Tag Archives: #psejclub

There’s no place like home? An exploration of the mechanisms behind plant litter–decomposer affinity in terrestrial ecosystems

This week’s post is by PSE member and star #psejclub commenter Relena Ribbons. If you’d like to write a guest post, please get in touch!

I was really excited to see a new article synthesizing recent publications on decomposition and litter affinity effects in New Phytologist by Austin et al. One of the most well-known examples of litter affinity effects is the Home Field Advantage (HFA) hypothesis, whereby litter decomposition is accelerated in its home environment. Given the importance of nutrient cycling in terrestrial systems the patterns observed in litter decomposition have attracted a large audience, and expansions and new hypotheses have been postulated including the substrate-matrix interaction (SMI) or the phenology-substrate match (PSM) hypotheses. The authors go on to briefly describe each of these hypotheses, while also providing examples that don’t align with HFA, and conclude the article by raising additional research questions and future directions to elucidate the mechanisms behind observed litter affinity affects. Following the yellow brick road on home field advantage leaves us asking more questions, which is a good thing.

I really liked that the authors provided the background on HFA, expanded on to SMI and PSM, as it serves as a logical trajectory of how these hypotheses have been developed, and provides a good introduction for readers who may not be familiar with litter affinity effects. The authors state that the most cited explanations for litter affinity effects result from a specialization of microbial community, which is due to a constant and chronic input of similar litter quality over time which results in a microbial community that is optimized to degrade those particular litter inputs.  However, the authors go on to assert that standard indices of lignin, C : N ratios, and nutrient content alone, may not be sufficient to explain an observed HFA. For example, recalcitrant litter decomposes more quickly in a less favourable home environment and simply as a function of its litter quality or site fertility (see  Vivanco and Austin 2008 for further insights to this particular point and figure 1- copied below). Furthermore, high-quality litter may decompose faster in a fertile microsite as a result of higher resource availability for decomposers independent of its origin, which is known as a priming effect.


What I found especially insightful was the section of this article discussing green leaf hitchhikers, and discussion incorporating the legacy of the phyllosphere community. I see the term rhizosphere used quite frequently in journal articles, but I have not had the same exposure to the term phyllosphere (which is used to refer to the above-ground parts of plants). The microbiology of the rhizosphere (refers to the belowground habits of plants, e.g. plant roots) has received more attention than the microbiology of the phyllosphere (see Vorholt’s 2012 Nature Review Microbiology publication for further discussion), which I found interesting as historically scientists have first explored above-ground components.

Austin et al. went on to discuss how green leaves can serve as a conduit for introducing not only the litter nutrients, but also serve as a vector for carrying fungi and bacteria from green leaves into the decomposer community. In effect, microbial community might be hitching a ride from green leaves, down to the leaf litter (as leaves senesce) and could jump-start decomposition, alter the microbial decomposer community, and ultimately play an important mechanistic role in explaining observed HFA effects. The authors further explored the potential connections between volatile organic compounds used in plant defences, as a means for attracting a specific decomposer community. This got me thinking about all those caterpillars I have seen crawling towards my garden this summer, and what their role might be in decomposition. The authors highlight that further exploration of macrofauna decomposers is also warranted (see figure 2 from their paper below as you contemplate whether there is more to the story of Eric Carle’s Very Hungry caterpillar).


I found this particularly interesting as I think about my own experimental work, and the potential intersection between pathogens and pests and observed patterns in litter decomposition and nutrient cycling. Has this paper jump-started any new lines of inquiry in your research? Are there any future directions you think the authors should have considered in this paper? Any points where you are confused, or wish the authors explained the concepts in more details? Are any of your looking at caterpillars differently after reading this article? Share your thoughts on Twitter and Facebook using the #psejclub tag.

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!

Seasonal not annual rainfall determines grassland biomass response to carbon dioxide

After a brief hiatus, journal club is back and this time we’re discussing a paper by Hovenden et al from Nature in May exploring the interaction between carbon dioxide and rainfall on plant biomass.

At this point it seems that we ecologists have a reasonably good idea of what effect many environmental variables – like water, temperature, and carbon dioxide – have on certain ecosystem parameters, though always with a few caveats and exceptions thrown in to keep it interesting.  However, our understanding of how these variables interact and the effects of these interactions, especially over various temporal and spatial scales, is still pretty woeful.

For example, we know that plants need water to grow, and when there isn’t enough water they stop growing – very straightforward. Plants also need CO2 to grow, and in general higher CO2 levels lead to higher plant biomass.  This is because increased CO2 allows for higher rates of photosynthesis and greater water use efficiency.  Due to the greater water use efficiency, we also expect that the effect of elevated CO2 (eCO2) on plant growth will be greater when water scarce.  Basically, with higher CO2­, plants can photosynthesize more per unit available water, so will be able to grow more before the water runs out compared to plants grown at lower CO2 levels.

As with so many things in ecology, what we predict is exactly what we see … except when we don’t.  If the relationship between water availability, eCO2 and plant biomass is so straightforward, biomass responses to eCO2 would always be positive and we would see the strongest responses in the driest years.  I bet you can see where this is going…

TasFACE ring

Photo credit: TasFACE website

Hovenden et al looked at data from a nine year FACE experiment in Tasmania (TasFACE) and found that the eCO2 effect was far from consistent across years.  Some years there was no discernable eCO2 effect on biomass, some years it was positive (like we’d expect) and one year it was actually strongly negative; and these responses were not correlated with annual rainfall or soil water availability.

