Monday, August 3, 2009

PS 20-171: Soil faunal distribution among different ecosystems using large scale molecular cloning and sequencing

Tiehang Wu1, Edward Ayres2, Richard D. Bardgett3, Diana H. Wall2, and James R. Garey1. (1) University of South Florida, (2) Colorado State University, (3) Lancaster University


Soil fauna play important roles in ecosystems and may greatly influence ecological processes.  However, patterns of global scale diversity for soil animals are poorly known, especially for mesofauna and microfauna.   Traditional morphological methods require specialized knowledge of each group of soil animals, which is influenced by the method with which animals are extracted from the soil and are extremely labor intensive.  We are studying the biodiversity of the entire soil animal community using large-scale sequencing of 18S rDNA extracted from around the globe.  We present results obtained from seven locations including boreal forests and tundra in Alaska and Sweden, tropical forests in Costa Rica and Peru, and a temperate forest in New Zealand.  At each site a 900m transect was established comprised of 4 evenly spaced plots (10 x10 m). Twenty soil cores were combined from each plot.  DNA was extracted from the soil samples of each plot and 18S rDNA amplified with metazoan-specific primers. The PCR products were cloned into libraries and individual clones sequenced. Sequences were compiled into OTUs using a 99% match criterion and OTUs were identified provisionally by BLAST searching. Community structure and biodiversity were analyzed using PrimerE and EstimateS software. 


We obtained 13,089 sequences from the seven different sites.  Based on 99% minimum matching percentage, we assigned the sequences to 1502 OTUs (operational taxonomic units).  Among these, 254 OTUs were obtained from the 2621 sequences of the boreal forest of Alaska; 303 OTUs from 2621 sequences of the tundra of Alaska; 212 OTUs from 1339 sequences of the boreal forest of Sweden; 271 OTUs from 1305 sequences of the tundra of Sweden; 240 OTUs from the 2552 sequences of the tropical forest of Costa Rica; 144 OTUs from the tropical forest of Peru; and 138 OTUs from 1315 sequences of the temperate forest of New Zealand.  Approximately 77% of all the OTUs were represented only once, indicating a large proportion of rare organisms in most soils. We compare the common species, diversity, and community structure among samples from the seven sites. The soil faunal composition under different ecosystems using molecular profiling will provide important information about global-scale patterns of diversity for the entire soil animal community and may allow a better understanding of the relationship between below ground diversity and above ground diversity.