Cultivating an Understanding of Microbial Diversity

Plant diversity, soil structure, and seasonality all influence microbial diversity in soil.

The Science

Biodiversity protects ecosystems from stressors, increases ecosystem services, and promotes sustainability by enhancing resilience. Researchers studied how plant growth, agricultural management, and season influence the diversity of microbial communities. Within soil clumps called aggregates, scientists saw that smaller soil aggregates had more bacterial and fungal diversity than larger ones. They also found that microbial diversity increases with plant diversity and changes seasonally. Larger soil aggregates were less diverse. But they had communities of microbes, known as microbiomes, that are more sensitive to environmental changes over the course of seasons.

The Impact

Understanding what controls the diversity and function of soil microbes can help researchers better predict how productive and healthy soil will be. This information can also help scientists predict how climate and environmental changes will influence the soil. Land-management services might use this knowledge to enhance biodiversity and the benefits soil provides to society.


Within soil systems, microbes maintain nutrient cycling, influence plant productivity, enhance drought tolerance, and impact soil health and fertility. However, the ecological rules that reinforce soil biodiversity and microbial activities are not clearly defined at a microbial scale. This study helps close an important knowledge gap by investigating how the spatial structure of soil is vital to understanding the impact of microbiomes on ecosystem and biogeochemical services. Historically, researchers have examined microbial diversity in soils at ecosystem or landscape scales. In this study, researchers chose different size soil aggregates as a way to represent microbially relevant scales. Over years and seasons, soil aggregate turnover is dynamic and thereby structures soil microbial habitats. Temporal data from different size soil aggregates and three different bioenergy management systems revealed discrete microbial communities. This research is pertinent to evaluating how different management practices impact spatially discrete microbial communities in the soil. Management practices that increase plant diversity across growing seasons, the authors demonstrate, influence soil aggregate habitats and therefore increase microbial diversity. The study underscores the importance of including both spatial and temporal dynamics in investigations in order to fully understand microbial community assembly and persistence in soil.

Principal Investigator

Kirsten Hofmockel
Pacific Northwest National Laboratory
[email protected]

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


This research was supported by the Office of Biological and Environmental Research, within the U.S. Department of Energy Office of Science, under award DE-SC0010775.


Upton, R. N., E. M. Bach, and K. S. Hofmockel. 2019. “Spatio-Temporal Microbial Community Dynamics within Soil Aggregates,” Soil Biology and Biochemistry 132, 58–68. DOI:10.1016/j.soilbio.2019.01.016.