Instead, Hovenden et al found that the biomass responses to eCO2 were strongly correlated with seasonal rainfall variability.  Higher rainfall in the summer resulted in a positive effect of eCO­2 on biomass, as we would expect.  Summer rain at the site tends to come in short, sharp bursts, so the increased water use efficiency would allow the plants to maintain growth for longer between rain events.  However, increased rain during the spring and autumn were correlated with a negative effect of eCO2 on biomass.  During these cooler, wetter periods plants don’t grow as much and it is likely that increased rain would leach nutrients from the soil.  This was supported by a strong negative relationship between spring rain and soil nitrogen availability.

It seems probable that such a relationship between seasonal rainfall and eCO2 effects on biomass could be seen throughout temperate and seasonally wet systems, and that this could have big implications for global carbon models.  It also highlights the importance of looking beyond plants to fully understand the mechanisms that drive responses to climate change.

I would love to see similar analyses of other FACE datasets to see if these trends are replicated in other systems.  It’s an important finding, but opens up lots of other interesting questions: How does vegetation type or soil type effect the relationship between seasonal rainfall and eCO2 effects on biomass?  Does seasonal temperature variability affect the relationship significantly?  What about increased nitrogen pollution or fertilisation – would increased nitrogen deposition overturn the negative relationship between high spring/autumn rain and the eCO2 effect on biomass?

As always, we’d love to hear what you think about the paper.  Is it the best paper you’ve ever read or do you think it contains some fundamental flaw? Does it raise interesting questions or link well with something else you’ve read recently?  Would you use similar methods or could you propose a better protocol?  Let us know in the comments or on twitter with hashtag #psejclub!

Finally, don’t forget about our joint meeting with the Plant Environmental Physiology group coming up in October.  All the details, including links for registration and abstract submission, are available here.  It’s going to great!

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!

Interactions with soil biota shift from negative to positive when a tree species is moved outside its native range

Pinus contorta

Pinus contorta. Image by Rudi Riet, Washington, DC, United States [CC-BY-SA-2.0], via Wikimedia Commons

This week’s paper is a Rapid Report by Gundale et al which appeared in New Phytologist in late January.  It also happens to be the paper we discussed at the Hawkesbury Institute for the Environment’s student journal club this week.

This study was a really good example of a home-away growth experiment, and showed some really striking results.  Seeds from Pinus contorta trees of known provenance were collected in Sweden, and then grown in soil from their native Canadian sites and their introduced

Swedish sites to look for differences in aboveground and belowground biomass.  Sounds simple?  It would be, but they didn’t just compare fresh soils containing whatever biota could contend with the 2mm sieve.  They also used sterilised soils from both countries, sterilised soils which had been cross-inoculated with soils from the opposite country, and included a fertilisation element to make it more interesting.

So what was the take-home message?  The clue is in the title, but the short version is that it’s all about the soil biota.  Seedlings grown in Swedish soils had much higher biomass (around 43% higher) than those grown in native their native Canadian soils, despite the Swedish soils having lower pH and nutrient availability.  When seedlings were grown in sterilised soils, the soil origin had no effect on biomass.  When seedlings were grown in sterilised soil from either country, but inoculated with soil biota from Sweden, biomass was again much greater than when sterilised soils were inoculated with Canadian soil biota.  The effect of soil biota was even greater than the effect of fertiliser on biomass.

Considering these different trials together, it becomes clear that not only did the Swedish biota have a strong positive effect on P. contorta seedling biomass, but that the Canadian biota actually had a negative effect on biomass. This provides evidence that better growth in soils from outside of the native range is probably down to a combination of pathogen release and positive biotic associations.

However, this evidence also highlights the gap in this paper – analysis of the soil biota itself.  We see the effects, but what are the actual differences in the bacterial, fungal, and/or mesofaunal communities?  Are there differences in community structure? Abundances or biomass? Activity?  All of these?  It would be great to see data on this, especially regarding known pathogens or ectomycorrhizal fungi associates.  I hope/suspect there may be another paper on the way exploring some this.

Overall, this was a really nicely designed project that asked interesting questions and addressed them in a very straightforward way.  The paper itself was well written.  It flows nicely and is easy to follow and understand even on a quick reading.  The methods made no attempt to disguise the logistical issues associated with transporting soils half way around the world, and the data analysis and presentation was simple and direct with no unnecessary frills or risk of misinterpretation.  All of these are elements that we should expect of any paper, but sometimes experiments are complex and difficult to describe, methodological detail gets glossed over in an attempt to meet word counts, and data are not easy to interpret.  While it is not possible to answer all questions with a glasshouse study, or to present all data with bar graphs, it is a nice reminder of the clarity with which we should try to communicate our work.

So now that I’ve had my say, exposing my soil ecology and science communication biases, we’d love to hear what you thought about the paper.  Was there anything you would have done differently?  What do you think the next steps should be?  What did you think of the tree provenance element of the study?  It didn’t show a significant effect here, but would it be worth pursuing in other systems?  How well do you think the results of this glasshouse study represent what’s happening in the natural communities?

You can let us know your take on this either in the comments or via twitter using the hashtag #psejclub.  We’d also love to hear from you If you have a suggestion for a paper you’d like us to discuss, or if you want to write a post yourself!

Pinus contorta native range.  Image by  Elbert L. Little, Jr., of the U.S. Department of Agriculture, Forest Service, and others http://esp.cr.usgs.gov/data/little/

Pinus contorta native range. Image by Elbert L. Little, Jr., of the U.S. Department of Agriculture, Forest Service, USGS

P. contorta range in Sweden.  Image by Philippe Rekacewicz, UNEP/GRID-Arendal

P. contorta range in Sweden. Image by Philippe Rekacewicz, UNEP/GRID-Arendal