A longitudinal study using 16s rRNA gene sequence analysis of soil amended or unamended with heat-treated poultry pellets contaminated with Salmonella Newport

Authors: SHAH, MANOJ - North Dakota State University; GRIM, CHRISTOPHER - Food And Drug Administration(FDA); JARVIS, KAREN - Food And Drug Administration(FDA); BERGHOLZ, TERESA - North Dakota State University; Sharma, Manan

Submitted to: International Association for Food Protection
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2019
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Introduction: Salmonella Newport is a foodborne pathogen frequently associated with outbreaks in produce. Several factors, such as the use of manure, temperature, and soil moisture have been shown to impact Salmonella survival in soil. Purpose: The purpose of this study was to investigate soil microbiomes by 16s rRNA amplicon sequencing, over a two-month period, in heat-treated poultry pellets (HTPP)-amended or unamended soils contaminated with and without Salmonella Newport. Methods: Salmonella Newport was inoculated at ~7.5 log CFU per gram dry weight into a total of six planters, three containing HTPP-amended soil and three without amendment. Six similar planters were also set up without Salmonella Newport inoculation. Soil samples were collected in duplicate from each planter on days zero, 21, 35, and 63, and six replicate samples from bulk and rhizosphere soil were also collected at days 35 and 63. 16s rRNA microbiome sequencing was performed on extracted metagenomic DNA. Results: Amended and unamended soils harbored very diverse microbiomes, with >1,500 taxa identified over all samples. The addition of HTPP introduced, or added certain taxa; namely, Pseudomonas (P. entomophila and P. fuscovaginae) and Bacilli (such as B. aryabhattai, B. asahii, B. arbutinivorans, and Rummeliibacillus stabekisii) to the soil. Some taxa remained constant during the 63 days of the study, such as Granulicella tundricola, and members of the Actinomycetales and the Rhodoplanes, while others increased in proportional abundances, such as Niastella, Devosia, Brevundimonas spp., and Sphingobacteriummultivorum. Salmonella persisted longer in amended soils, ranging from 5% relative abundance on day 0 to 0.1% on day 63. In unamended soils, Salmonella was undetected after day 21. Salmonella was also detected in rhizosphere soil at day 35 but declined to undetectable levels by day 63. Significance: The soil amendment resulted in an increase in abundance of some members of the microbiome without an overall impact on the diversity and promoted the survival of Salmonella.