Soil is a substance composed of minerals and organic matter that supports plant life. The properties of soil do not remain constant due to the influx and efflux of rainfall and the organic matter which it derives from decaying organic matter. Therefore, the soil properties are different across different soil types and can change with environmental factors can fluctuate with the seasons. According to FAWN, the State of Florida has two seasons, wet and dry. The two seasons are classified based on the average rainfall (FAWN, 2002).
Soil can be valuable evidence in an investigation. Soil has been analyzed by various methods like microscopic and chemical to act as evidence in investigations (Junger, 1996; McVicar & Graves, 1997; Srodon et al., 2001). It has been recently examined biologically (Suzuki et al., 1998; Mills et al., 2003; Mills et al., 2006). The recent advances being that soil types can be distinguished based on their biotic content (Moreno et al., 2006). Amplicon length heterogeneity PCR (LH-PCR) is a method that can be used to identify hypervariable regions such as 16S rRNA genes. 16S rRNA heterogeneity has been used widely to identify structural patterns in microbial communities from variety of samples (Suzuki et al., 1998).
Zhou et al. has shown that that the microbial communities present in the soil are affected by soil type (Zhou et al., 2002), and any manipulation in soil will affect the microbial diversity observed in the soil type (Girvan et al., 2003). The obtained soil DNA profiles were analyzed using bioinformatics tools. These tools have been validated as to be able to classify microbial community profiles across varied sample types.
Objectives: The aim of the research is to use microbial community profiling and bioinformatic tools to analyze and classify soil from different soil types across the Miami-Dade County. And also aid in establishing a searchable soil profiling database. For this study, the DNA profiles were generated using amplicon length heterogeneity (LH-PCR) with the four taxa, Bacteria, Fungi, Archaea and Plant.
Materials and Methods:
USDA has classified the soil in Miami-dade County into six different types. The classifications are as follows, soil type one: Urban Land-Udorthents, two: Lauderhill Dania-Pahokee, three: Rock Outcrop-Biscayne-Chekika, four: Perrine-Biscayne-Pennsuco, five: Krome Association, and six: Perrine-Terra Ceia-Pennsuco (USDA). Soil samples were collected from soil type one. Four transects were collected from soil type one. Each transect was 100 m in length and six subplots of (1 m2) were haphazardly collected along the transect. From each subplot six samples (A-F) were collected. A total of 36 samples were collected from a transect. The samples were collected in the wet (August – January) as well as the dry (February- July) season as defined by Florida Automated Weather Network (FAWN, http://fawn.ifas.ufl.edu/). The two seasons are classified based on the average rainfall (FAWN, 2011). Soil samples were collected from the top 5 cm with a 2cm diameter soil corer.