Molecular Ecology

A few years back, I began working on a collaborative project led by Greg Bonito to examine fungal and bacterial communities associated with plant roots.  We used next-generation sequencing on the 454 GS-FLX platform for profiling using four different loci (one bacterial and three fungal).  The fungal ITS and LSU primers were identical to those used in my recent Mycosphere paper (Hodkinson & Lendemer 2013), and the 16S primers are the ones I designed for my Environmental Microbiology paper from a couple of years back (Hodkinson et al. 2012).  The paper is finally out in Molecular Ecology; check it out!

- Brendan

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References

Bonito, G., H. Reynolds, M. S. Robeson, J. Nelson, B. P. Hodkinson, G. Tuskan, C. W. Schadt, and R. Vilgalys. 2014. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Molecular Ecology 23(13): 3356-3370.
Download publication (PDF file)

Hodkinson, B. P., and J. C. Lendemer. 2013. Next-generation sequencing reveals sterile crustose lichen phylogeny. Mycosphere 4(6): 1028-1039.
Download publication (PDF file)
Download data and sequence-processing scripts (ZIP archive)
Download Ascomycota LSU alignment and analysis files (ZIP archive)
Download Arthoniales LSU alignment and analysis files (ZIP archive)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology 14(1): 147-161.
Download publication (PDF file)
View publication (publisher's website)Download supplementary phylogeny (PDF file)
Download data and analysis file archive (ZIP file)

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[Support for my work on this project was provided in part by the National Science Foundation under awards EF-0832858, DEB-1011504, and DEB-1145511.]