Tuesday, January 24, 2012

Lichenology Conference in Thailand

I recently attended the 7th International Association for Lichenology Symposium in Bangkok, Thailand.  It was a great conference with many exciting presentations about the most cutting-edge lichen research!  Besides networking, presenting, and listening to talks, I also took a few hours to do some sightseeing around the city.  Here are some photos:


See more photos from the conference here!

- Brendan

Thursday, January 5, 2012

Lichen Taxonomy

This week a new issue of the journal Opuscula Philolichenum came out. It contains two pieces to which I contributed. The first is an announcement of the new International Committee for the Nomenclature of Lichens and Allied Fungi (ICNLAF), which was formed only very recently (Lendemer et al. 2012). The second is an annotated phylogenetically based summary of lichen taxonomy that I have put together based on the system in use at the New York Botanical Garden (NYBG) (Hodkinson 2012). This will be up on the internet in a format that can be continually updated as our understanding of the organisms evolves. Hopefully it can serve as a useful guide for lichen herbarium/data managers wishing to arrange taxa within a higher-level framework.

Here is the official announcement from the editor:
"The latest issue (volume 11, number 1) of Opuscula Philolichenum is now available online at http://sweetgum.nybg.org/philolichenum/ free of charge as is tradition. This is the first volume to be published in the new age of electronic publication as sanctioned in Melbourne last year. As was noted in the previous issue, the journal has ceased its print run (although one copy is still deposited in the library at NYBG). Volumes will also now consist of multiple numbers, published throughout the year.
"The current issue comprises five contributions covering a diverse array of topics. This includes a higher level taxonomic scheme for lichen-forming fungi that synthesizes current literature. The system may be particularly useful to those wishing to organize herbaria using a phylogenetic system as is common practice in vascular plants. Also included are contributions to our understanding of Hypogymnia in eastern Asia, Parmeliella in South America, and Acarospora in South America. Those who have been following the changes in generic concepts in Acarosporaceae, particularly pertaining to Silobia, will be interested in the discovery by Linda in Arcadia and Kerry Knudsen that Myriospora is actually an earlier available name for Silobia. The authors make the appropriate new combinations and place the taxa previously assigned to Myriospora in a new genus.
"In addition to the above contributions the issue contains the notice of the formation of an International Committee for the Nomenclature of Lichens and Allied Fungi. A group that that aims to work with IAL and various bodies (ICNF, NCF) in the event that matters of nomenclatural governance are formally delegated to special committees by the IBC/IAPT."


Hodkinson, B. P. 2012. An evolving phylogenetically based taxonomy of lichens and allied fungi. Opuscula Philolichenum 11: 4-10.
Download publication (PDF file)

Lendemer, J. C., M. N. Benatti, T. L. Esslinger, J. Hafellner, B. P. Hodkinson, K. Knudsen, and J. Kocourkov√°. 2012. Notice of the formation of the International Committee for the Nomenclature of Lichens and Allied Fungi (ICNLAF). Opuscula Philolichenum 11: 1-3.
Download publication (PDF file)

Tuesday, January 3, 2012

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



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.