Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

Authors: ERLANDSON, SONYA - Orise Fellow; Neupane, Dhurba; Osborne, Shannon; Lehman, R - Michael

Submitted to: Environmental Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/21/2024
Publication Date: 5/7/2024
Citation: Erlandson, S.R., Ewing, P.M., Osborne, S.L., Lehman, R.M. 2024. Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations. Environmental Microbiome. 19(1), 1-15. https://doi.org/10.1186/s40793-024-00571-8.
DOI: https://doi.org/10.1186/s40793-024-00571-8

Interpretive Summary: Soil bacteria and fungi are critical to soil processes and plant growth which translates to significant influence on agronomic and environmental outcomes. However, assessing the active component of these communities – the taxa responding to management, interacting with plants, and cycling nutrients – remains challenging due to the overall high soil microbial diversity. We tested a method, “sterile sentinels”, to sample the most actively growing microbes in agricultural soils. The sterile sentinel method attempts to improve assessment by incubating uncolonized and standard soil within a root exclusion bag in the field. The method provided greater resolution in identifying management effects on bacterial community structure and allowed inference of management effects on plant-associated bacteria and fungi. Sentinel results therefore provided complementary information about soil microbial communities to that of bulk soil samples. Further testing across sites and deployment schemes will enable assessment of the transferability of these results. The method also allowed easy and standardized sample collection without specialized equipment. When combined with rapid-turnaround sequencing technologies, we anticipate this method will facilitate routine and large-scale assessment of critical soil microbes, ultimately leading to better prediction and management of their role in agricultural systems.

Technical Abstract: Background: Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, “sterile sentinels,” for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method. Results: Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations. Conclusions: Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.