Thursday, January 21, 2010

The Lichen as a Microcosm

In the spirit of the International Year of Biodiversity, I thought it would be appropriate to open a discussion about an unexplored environment in which we are currently finding an amazing number of new lineages of organisms that were not previously known to science. The environment of which I speak is: The Lichen! There is an ever-increasing body of evidence to show that the lichen exists not simply as a dual partnership between a fungus and an alga, but as a microcosm comprised of a diverse assemblage of specific microbial lineages.

Researchers often go to exotic locations and so-called 'extreme' environments to find new organisms, but in order to find a treasure-trove of new organismal lineages, all we really have to do is look more closely at some of the common, ordinary micro-environments such as lichens. Recently, a microbiotic survey of lichens involving molecular cloning has uncovered an entirely new lineage of bacteria from the order Rhizobiales (Hodkinson and Lutzoni 2009) that seems to thrive in association with a diversity of lichens. Additionally, the survey uncovered a great deal more bacterial diversity that has yet to be studied in depth.

Another recent study found an entirely new lineage of Cyanobacteria that seems to be exclusively associated with lichens (Lücking et al. 2009). However, the interesting aspect of this story is that the cyanobacterial lineage is associated with several diverse lineages of lichen-forming fungi that bare no resemblance to one another and share no common ancestry. It seems that the members of this cyanobacterial lineage may have evolved to be 'good symbionts' and have subsequently been adopted by several ecologically similar lineages of lichenized fungi. The authors draw the analogy of crop domestication by humans, with Cyanobacteria as the 'crops' being shared by several specific groups of fungi.

Though lichens are known to have a dominant fungal partner, it has recently been discovered that healthy lichen thalli also host various undescribed lineages of 'endolichenic' fungi (fungi that inhabit seemingly healthy lichens and do not reveal any outward signs of their existence). Phylogenetic analyses of these fungi suggest that lichens may act as cradles of microbial diversification, and that the endolichenic state may facilitate transitions to other lifestyles (e.g., living inside of plants; Arnold et al. 2009).

As mentioned before, 'extreme' environments are often thought to be good places to search for undiscovered diversity. However, the definition of an 'extreme' environment has perhaps been too narrow. In a sense, the lichen thallus can be seen as an extreme micro-environment, since lichen-forming fungi often produce abundant acidic secondary compounds that may serve to eliminate some of the common, or 'weedy', environmental microbes. This would open up the environment of the lichen thallus for other microbial lineages, and potentially lead to the co-evolution of specific microbes alongside with their lichen hosts.

In addition to the microbial diversity found in lichen thalli, lichenologists are still hard at work constantly defining new lichen species (species of lichens are named based on the identity of the major fungal partner). Though some of these species are actually rather conspicuous and distinctive, various issues (lack of adequate collections, confusion based on solely morphological evaluations) have left many species without names. Now, using molecular tools to test hypotheses based on careful morphological/chemical/ecological evaluations, many new species are being discovered and the boundaries of others are being more clearly defined (e.g., Lendemer and Hodkinson 2009, Lendemer and Hodkinson 2010, Hodkinson and Lendemer 2010).

But let us not forget the algae in this whole story! It has been known for quite some time that lichen-forming fungi associate with a great diversity of specific algal lineages (for summaries see, e.g., Miadlikowska et al. 2006 and Goward 2009). However, recent molecular investigations have revealed the fact that there is often much greater genetic diversity within each of these lineages than previously suspected (e.g., Skaloud and Peksa 2010).

The amazing microcosm known as the 'lichen' has much left to reveal about the overall biodiversity of life on Earth. The study of the 'Lichen Microbiome' is an emerging field that will continue to grow as culturing techniques improve and molecular tools become more accessible and more advanced. What remains clear at this point is that there is much more to the lichen than the simple 'fungus and alga' model that is so well-known these days.

-Brendan Hodkinson, Duke University

Works Cited:

Arnold, A. E., J. Miadlikowska, K.L. Higgins, S.D. Sarvate, P. Gugger, A. Way, V. Hofstetter, F. Kauff, and F. Lutzoni. 2009. A phylogenetic estimation of trophic transition networks for ascomycetous fungi: Are lichens cradles of symbiotrophic fungal diversification? Systematic Biology 58:283-297.
Download publication (PDF file) 

Goward, T. 2009. Twelve readings on the lichen thallus VII - Species. Evansia 26(4): 153-162.
Download publication (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: 163-180.
Download publication (PDF file)
Download alignment (NEXUS file)

Hodkinson, B. P., and J. C. Lendemer. 2010. Molecular analyses reveal semi-cryptic species in Xanthoparmelia tasmanica. Bibliotheca Lichenologica: in press.
Download draft (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2009. The Wisdom of Fools: new molecular and morphological insights into the North American apodetiate species of Cladonia. Opuscula Philolichenum 7: 79-100.
Download publication (PDF file)
Download alignment (NEXUS file)

Lendemer, J. C., and B. P. Hodkinson. 2010. A new perspective on Punctelia subrudecta in North America: previously-rejected morphological characters corroborate molecular phylogenetic evidence and provide insight into an old problem. The Lichenologist 42(4):  405-421.
Download publication (PDF file)
Download alignment (NEXUS file)

Lücking, R., J.D. Lawrey, M. Sikaroodi, P.M. Gillevet, J.L. Chaves, H.J.M. Sipman, and F. Bungartz. 2009. Do lichens domesticate photobionts like farmers domesticate crops? Evidence from a previously unrecognized lineage of filamentous cyanobacteria. American Journal of Botany 96: 1409-1418.
Download publication (website)

Miadlikowska, J., F. Kauff, V. Hofstetter, E. Fraker, M. Grube, J. Hafellner, V. Reeb, B. P. Hodkinson, M. Kukwa, R. Lücking, G. Hestmark, M. Garcia Otalora, A. Rauhut, B. Büdel, C. Scheidegger, E. Timdal, S. Stenroos, I. Brodo, G. Perlmutter, D. Ertz, P. Diederich, J. C. Lendemer, P. May, C. L. Schoch, A. E. Arnold, C. Gueidan, E. Tripp, R. Yahr, C. Robertson, and F. Lutzoni. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98: 1088-1103.
Download publication (PDF file)
Download supplement (PDF file)
Download alignment (zipped NEXUS file)

Skaloud, P., and O. Peksa. 2010. Evolutionary inferences based on ITS rDNA and actin sequences reveal extensive diversity of the common lichen alga Asterochloris (Trebouxiophyceae, Chlorophyta). Molecular Phylogenetics and Evolution 54(1): 36-46.
Download publication (website)

Monday, January 18, 2010


Welcome to the brand new 'Squamules' blog!

This is a place for the random thoughts and musings of Brendan Hodkinson (Lichenology, Duke University). Feel free to comment and join the conversation!

squa·mule (skwä-myl)
A small, loosely attached thallus lobe of certain lichens.
[Latin squmula, diminutive of squma, scale.]

Squamules.blogspot is part of 'Squam Blogs', a division of 'Squamules Unlimited'.