An Assessment of Fungal Diversity Using Oligonucleotide Fingerprinting of rRNA Genes, A Macroarray-based Technique

Environmental controls over the diversity and community composition of microbial decomposers are poorly understood. In this experiment, we examined the effects of litter quality and competitive exclusion on fungal diversity. Specifically, we expected to see greater fungal diversity in litter containing higher nitrogen concentrations in that this high quality substrate would be able to support fungal groups with a range of nutrient requirements. Additionally, to test the competitive exclusion principle that a limited number of decomposer groups can be supported by a given substrate, we excluded from the litter one phylum of decomposer fungi, the Ascomycota. An increase in diversity within the remaining fungal phyla would indicate a release from competitive exclusion. To test these hypotheses, we performed a decomposition experiment in a boreal forest near Delta Junction, Alaska. Senescent leaves of Populus tremuloides (quaking aspen) from two sites that varied in soil fertility were collected in fall 2002. Leaves from the more fertile site had nitrogen concentrations of 2.26%, and those from the less fertile site had nitrogen concentrations of 1.59%. Leaves were placed into 1-mm mesh bags and incubated in a third site from September 2002 to July 2003. The fungicide Benomyl, which eliminates Ascomycetes, was applied to a subset of the bags at the onset of decomposition. Directly following collection, active fungal DNA was isolated using a nucleotide analog probe. Fungal communities were characterized by oligonucleotide fingerprinting of rRNA genes, a macroarray-based technique. Cluster analyses of fingerprints identified fungal groups representing taxonomic levels ranging from genus to class. The number of fungal groups in each treatment was approximated using the Chao1 estimator. A total of 524 ± 10 fungal groups were estimated to occur across all treatments, with less than 60 of these groups previously identified in Genbank. We found that litter quality did not strongly affect fungal diversity, since the number of fungal groups did not differ significantly between site of litter origin (P = 0.0691). However, the overall fungal diversity in the fungicide treatment was significantly reduced compared to the control (P = 0.0358). This indicates that the remaining fungal groups did not completely radiate to fill all available niches following the elimination of competitors. Thus, we did not find strong evidence for competitive exclusion as an important control over the microbial community composition in this system. An additional analysis of the diversity of non-Ascomycetes across treatments will be conducted to further elucidate any potential role of competitive exclusion.