Metataxonomics Characterization of Soil Microbiome Extraction Method Using Different Dispersant Solutions

Abstract

Soil health is essential for maintaining ecosystem balance, food security, and human well-being. Anthropogenic activities, such as climate change and excessive agrochemical use, have led to the degradation of soil ecosystems worldwide. Microbiome transplantation has emerged as a promising approach for restoring perturbed soils; however, direct soil transfer presents practical limitations for large-scale applications. An alternative strategy involves extracting microbial communities through soil washing processes, but its success highly depends on proper microbiota characterization and efficient extraction methods. This study evaluated a soil wash method using four different dispersant solutions (Tween-80, NaCl, sodium citrate, and sodium pyrophosphate) for their ability to extract the majority of microbial cells from Antarctic and Crop soils. The extracted microbiomes were analyzed using 16S rRNA gene metataxonomics to assess their diversity and abundance. We found that some treatments extracted a greater proportion of specific taxa, and, on the other hand, some extracted a lower proportion than the control treatment. In addition, these dispersant solutions showed the extraction of the relevant microbial community profile in soil samples, composed of multiple taxa, including beneficial bacteria for soil health. Our study aims to optimize DNA extraction methods for microbiome analyses and to explore the use of this technique in various biotechnological applications. The results provide insights into the effect of dispersant solutions on microbiome extractions. In this regard, sodium chloride could be optimal for Antarctic soils, while sodium citrate is suggested for the Crop soils.

Keywords: 16S rRNA gene metataxonomics; dispersant solutions; metabarcoding; metataxonomics; microbiome transplantation; soil bioremediation.

Figure 1

Taxonomic composition and diversity analyses of Antarctic and Crop soil microbiomes extracted using different dispersant solutions. (A,E) Relative abundance of bacterial phyla in Antarctic and Crop soils, respectively. (B,F) Relative abundance at genus level in Antarctic and Crop soils, respectively. (C,G) Principal Coordinates Analysis (PCoA) based on Bray–Curtis dissimilarity matrix showing beta diversity of microbial communities in Antarctic and Crop soils, respectively. (D,H) Alpha diversity analysis using Chao1 index for Antarctic and Crop soils, respectively. Treatments included no treatment control (nt), Tween-80, sodium chloride, sodium citrate, and sodium pyrophosphate. Data show differences in microbial composition and diversity across treatments.