Microbial Metagenomic Profiling Of Urban Land Udorthents Biology Essay


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).

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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:

Sample collection:

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.

Physical analysis:

The pH of the soil samples was analyzed with an AB151 pH meter (Fisher Scientific, Suwanee, GA) according to the manufacturer's protocols for soils. The moisture content was determined using a Hydra Probe® Soil Sensor (Stevens® Water Monitoring System, Inc.) according to the manufacturer's specification in the lab. The temperature of the sites was monitored using temperature probes (I-button® Devices).

DNA Extraction and Quantification

Soil DNA was extracted with the Fast DNA Spin Kit for Soil® (MP Bio, Solon, OH) (Mills et al., 2003) using the FastPrep®-24 System homogenizer .The extracted DNA was quantified using the BioRad Fluorescent DNA Quantitation Kit and ModulusTM Microplate Multimode Reader. The DNA samples were diluted to a stock concentration of 20ng/µl and the remaining sample volumes were stored at -20C°. Extracted DNA was checked for its quality on a 1% agarose yield gel.


The soil DNA was amplified using multiplex LH-PCR and two duplexes, one for bacteria and fungi and one for plant and archaea. Universal primers for the four taxa were used. 16S rRNA gene was used for bacteria and archaea (Suzuki et al., 1998, Delong, 1992 and Cocolin et al., 2001, the ribosomal internal transcribed spacer region (ITS) for fungi (White et al., 1990), and the chloroplast trnL intergenic region for plants (Taberlet et al., 1991). The forward primers were labeled with the blue 6-FAM dye. The optimized concentrations of PCR reagents for both duplexes are 1X reaction buffer, 2.5mM MgCl2, 250 µm dNTPs (Promega, Madison, WI), 1% BSA (fraction V, Fisher Scientific, Pittsburgh, PA), 1% DMSO (Promega, Madison, WI), various µm of primers, 2ng DNA, and 0.5 U DNA polymerase AmpliTaq Gold DNA PolymeraseTM (Applied Biosystems, Foster City, CA), and diethylpyrocarbonate-treated (DEPC) water to a final volume of 20µL. Same program was used to amplify each duplex using a 9700TM thermocycler (Applied Biosystems, Foster City, CA). The following parameters were used; an initial 10 minute denaturing step at 95°C, 25 cycles of denaturation at 95°C annealing at 52°C and extension at 72°C each for 30 seconds with a final extension at 72°C for 10 minutes. The four taxa were each run individually and in duplex, with control DNAs and soil samples.

Capillary Electrophoresis (CE):

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The amplified PCR products were used for amplicon length heterogeneity (LH-PCR). The sample for CE separation was prepared by mixing 0.5 µl of the PCR product with 9 µl of Hi-DiTM formamide containing a 96:1 ratio of Hi-DiTM and GeneScanTM LIZ 600TM (Applied Biosystems, Foster City, CA). GeneScanTM LIZ 600TM was fluorescently labeled size standard. DS-33 matrix and filter set G (6FAM™, VIC™, NED™ PET™, and LIZTM) were used (Applied Biosystems, Foster City, CA). The PCR products were denatured by heating at 95°C for two minutes and then immediately snap cooled on ice for five minutes. The samples were then electrokinetically injected at 15 kV for five seconds and run at 60°C on an ABI PrismTM 310 (Applied Biosystems, Foster City, CA) using Performance Optimized Polymer 4 (POP4) (Applied Biosystems, Foster City, CA) with laser power at 9.9mW and capillary length of 45.72 cm, and a run time of 28 minutes per sample.