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.]

Saturday, February 15, 2014

New Species: Lepidostroma winklerianum

There has recently been amazing burst of discovery in what is now known as the order Lepidostromatales. Until 2007, only one of the species that is now in the order had been described. Then, in a series of recent papers, five new species have been described. The most recent new species is Lepidostroma winklerianum, named after Sieghard Winkler, one of the authors who first described the genus Lepidostroma.

Morphology and anatomy of thallus squamules of Lepidostroma winklerianum
(a–b) Fully grown and young squamules. [scale=1 mm] 
(c) Section through squamule.  [scale=100 μm]
(d) Photobiont cells.  [scale=10 μm]
(e) Upper cortex in section view. [scale=10 μm]
(f) Upper cortex in surface view. [scale=10 μm]

Here is a key to the currently-known species in the order Lepidostromatales:

1a Thallus crustose, undifferentiated, lacking distinct cortical structures (Sulzbacheromyces); basidiomata clavarioid; Neotropics (northeastern Brazil) ... Sulzbacheromyces caatingae
1b Thallus microsquamulose to squamulose, with distinct cellular cortex; basidiomata clavarioid or club-shaped ... 2

2a Thallus microsquamulose, composed of contiguous glomerules with cortex formed by distinctly lobate, jigsaw-puzzle-shaped cells (Ertzia), medulla absent; basidiomata clavarioid; tropical Africa (Rwanda) ... Ertzia akagerae
2b Thallus distinctly squamulose, composed of scattered to dense, rounded to reniform squamules with cortex formed by polygonal or jigsaw-puzzle-shaped cells (Lepidostroma), medulla present; basidiomata clavarioid or club-shaped ... 3

3a Basidiomata clavarioid; squamules lacking raised margin and maculae; photobiont layer above medulla, more or less uniform, with scattered cells throughout medulla and in lower portion of squamules; photobiont cells lacking pyrenoids; Neotropics (Costa Rica, Colombia) ... Lepidostroma calocerum
3b Basidiomata club-shaped; squamules with conspicuous, slightly raised white margin, their surface maculate; photobiont layer below medulla, forming pyramidal columns protruding upwards; photobiont cells with pyrenoid(s) ... 4

4a Upper cortex with jigsaw-puzzle-shaped cells in surface view; tropical Africa (Rwanda) ... Lepidostroma rugaramae
4b Upper cortex with polygonal cells in surface view; Neotropics (Mexico) ... 5

5a Squamules 1.5–3 mm diam.; upper cortex multi-layered; basidia 2-sterigmate ... Lepidostroma vilgalysii
5b Squamules 0.5–1.5(–2) mm diam.; upper cortex single-layered; basidia 4-sterigmate ... Lepidostroma winklerianum


Hodkinson, B. P., B. Moncada, and R. Lücking. 2014. Lepidostromatales, a new order of lichenized fungi (Basidiomycota, Agaricomycetes), with two new genera, Ertzia and Sulzbacheromyces, and one new species, Lepidostroma winklerianumFungal Diversity 64(1): 165-179.
Download publication (PDF file)
View publication (website)

[This work was supported in part by the National Science Foundation under DEB-0715660.]