Fungal genes for ecosystem-related traits

From: Treseder KK, Lennon JT. 2015. Fungal traits that drive ecosystem dynamics on land. Microbiology and Molecular Biology Reviews 79:243-262.

Functional genes can indicate the genetic potential of fungal taxa to carry particular traits, and they are especially informative if their function has been empirically verified in mutant or transcription assays in at least one fungus (1-3). Of course, possession of a gene does not mean that gene is expressed or translated (4-6). Nevertheless, it is a useful tool to supplement empirical measurements of traits of fungal taxa (7), which can be limited owing to logistical challenges such as difficulty generating laboratory cultures or measuring functions in situ. Moreover, we can use functional genes to document linkages among traits within whole genomes. Where possible, we have identified experimentally-verified functional genes encoding ecosystem-related traits in fungi, and listed them in the table below.

For some enzymes, additional care must be taken to ensure that the functional gene encodes enzymes that are active in the appropriate sites. For example, fungi use chitinases internally to re-organize their own cell walls (8), and we would not consider this process to contribute to N depolymerization in soils. Nevertheless, gene GH18-5 has been verified as an extracellular chitinase, based on its sequence (8), mutation assays (9), the activity of purified protein (10), and secretion into growth medium (11). Moreover, in Trichoderma, its transcription is induced by C and N starvation (8, 12). Altogether, it is a good candidate as a standard extracellular chitinase used by fungi to acquire C or N, so we have listed it as such in Table 1. Likewise, only membrane transport proteins that internalize compounds from the environment are relevant for immobilization of nutrients, even though fungi use these proteins for intracellular transport as well. Thus, only functional genes for transporters that operate in the outer membrane are included in the table.

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