Understanding the soil microbiome of a montane longleaf pine ecosystem: does choice of soil DNA extraction method matter?
Abstract (300 words maximum)
The longleaf pine (Pinus palustris Mill) is an ecologically diverse and resilient ecosystem. However, its range in the southeastern United States has significantly declined due to anthropogenic changes. Understory herbaceous plants play a significant role in maintaining its diversity and providing fuel for surface fires necessary for this pyrophytic ecosystem. Soil microbes are crucial to plant functions such as nutrient acquisition, plant health, and growth. Our long-term ecological study of the soil microbiome of a longleaf pine restoration site aims to understand factors that may influence the soil microbial community, such as seasonal changes, soil chemistry, restoration practices, and forest age. For this, in our analysis, it is necessary to consider the methodology and its potential role in influencing the characterization of the microbiome. Hence, the soil DNA extraction kits used are critical. Between 2021 and 2023, we used the DNeasy PowerSoil kit (original) for our soil DNA extractions. Then, after its discontinuation, starting in March 2023 we used the DNeasy PowerSoil Pro kit (new). We aim to answer the question: how do the two kits compare in terms of purity of DNA extracted and bacterial community representation? DNA was extracted from frozen soil samples collected at Sheffield Wildlife Management Area (WMA) in March, July, and November 2023 using the original kit. Extracted DNA concentrations were measured using a NanoDrop spectrophotometer to test for purity and DNA was sent to LC Sciences for 16S rRNA sequencing to identify bacterial composition. Results obtained from both kits will be compared. Investigating differences in DNA extraction kits used for our study is crucial for scientific rigor and replicability. Ultimately, our efforts will contribute to the understanding of soil DNA extraction methodology and the scarce knowledge base of the soil microbiome of the longleaf pine ecosystem.
Academic department under which the project should be listed
CSM - Ecology, Evolution, and Organismal Biology
Primary Investigator (PI) Name
Paula Jackson
Understanding the soil microbiome of a montane longleaf pine ecosystem: does choice of soil DNA extraction method matter?
The longleaf pine (Pinus palustris Mill) is an ecologically diverse and resilient ecosystem. However, its range in the southeastern United States has significantly declined due to anthropogenic changes. Understory herbaceous plants play a significant role in maintaining its diversity and providing fuel for surface fires necessary for this pyrophytic ecosystem. Soil microbes are crucial to plant functions such as nutrient acquisition, plant health, and growth. Our long-term ecological study of the soil microbiome of a longleaf pine restoration site aims to understand factors that may influence the soil microbial community, such as seasonal changes, soil chemistry, restoration practices, and forest age. For this, in our analysis, it is necessary to consider the methodology and its potential role in influencing the characterization of the microbiome. Hence, the soil DNA extraction kits used are critical. Between 2021 and 2023, we used the DNeasy PowerSoil kit (original) for our soil DNA extractions. Then, after its discontinuation, starting in March 2023 we used the DNeasy PowerSoil Pro kit (new). We aim to answer the question: how do the two kits compare in terms of purity of DNA extracted and bacterial community representation? DNA was extracted from frozen soil samples collected at Sheffield Wildlife Management Area (WMA) in March, July, and November 2023 using the original kit. Extracted DNA concentrations were measured using a NanoDrop spectrophotometer to test for purity and DNA was sent to LC Sciences for 16S rRNA sequencing to identify bacterial composition. Results obtained from both kits will be compared. Investigating differences in DNA extraction kits used for our study is crucial for scientific rigor and replicability. Ultimately, our efforts will contribute to the understanding of soil DNA extraction methodology and the scarce knowledge base of the soil microbiome of the longleaf pine ecosystem.