Tag Archives: fungi

Sequencing meta-analysis workshop, Manchester, 18-20 May 2015

We are organizing a workshop to bring together ecologists and bioinformaticians to work on a meta-analysis of sequencing data with the aim of exploring patterns in belowground biodiversity.

The description and biogeography of belowground biodiversity is severely lagging behind that of aboveground diversity. This is despite increasing recognition of the importance of soil organisms for ecosystem functioning, including carbon and nitrogen cycling, and feedbacks to plant community composition, which underlie ecosystem services such as food production and climate mitigation. Moreover, recent evidence suggests that patterns of belowground biodiversity might not follow those of aboveground biodiversity. Thus, belowground biodiversity offers a unique opportunity to test and develop ecological theory. However, bringing together soil biodiversity data is challenging, especially when it comes to sequencing data, because pipelines and metadata are not standardized.

Confirmed speakers/leaders of the workshop are:

Dr Kelly Ramirez, Netherlands Institute of Ecology, the Netherlands and GSBI

Dr Rob Griffiths, CEH Wallingford, UK

Dr Jennifer Talbot, Boston University, USA

-Dr Hyun Soon Gweon, CEH Wallingford, UK

Dr John Davison, University of Tartu, Estonia

The aim of this workshop is to bring together ecologists and bioinformaticians to do a meta-analysis of sequencing data of soil microbial communities. Both publicly available data and participants’ data will be used, and the anticipated outcome is a publication in a peer-reviewed journal. The workshop will consist of lectures by our invited speakers to highlight recent advances, and participants will be expected to give a short presentation about their background and expertise. The majority of time will be spent identifying ecological questions to address with the data, analyzing the data in novel ways, and drafting a manuscript.

Spaces for this workshop are limited, and we are seeking motivated ecologists and bioinformaticians of all career stages to participate in, and contribute to, the workshop. Participants are expected to bring their own dataset of soil microbial (principally bacterial) community sequencing data (including metadata), and to have some experience in analyzing sequencing data.

The call for participants is now open. Applications should consist of a one-page CV, description of the dataset(s) that the applicant will bring to the workshop, and a statement (500 words maximum) of what the applicant will contribute to, and hopes to get out of, the workshop, including proposed hypotheses to be explored during the workshop.

Send your application to besplantsoileco@gmail.com before April the 10th 5pm. Applicants will be notified whether they have been selected for the workshop by April the 17th. For questions email Franciska de Vries: franciska.devries@manchester.ac.uk

Registration fee: £75 (students)/£100 (BES members)/£125 (others)

 

Flyer

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!

Soil biodiversity and soil community composition determine ecosystem multifunctionality

This paper, by Cameron Wagg et al., which was published online early in PNAS last month, describes the results of a very interesting experiment in which the authors manipulated soil biodiversity and measured the effect of these manipulations on a range of ecosystem functions.

More specifically, they created a gradient of reduced soil biodiversity (including a range of faunal and microbial groups) by sieving the soil through a number of decreasing mesh sizes, adding the fraction that passed through the sieve to sterilized soil, while also adding the sterilized fraction that remained on top of the sieve. They then grew plant communities consisting of common grasslands species in the soil for 14 and for 24 weeks, in two separate experiments. At the end of the first experiment, and after 12 and 24 weeks of the second experiment, they measured plant diversity and productivity, carbon sequestration, litter decomposition, nitrogen turnover, N2O emission, phosphorus and nitrogen leaching as ecosystem functions, and fungal and bacterial diversity (by TRFLP), mycorrhizal root colonization (microscopically), and nematode abundance (microscopically).

They then used these data to relate the ecosystem functions measured to the soil biodiversity treatments. In addition, they calculated z-scores for the range of ecosystem functions measured as well as for all groups of organisms quantified, and regressed these against each other to answer the question whether ecosystem multifunctionality is related to soil biodiversity. This approach, of summarising a number of ecosystem processes into one ecosystem multifunctionality index, has been used previously by Maestre et al. (2012).

