Temporal and spatial dynamics of bacterial and fungal microbiomes in nursery soils post-steaming

Authors: CRANDALL, SHARIFA - Pennsylvania State University; Miles, Asha; CHUNG, TAEJUNG - Pennsylvania State University; CLOUTIER, MARA - Pennsylvania State University; GARCIA-RODRIGUEZ, RAYMOND - Pennsylvania State University; SCHWEIGKOFLER, WOLFGANG - Dominican University Of California; COURADEAU, ESTELLE - Pennsylvania State University

Submitted to: PhytoFrontiers
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2022
Publication Date: 10/31/2022
Citation: Crandall, S.G., Miles, A.M., Chung, T., Cloutier, M.L., Garcia-Rodriguez, R., Schweigkofler, W., Couradeau, E. 2022. Temporal and spatial dynamics of bacterial and fungal microbiomes in nursery soils post-steaming. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-07-22-0071-R.
DOI: https://doi.org/10.1094/PHYTOFR-07-22-0071-R

Interpretive Summary: Plant pathogens can be eliminated from nursery soils by applying heat in a process known as steam sterilization. What isn’t known is the impact this has on soil ecosystems and nutrient composition that contribute to plant health. This manuscript investigates changes in soil chemistry and fungal and bacterial microbiomes on topsoil and subsoil 1 day, 2 months, and 5 months after steam sterilization. The purpose of this work is to help nursery practitioners decide whether they should add bioproducts and fertilizers to adjust soils post-steaming and to target amendments that support soil and plant health.

Technical Abstract: A major concern for plant nurseries and land stewards is managing pathogens that cause soilborne diseases. Plant pathogens can cause disease which costs nurseries millions of dollars in lost revenue. These pathogens also disperse and spread into the environment from nursery soil and plants used for out-plantings in wild and managed landscapes. Recent research shows that steaming soil and plant pots at high temperatures can effectively kill plant pathogens, however, few studies investigate how the soil microbiome responds to steaming, namely: (1) how does it cause shifts in the microbial community compositon and diversity overtime, (2) quantify the most abundant and dominant bacterial and fungal communities at diferent time points including functionally important taxa such as plant pathogens and (3) influence the soil chemistry post-steaming. We conducted a controlled experiment where nursery soil underwent a steaming event within a rectangular mesocosm (2.04 x 3.55 x 0.25 m) located at the National Ornamentals Research Site at Dominican University (NORS-DUC) (San Raphael, C.A., U.S.A). Soil samples were collected at various time points up to 5 months post-steaming. A total of 32 soil samples were used for DNA extraction and 18 for chemical analysis. 16S rRNA gene and ITS genetic markers were used for amplicon high-throughput sequencing methods to identify the bacterial and fungal soil microbiome. Results indicate that microbial diversity and composition changed overtime, but that soil depth was not an important factor. Important bacterial taxa that were found were Firmicutes, especially 1 day post-steaming, and common fungal taxa included Aspergillus sp.. Cladosporium, sp. and Pseudallescheria, sp.. Soil chemistry levels for nutrients such as B, C, Cl, K, Mg, SO4, Zn in addition to essential soil properties such as CEC, gypsum, moisture, and SAR changed significantly with soil recovery. These results can help nursery practitioners to make informed decisions regarding if and when to add bioproducts, fertilizers or synthetic microbial communites or make adjustments to the soil chemistry post-steaming to promote soil and plant health.