Friday, February 28, 2014

Alternative Nitrogen Fixation

During my dissertation research, I found an interesting set of genes in the metatranscriptome of Peltigera praetextata. They were vnfDG and vnfN, two genes in the alternative, vanadium-dependent nitrogen fixation gene cluster. The interesting thing about this was that nitrogen fixation in lichens has always been attributed to the standard molybdenum-dependent system. These gene fragments were very similar to ones from Anabaena, cyanobacteria that are not known to be lichen photobionts, but are closely related to Nostoc, the cyanobiont in Peltigera. After examining metagenomes from other Peltigera species (all associated with Nostoc) and running further analyses, I found that the presence of the vnf gene cluster seems to be widespread (in all five samples checked from five Peltigera species from all over the world). Analyses revealed that the Peltigera-associated sequences all form a group close to, but separate from, Anabaena, which is entirely consistent with them being derived from the main photobiont, Nostoc. Therefore, it seems that lichens with cyanobacteria are actually using both the standard nitrogen-fixation system and an alternative, vanadium-dependent one.

This work could have sweeping implications for studies of biogeochemistry, since certain ecosystems, especially those in the tundra, are dominated by lichens. Ecosystem-wide nitrogen fixation rates are often inferred based on the acetylene-reduction assay (ARA). To interpret the results of this assay, a conversion factor based on the standard molybdenum-dependent system is typically used. However, if a substantial portion of the nitrogen fixation is taking place via alternative means, the standard conversion factor could produce wildly inaccurate interpretations. Even if one is willing to consider that a different conversion factor should be used, determining the proper conversion factor may become especially problematic since the proportion of standard to alternative nitrogen fixation could vary greatly based on the season or micro-environment. Therefore, a greater understanding of vanadium, molybdenum, and nitrogen dynamics may be needed before we can continue to rely blindly upon the commonly-used ARA for ecosystem-wide studies.

Peltigera rufescens, a lichen with a cyanobacterial photobiont from the genus Nostoc, in the Alaskan tundra.

- Brendan



Hodkinson, B. P., J. L. Allen, L. L. Forrest, B. Goffinet, E. Sérusiaux, Ó. S. Andrésson, V. Miao, J.-P. Bellenger, and F. Lutzoni. 2014. Lichen-symbiotic cyanobacteria associated with Peltigera have an alternative vanadium-dependent nitrogen fixation system. European Journal of Phycology 49(1): 11-19.
Download publication (PDF file)
Download supplementary table (PDF file)
Download vnfD alignment and analysis files (ZIP archive)
Download vnfN alignment and analysis files (ZIP archive)
Download script for editing GenBank-derived FASTA files (PERL script)


[This work was supported in part by the National Science Foundation under grants OCI-1053575 and DEB-0919284.]

1 comment:

  1. You should make a book of all of these beautiful pictures. Or at least a website dedicated to them because these are really cool.