Their findings are very interesting and will make a lot of soil ecologists very happy: they find that a number of the individual ecosystem functions are reduced with declining biodiversity, but also that ecosystem multifunctionality is positively correlated with overall soil biodiversity.

When taking a closer look at the data, it becomes clear that the reduction in soil biodiversity varies between groups and isn’t linear with the decreasing mesh sizes – mycorrhiza and nematodes drop down sharply after the third ‘dilution’, whereas the other parameters show a more gradual decline. The authors have taken this into account by not only relating ecosystem functioning to the diversity treatments, but also to the abundance and diversity of individual groups. When taking a closer look at this, it becomes clear that the microbial properties measured have a far stronger effect than nematode abundance. In addition, the effect of reduced soil biodiversity on a range of functions is indirect, through effects of plant productivity and diversity.

Of course, it is very easy to criticise aspects of this study. You can question whether bacterial and fungal diversity, microbial biomass, mycorrhizal colonization, and nematode abundance together are a realistic representation of soil biodiversity. For example, why was nematode diversity not assessed? And why not higher trophic levels, such as Collembola and mites? Microbes and nematodes are only a fraction of the soil food web (Fig. 1). With the current analyses, the title ‘Soil microbial diversity and community composition determine ecosystem multifunctionality’ might have been more appropriate.

A (simplified) example of a soil food web, with the groups measured by Wagg et al. (2014) indicated by the dashed line.

A (simplified) example of a soil food web, with the groups measured by Wagg et al. (2014) indicated by the dashed line.

Also, it would have been interesting to see root biomass in addition to mycorrhizal colonisation – a number of recent papers point to the importance of roots for ecosystem functioning (e.g. Orwin et al. 2010, Grigulis et al. 2013)

A more technical comment relates to the measurement of nitrogen turnover – this was assessed by measuring the uptake of 15N from Lolium multiflorum litter into aboveground L. multiflorum biomass. So, this measurement might be a proxy for L. multiflorum biomass, which decreases with decreasing soil biodiversity, rather than for nitrogen turnover.

On another note, and I would be very interested in other people’s opinion, I am wondering about the value of using an index for ecosystem multifunctionality. True, this averages across ecosystem functions and can therefore inform management to optimize overall ecosystem functioning. However, are the ecosystems that have the greatest average functioning really the most sustainable, and thus, desirable ecosystems? Are all ecosystem functions equally important? There might be trade-offs between different ecosystem functions – for example between crop yield and nitrogen retention, or between decomposition and carbon sequestration. We might want to optimize a certain function in a certain area, of which we already know that it has potential in delivering a certain function, rather than promoting multifunctionality across the board. For example, peatlands store large amounts of carbon because of their low decomposition rates, and agricultural production systems have high yields but low carbon sequestration.

However, in this paper, the multifunctionality index serves the purpose of summarizing overall ecosystem functioning, which shows a strong and positive relationship with soil biodiversity. Done like this, it summarizes a range of measurements that non-specialists might struggle to interpret – thus, it simplifies and reinforces the message of the paper that soil biodiversity determines ecosystem functioning.

Experiments like this require an enormous amount of work, and you simply can’t include everything. It is incredibly difficult to modify soil biodiversity without simultaneously changing soil properties, and the authors of this paper have achieved this by used an elegant method of reducing soil biodiversity. Thus, in contrast to many earlier studies, they were truly able to mechanistically elucidate the role of groups of soil organisms in ecosystem functioning.

This paper adds to the growing body of literature that soil biodiversity plays a crucial role in ecosystem functioning, and highlights the importance of conserving, and promoting, soil biodiversity. That’s what I like to hear!

#psejclub discusses: plants, fungi, competition and carbon storage

It’s nearly two weeks since Franciska wrote the first post for our journal club (#psejclub), about a paper published in Nature, entitled ‘Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage‘. Her thoughts on the paper prompted an interesting discussion, which you can catch up on here.

Keep your eyes peeled for a new #psejclub post in the next couple of days!