Author Archives: Mike

About Mike

I'm a postdoctoral research fellow in the Botany Department at Trinity College Dublin, where my research focuses on estimating greenhouse gas emissions from agricultural soils at the national scale, using process-based models.

Be sociable with Plants-Soils-Ecosystems

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It’s been a while since we’ve had any posts on this blog, but that doesn’t mean that all is quiet behind the scenes at Plants-Soils-Ecosystems! The committee is planning some exciting activities for next year – watch this space.

In the meantime, you can connect with the special interest group, find out about studentships and job opportunities, and network with other members of the group via our social media feeds! Like us on Facebook and follow us on Twitter. Help your special interest group reach 1000 followers before Christmas!

Image: Wikimedia Commons CC BY-SA 2.5

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You, me, and the EMP (Earth Microbiome Project)

In this guest post, Dr. Dorota Porazinska of the University of Colorado introduces the Earth Microbiome Project (EMP), an initiative to understand microbial communities, their diversity and function at the global scale, and explains how researchers can help the EMP as part of their own research projects. Communities like Plants-Soils-Ecosystems provide great environments for connecting like-minded researchers and encouraging collaboration – if you’re interested, read on, and get in touch! Now, over to Dorota:

The EMP was initiated in 2010 to understand patterns in microbial communities across different spatial, temporal and evolutionary scales, to understand the functional basis for these patterns, and to provide a portal for the analysis and visualization of the data. The EMP has primarily generated data from amplicon sequencing of Bacteria and Archaea to date, although expansion to other taxa including eukaryotes and viruses, and other forms of data generation including metagenomics, metatranscriptomics, and metabolomics, is anticipated in future.

emp-logo

The EMP is a massively collaborative project. Individual projects are stand-alone, hypotheses-driven studies contributed by PIs from around the world. The EMP has generated 16S rRNA profiles for >30,000 samples representing >40 ecological biomes, including oceans, sediments, rivers, lakes, human, plant- and animal-associated ecosystems. Soils constitute ~10% of these samples, and although many project contributions to date have been from agricultural sites from the North American meridian, the EMP results to date confirm our expectations of these ecosystems: high diversity, many novel taxa, and limited community overlap among biomes and geographic locations.

emp-wordle

The success of the EMP depends on your participation.

If you join the EMP, we will:

  • Extract DNA and sequence 16S rRNA amplicons free of charge using standardized protocols
  • Archive the data and make it publically available
  • Perform initial analysis of the sequencing data (quality-filtering, OTU-clustering, taxonomy assignment, and beta diversity analyses integrated with a vast database of other studies)

To join the EMP, we ask that you submit:

  • A one-paragraph proposal that describes your study, focusing on what the samples are and what spatial, temporal or evolutionary questions your sample set addresses in the microbial world
  • Information about each sample (“sample metadata”) that must be provided in standardized format (the EMP will assist with this) prior to sample receipt

For detailed information about goals and protocols, please visit the EMP website. Note the EMP data release policy, which is that all data are made freely available to the community upon sequencing.

For specific questions about submission of the proposal and the mandatory metadata, please email: dorota dot porazinska at colorado dot edu

PSE journal club: Vegetation exerts a greater control on litter decomposition than climate warming in peatlands

A bright, blustery day in England’s north Pennines. Fluffy cotton grass heads bob and bounce on the breeze. On the side of a hill, a strange array of hexagonal, knee-high structures glint and sparkle. Four figures, hunched against the wind, move methodically along jaunty wooden boardwalks, which rest on the blanket bog, crouching at each hexagon in turn. Welcome to Moor House National Nature Reserve, the site of an experiment designed to investigate how a warmer climate will affect the speed with which plant litter is recycled back into the soil, and ultimately the atmosphere.

One of the inherent difficulties associated with upland experiments.

One of the inherent difficulties associated with upland experiments.

If you’re wondering about the shift in tone in the opening paragraph of this #psejclub post compared to some of the others, it’s because I was there. I helped to set up and sample the aforementioned experiment, which is located a few hundred metres away from where I did my PhD fieldwork, in exchange for help with my own work, so I have to admit to having a degree of personal bias! I do think that the work is of general interest, though, and conveys some important findings about litter decomposition in peatlands that will help us to build a picture of how these key processes might change as plant communities shift in response to climate change.

The paper, currently a preprint in ESA Ecology, describes an experiment that uses a combination of open-top, passive warming chambers and plant removal treatments to investigate how the presence of certain plant functional types and warmer temperatures affect rates of litter decomposition. The authors used litter bags, filled with the litter of each plant functional type and buried in plots beneath the plant removal and warming treatments. In all, there were eight treatments (combinations of graminoid, shrub and bryophyte removal, a bare plot and a control with no plants removed), replicated over four blocks, with half the plots warmed by the passive chambers.

So how do peatland processes respond to warming?

So how do peatland processes respond to warming?

The main finding of the paper is that presence or absence of plant functional groups had a stronger effect on peatland litter decomposition than the warming of approximately 1°C achieved by the passive chambers. Removing the shrubs from the peatland resulted in faster decomposition of graminoid and bryophyte litter, after two years. Litter identity was also important – in the first year of the experiment this was the main factor controlling rates of litter decomposition, with bryophyte litter decomposing most slowly, followed by shrubs and graminoids. After two years, the live plants present in the plot (i.e. presence of shrubs) were more important than the litter identity. Warming affected the composition of the bacterial community, while the fungi responded more strongly to the presence of shrubs.

