framework for soil health assessment, we not only used traditional indicators, such as chemical and physical measures, but also assessed metagenomics data of soil by land use to identify the major factors influencing the microbial structure in soil. Moreover, major keystone species were identified. Furthermore, the microbial genetic diversity of generally healthy surface soil, such as forests, farmland, and parks, was determined. These findings provide basic data for exploring soil health-related biomarkers.
Highlights
Living organisms in soil, including the soil microbiota, play important roles in supporting life on earth
Next-generation sequencing (NGS)-based molecular techniques have been used to study soil microbial diversity and soil microorganisms useful for producing high-quality plants. These studies reported the bacterial and fungal diversity according to the specific treatment of field soil; microbial diversity according to soil depth on a poplar farm; association between soil depth and native and exotic plant species; and comparison of the soil microbiota in natural and re-seeded grassland [2–5]
The results suggested that the soil depth is a major factor affecting the networking between the microbiota structure and abiotic factors, including interactions with fungi at approximately 1 m below the soil surface and microbial diversity at depths of 0–20 and ≥21 cm
Summary
Living organisms in soil, including the soil microbiota, play important roles in supporting life on earth. Compared to soil indicators based on physical and chemical measures that can be used to assess soil quality, bioindicators remain controversial These indicators typically have key functions and important regulatory roles (known as keystone species), identifying specific keystone markers within the vast functional redundancies of the soil microbiota remains challenging [1]. Next-generation sequencing (NGS)-based molecular techniques have been used to study soil microbial diversity and soil microorganisms useful for producing high-quality plants (agricultural soil environment and agriculture-related microorganisms). These studies reported the bacterial and fungal diversity according to the specific treatment of field soil; microbial diversity according to soil depth on a poplar farm; association between soil depth and native and exotic plant species; and comparison of the soil microbiota in natural and re-seeded grassland [2–5]. The results demonstrated that the surface soil has important effects on plant growth
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