Event Title

ES5 -- Microbial Soil Community Profiling of Recreational Areas near a Pond at Grace Street Park in Greenwood, South Carolina through Illumina MiSeq sequencing

Location

URC Greatroom

Start Date

8-4-2022 10:30 AM

Description

City parks and urban environments contain diverse urban microbiomes that contribute to the health of urban systems through pollution degradation and the driving of biochemical cycles and soil processes (Li et al. 2009, Cusack et al. 2011, Escobedo et al. 2011, Strohbach and Haase 2012, Han et al. 2017, Kirchman 2018, Deng et al. 2020). The activity and composition of soil microbial communities are generally impacted by dominant plant species in the parks present as well as the presence of polluted material, agricultural products, and animal waste products (Hartmann et al. 2009). In recent studies, recreational parks in densely populated cities have been shown to support larger proportions of antibiotic resistant pathogens, which could make fighting against city park pests, more difficult and economically challenging in the future (Delgado-Baquerizo et al. 2021). After a brief literature review, it was noted that very little research has been published on the diversity and bioactivity of soil microbial communities in public parks and urban recreational areas. Soil samples were collected from recreational areas throughout Grace Street Park in Greenwood, South Carolina. These areas included a dog park, playground, pond banks and hiking trails. Each soil sample was analyzed independently for microbial community analyses. DNA was extracted from 2.5 g of soil using Quiagen DNeasy PowerSoil Pro Kit following the standard manufacturer's protocol. Concentrations of extracted DNA were assessed using a Nanodrop spectrophotometer to ensure successful DNA extraction and quantification for sequence library preparation. DNA samples were sent to University of Michigan’s Microbiome Core (Ann Arbor, MI) for library preparation and next generation sequencing. The V4 region of the 16S rRNA gene was amplified for downstream sequencing with the commonly used primers 16Sf-V4 (515f) and 16Sr-V4 (806r) and a previously developed protocol (Caporaso et al. 2012; Kozich et al. 2013). Sequencing was accomplished via a MiSeq high-throughput sequencer (Illumina, San Diego, CA). Acquired DNA sequences were filtered for quality and analyzed using MOTHUR v 1.47.0 (Schloss et al. 2009) following the MiSeq SOP (available at https://www.mothur.org/) with modifications. This study has provided an initial characterization of microbial communities in the recreational areas at Grace Street Park in Greenwood, South Carolina.

This document is currently not available here.

Share

COinS
 
Apr 8th, 10:30 AM

ES5 -- Microbial Soil Community Profiling of Recreational Areas near a Pond at Grace Street Park in Greenwood, South Carolina through Illumina MiSeq sequencing

URC Greatroom

City parks and urban environments contain diverse urban microbiomes that contribute to the health of urban systems through pollution degradation and the driving of biochemical cycles and soil processes (Li et al. 2009, Cusack et al. 2011, Escobedo et al. 2011, Strohbach and Haase 2012, Han et al. 2017, Kirchman 2018, Deng et al. 2020). The activity and composition of soil microbial communities are generally impacted by dominant plant species in the parks present as well as the presence of polluted material, agricultural products, and animal waste products (Hartmann et al. 2009). In recent studies, recreational parks in densely populated cities have been shown to support larger proportions of antibiotic resistant pathogens, which could make fighting against city park pests, more difficult and economically challenging in the future (Delgado-Baquerizo et al. 2021). After a brief literature review, it was noted that very little research has been published on the diversity and bioactivity of soil microbial communities in public parks and urban recreational areas. Soil samples were collected from recreational areas throughout Grace Street Park in Greenwood, South Carolina. These areas included a dog park, playground, pond banks and hiking trails. Each soil sample was analyzed independently for microbial community analyses. DNA was extracted from 2.5 g of soil using Quiagen DNeasy PowerSoil Pro Kit following the standard manufacturer's protocol. Concentrations of extracted DNA were assessed using a Nanodrop spectrophotometer to ensure successful DNA extraction and quantification for sequence library preparation. DNA samples were sent to University of Michigan’s Microbiome Core (Ann Arbor, MI) for library preparation and next generation sequencing. The V4 region of the 16S rRNA gene was amplified for downstream sequencing with the commonly used primers 16Sf-V4 (515f) and 16Sr-V4 (806r) and a previously developed protocol (Caporaso et al. 2012; Kozich et al. 2013). Sequencing was accomplished via a MiSeq high-throughput sequencer (Illumina, San Diego, CA). Acquired DNA sequences were filtered for quality and analyzed using MOTHUR v 1.47.0 (Schloss et al. 2009) following the MiSeq SOP (available at https://www.mothur.org/) with modifications. This study has provided an initial characterization of microbial communities in the recreational areas at Grace Street Park in Greenwood, South Carolina.