Endemism and functional convergence across the North American soil mycobiome

I’m really interested in scale. The world we live in is full of things that are doing things, sometimes to other things, and how we see those things (doing things to things) depends fundamentally on how close we are to them. Take soil as an example: from about 170 cm up, it looks brown, reasonably inert, and good for growing plants in. However, assume that you’re about a thousand times smaller, and the soil becomes a much more interesting, and probably quite frightening, place. Everywhere you look, there are mites, larvae, worms, beetles, and sticky white chords, clinging to vast, pipe-like plant roots. And it’s those strange, white chords that are the topic of today’s #psejclub paper.

Ectomycorrhizal mycelium with some white spruce roots (André-Ph. D. Picard, CC BY-SA 3.0)

The paper, by Jennifer Talbot, Kabir Peay, and several others, appears in PNAS. The authors wanted to study the community structure of soil fungi and their contribution to ecosystem functions, like soil nutrient cycling, across the continental USA. In order to capture differences in functioning at a variety of scales, soil sampling in the study was nested (see Supplementary Figure S1): at the broadest level, sites were chosen from three different regions of the USA (1000 km); within regions, different landscapes were sampled (100 km); in each plot within a landscape unit, thirteen soil samples were taken at increasing distances apart along three transects (40 km). To look at the effect of scale without the confounding influence of plant community, the study focuses on a single plant family, the Pinaceae, which occur across North America. The authors determined fungal community composition from soil DNA by sequencing the internal transcribed spacer (ITS) region using primers ITS1f and ITS4, clustering the sequences into taxonomic units. To assess the functioning of the soil fungi, the authors used the activity of seven extracellular enzymes involved in carbon and nutrient cycling. Finally, each soil core was split into an organic and a mineral horizon, which were analysed separately.

I was attracted to this paper initially by the implication of scale in the title, and the fact that I misread ‘mycobiome’ as ‘microbiome’. After skim-reading the paper and wondering ‘But what about the bacteria, mites, nematodes, etc.?’ I realised my mistake. The results are interesting: while fungi were highly endemic, the activity of their enzymes was broadly similar across large scales, varying with soil chemistry at smaller scales. The authors suggest that this provides evidence for a high level of functional redundancy in fungal communities at large spatial scales; function has little to do with structure. They argue that efforts to include the soil fungal community in biogeochemical models would be better focused trophic groups rather than identity, which is good news for modellers!

While the study does ‘only’ consider fungi in stands of Pinacaea, it does so at a range of scales, encompassing the continental to plot-level. The way that scale was incorporated into the sampling design is probably the best thing about this study, for me, because it provides a way of examining how ecosystem structure is related to function across increasing scales, in a way that I can imagine applying to other groups of organisms. On that note, it would be very interesting to see this approach applied to other functional groups, particularly those with contrasting degrees of mobility, to see if the same conclusions can be drawn: what about bacteria, mites, or earthworms? Might we expect to see the same degree of endemism in organisms that move around more? How does endemism belowground relate to ‘lifestyle’?

Another interesting angle to pursue could include disturbance. The fungi and fungal functions characterised in the study were from predominantly natural ecosystems; how does the disturbance embodied in, for example, conversion of grassland to agriculture, affect the functioning of soil communities, at a range of scales? I wonder how feasible it would be to combine the sequential sieving approach from the previous #psejclub paper with the scale methodology presented in this one.

This is a really interesting paper, suggesting that no matter which soil you zoom into, all the fungi (those strange white chords from earlier) are clubbing together to basically the same end, in Pinaceae forest anyway. I enjoyed reading it, and liked the figures, particularly the use of colour to show different regions. I wonder why the authors didn’t use different shapes the represent the different soil horizons – it’s very difficult to tell the difference between a small circle and a slightly larger one – but that’s a minor gripe. And now it’s over to you: the #psejclub readers and contributors. What did you think? Are there elements you think could have been handled better? Where would you go from here? Tweet your thoughts using #psejclub, post them in the Facebook group, or comment on this post – I’m looking forward to hearing from you!


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