Microbial Ecology

, Volume 60, Issue 3, pp 606–617 | Cite as

Soil Microbial Communities Associated with Douglas-fir and Red Alder Stands at High- and Low-Productivity Forest Sites in Oregon, USA

  • Stephanie A. Yarwood
  • Peter J. Bottomley
  • David D. Myrold
Soil Microbiology

Abstract

Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed spacer region), eubacterial 16S rRNA, and archaeal 16S rRNA primers. Population size was measured with quantitative (Q)-PCR and composition was examined using length heterogeneity (LH)-PCR for fungal composition, terminal restriction fragment length (T-RFLP) profiles for bacterial and archaeal composition, and sequencing to identify dominant community members. Whereas fungal and archaeal composition varied between sites and dominant tree species, bacterial communities only varied between sites. The abundance of archaeal gene copy numbers was found to be greater in coastal compared to montane soils accounting for 11% of the prokaryotic community. Crenarchaea groups 1.1a-associated, 1.1b, 1.1c, and 1.1c-associated were putatively identified. A greater abundance of Crenarchaea 1.1b indicator fragments was found in acidic (pH 4) soils with low C:N ratios under red alder. In coastal soils, 25% of fungal sequences were putatively identified as basidiomycetous yeasts belonging to the genus Cryptococcus. Although the function of these yeasts in soil is not known, they could significantly contribute to decomposition processes in coastal soils distinguished by rapid tree growth, high N content, low pH, and frequent water-saturation events.

Notes

Acknowledgments

Support was provided by grants from the USDA NRICGP, the National Science Foundation IGERT Program, and the HJ Andrews LTER fund. Thanks go to Rockie Yarwood and Elizabeth Brewer for assistance in sample collection and preparation and to Kenneth Stedman for providing Sulfolobus solfataricus DNA and Joseph Spatofora for providing Haematonectria haematococca DNA. A portion of this research was conducted at the HJ Andrews Experimental Forest, which is funded by the US Forest Service, Pacific Northwest Research Foundation. Thank you also to Oregon State University’s Center for Genome Research and Biocomputing for Q-PCR facilities and genotyping analysis and to the University of Washington High Throughput Genomic Sequencing Unit.

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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Stephanie A. Yarwood
    • 1
  • Peter J. Bottomley
    • 1
    • 2
  • David D. Myrold
    • 2
  1. 1.Department of MicrobiologyOregon State UniversityCorvallisUSA
  2. 2.Department of Crop and Soil ScienceOregon State UniversityCorvallisUSA

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