Environmental Microbiology

Just yesterday I had an article come out in print in Environmental Microbiology (Hodkinson et al. 2012a) that represents the central chapter of my doctoral dissertation (Hodkinson 2011). It has been published as part of a special issue on 'Omics' and their utility in environmental microbiology and microbial ecology. The study uses 16S rRNA gene sequence data (generated both through molecular cloning and pyrosequencing) to illuminate the bacterial diversity found in lichens. There are a number of interesting discoveries presented, e.g.:
- lichens harbor complex, diverse bacterial communities
- mycobiont, photobiont, and geography are all significant factors in determining bacterial community composition in lichens
- the most taxonomically diverse group is the order Rhizobiales (which contains many symbiotic nitrogen fixers... and many of the groups found within lichens have members that are symbiotic nitrogen fixers)
- the LAR1 (Lichen-Associated Rhizobiales #1; Hodkinson & Lutzoni 2009) lineage is one of the most abundant lineages and seems to be nearly exclusive to lichens
- Acidobacteria is also extremely common, which could potentially be a result of the abundant acidic secondary compounds produced by lichens.

In addition to the above findings (along with the exciting future directions that they point to!), the paper presents many scripts and protocols for managing and analyzing large 16S rRNA gene sequence data sets (Hodkinson et al. 2011). Many of the scripts and protocols that I have posted elsewhere on this blog were derived from the studies that led to this publication. For much of my future research I plan to tweak these scripts and re-purpose them for all sorts of exciting and interesting new applications!

I'll be giving a talk next Monday on this work at the International Association for Lichenology conference (IAL-7) in Bangkok, Thailand (Hodkinson et al. 2012b). I hope to see some of you there!

- Brendan

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References

Hodkinson, B. P. 2011. A phylogenetic, ecological, and functional characterization of non-photoautotrophic bacteria in the lichen microbiome. Doctoral Dissertation, Duke University, Durham, NC.
Download Dissertation (PDF file)

Hodkinson, B. P., and F. Lutzoni. 2009. A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales. Symbiosis 49(3): 163-180.
Download publication (PDF file)
Download nucleotide alignment (NEXUS file)
View Dryad data package (website)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2011. Data from: Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Dryad Digital Repository. doi:10.5061/dryad.t99b1

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012a. Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome. Environmental Microbiology 14(1): 147-161. [doi:10.1111/j.1462-2920.2011.02560.x]
Download publication (PDF file)
Download supplementary phylogeny (PDF file)
View data and analysis file webportal (website)
Download data and analysis file archive (ZIP file)

Hodkinson, B. P., N. R. Gottel, C. W. Schadt, and F. Lutzoni. 2012b. Pyrosequencing reveals previously unknown phylogenetic, metabolic and ecological complexity within the lichen microbiome. In: IAL-7, International Association for Lichenology, Bangkok, Thailand, in press.