Elevation Gradient (EG) Soil Microbial diversity FAME and TRFLP data



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Soil fungal communities respond to multiple abiotic and biotic factors that change along elevation gradients. The limited information available on fungi and microbial processes along elevation gradients is primarily from temperate areas and very few from tropical regions. This study documents changes in fungal and bacterial diversity, and abundance and composition of microbial functional groups along a subtropical elevation gradient.

Date Range: 
2003-03-01 00:00:00 to 2004-12-31 00:00:00



Additional Project roles: 

Name: Carlos A. Cruz Role: Associated Researcher
Name: Luis M. Garcia Role: Associated Researcher


The elevation gradient is located in eastern Puerto Rico and is composed of five forest types each with characteristic vegetation. Soil samples were collected every three months from March 2003 thru December 2004. Soil fungal and bacterial communities were analyzed using fatty acid methyl esters (FAME) and TRFLP profiles.

In each forest type, five plots of 5 x 5 m were established and soil samples were collected every three months starting in March 2003 thru December 2004. A polyvinyl chloride plastic tube 5 cm in diameter and 10 cm in length was used to take a random core sample from each plot after removal of surface litter. A total of 150 soil cores were analyzed but only 79 of these yielded usable DNA extractions. Samples were stored in sterile plastic bags at -20°C for fatty acid or DNA extraction. Each sample was subdivided by depth into 0-5 and >5-10 cm strata. Fatty acids were extracted directly from 3 g of soil using the method for ester linked fatty acid methyl ester (EL-FAME). Briefly, the method used a mild alkaline methylation followed by pH neutralization with 1M acetic acid and FAME extraction using hexane. Extracts were cleaned using a NH2 column to remove humic substances. Samples were stored at -20°C until analyzed. Samples were analyzed in a GC-MS (Hewlett Packard 6890). DNA was extracted from 0.3 g of sample using MoBio Ultra Clean Soil DNA Isolation Kit. The 16S bacterial rDNA was amplified using primers 27F-FAM and 1525R, and digested with MnlI. The fungal ITS region was amplified using primers ITS1-FAM and ITS4, and digested with HaeIII. Samples were analyzed in an ABI 3130 using GenScan 500 Liz Size Standard.


<p>A polyvinyl chloride plastic tube 5 cm in diameter and 10 cm in length was used to take a random core sample from each plot after removal of surface litter.</p>

<p>GC-MS (Hewlett Packard 6890) used to analize soil samples.</p>

<p>A MoBio Ultra Clean Soil DNA Isolation Kit was used to extract DNA from sample</p>

<p>A ABI 3130 using GenScan 500 Liz Size Standard was used to analize digested samples</p>

Additional information: 

Results: Our results produced humped distributions for Shannon diversity of FAME and fungal to bacteria (F:B) ratios. Both microbial communities differed significantly among forest types. TRFLP were more frequently unique to forest types in fungi than bacteria. In multiple linear regression (MLR) models, soil moisture was predictive for all but Actinomycete FA abundance, and forest type contributed significantly to these same models for F:B ratios and all FA except for Gram negative 10Me18:0 and Gram positive 15:0. Diversity in this elevation gradient is higher at mid-elevations. Most G negative and G positive bacterial FAME were positively related to soil pH in MLR models, lower pH in mid-elevation forest soil may suppress bacteria favoring fungi. Conclusion: These data can be used as a benchmark for monitoring changes in microbial communities along elevation gradients caused by natural and anthropogenic disturbances, as well as global and regional climate changes.



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