While these results are compelling, they should be taken with caution, as the authors suggest: since the duration of the experiment was two years, further interesting effects resulting from the decomposition of shrub and bryophyte litter, which happens more slowly than in graminoids, might not have been captured. After four or five years, the decomposition of more recalcitrant litter could reveal more interesting effects. The same is true for the warming treatment: given a longer study period, the effect of 1°C warming on plant litter decomposition might become more important. It is, however, easy to write ‘more long-term experiments needed!’ while, in reality, the amount of effort required to maintain the plant removal treatments and warming chambers in the harsh upland environment of the Pennines represents a considerable hurdle. And one has to motivate one’s volunteers to see past the inherent absurdity of weeding a moorland!

Overall then, what’s the message? Dead or alive, whether you’re graminoid, shrub or bryophyte seems to exert much stronger control on litter decomposition rates in peatlands than temperature. While warming doesn’t have much of an effect on plant decomposition, it does affect the bacterial community in the peat, which might have important implications for graminoid decomposition, since bacteria are well-equipped to munch through labile substrates. Fungi respond when you take away the shrubs, which provide the more recalcitrant litter they’re specialised for dealing with, and might therefore moderate the response of the peatland carbon cycle to warming. Given a longer time period, more effects may emerge from this experiment.

I’m interested to know about the responses of decomposition processes in other ecosystems to warming and plant functional group removal. In grasslands, for instance, what happens when you increase the ambient temperature and remove the nitrogen fixers? Of course, these sorts of studies require a sufficiently long period to become stable and start producing results. In a time of apparently perpetually shrinking budgets, what’s next for long-term field experiments in ecology and biogeochemistry? What are the current barriers to their deployment, or do we in fact have enough to answer our more pertinent questions? Let me know what you think – get involved by commenting on this post, and posting on Twitter and Facebook using the #psejclub tag. I’m looking forward to hearing from you!

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!

Eutrophication weakens stabilizing effects of diversity in natural grasslands

This letter, by Yann Hautier and many others, appeared in Nature ten days ago. Its focus is grasslands, and what happens to their [above-ground] diversity when you add fertiliser. I was drawn to this paper by the simple message communicated in the title, and the universality implicit in ‘natural grasslands’. Excellent; a succinct study of the effects of excessive nutrients on the modulation ecosystem functioning by diversity – read on!

It’s immediately apparent that the strength of this work lies in the size and global reach of its dataset. The authors utilised an established network of experiments looking at the relationships between fertilization, diversity and production in grasslands: the Nutrient Network (NutNet). This allowed the authors to address their hypotheses using data collected from 41 different grasslands, spanning five continents. One of the major advantages of using sites in an established network is that methods are broadly standardised; this goes some way towards ensuring that, while the sites encompass a wide range of variation in grassland types, the data are comparable between sites. In the extended methods section, the authors describe the sensitivity analyses they performed to check that distinctive sites (subject to strong seasonality, or anthropogenic influence, for example) did not unduly influence their results.

So what did the authors measure? They chose above-ground net primary productivity (ANPP) as their response variable, which they estimated by measuring above-ground live biomass at each site. The authors also introduced two related concepts: the stability of ANPP and species asynchrony; stability of ANPP increases as species asynchrony increases and the productivity of individual species fluctuates in response to the environment at different rates. This is a neat idea: in an asynchronous community, a decline in the productivity of one species is more liekly to be compensated for by another, and so the productivity of the community as a whole is more likely to remain stable.

To arrive at their finding that the application of fertiliser weakens the stabilising effect of diversity, the authors observed that, while the temporal variation of ANPP decreased at higher diversities in the unfertilised communities, it increased at higher diversities in the fertilised communities. The increased variation in ANPP, combined with lower species asynchrony in fertilised communities, led the authors to conclude that [over]-fertilisation of grasslands can reduce the stability of their productivity. Importantly, the authors showed that the loss of diversity caused by fertilisation didn’t affect species asynchrony.

While I initially found this article difficult to get to grips with, due to the introduced concepts and number of scatterplots and lines to compare, but now that I get it, I agree with the results. One of the best aspects of this study is that it draws its conclusions from a controlled experiment, rather than observational correlations. I think the work also raises a number of further questions, which would be interesting to address using NutNet or a similar project.

  • The authors used species richness as their measure of diversity. What about functional diversity? Perhaps some groups (grasses, forbs, legumes) respond to fertilisation more than others?
  • While ANPP is certainly likely to be related to below-ground productivity, it would be interesting to see whether stability of below-ground productivity showed the same patterns in response to fertilisation. Are there other ecosystem functions that are worth measuring? What about carbon and nitrogen cycling? These functions obviously come with the caveat that they are much more difficult to measure (you can’t just see them, unlike plants), but if it was feasible, what patterns might we expect to see?
  • The amount of fertiliser applied in the study was quite high. Do we see the same results at lower concentrations?
  • There were no sites in South America – do we think this is likely to have biased the result significantly?

Now that I’ve had my say, it would be great to hear yours; did you find this paper interesting, do you think its conclusions are valid? How might you have done things differently? Do you think there are specific lessons to be learnt? Please get in touch by commenting on this post, or on Twitter or Facebook using the hashtag #psejclub. I’m looking forward to hearing from you!

#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!