Tag Archives: soil

International Year of Soils (#IYS2015)

Perhaps you have already heard the buzz about soils, and why everyone should be thinking about them this year, and every year; 2015 is the International Year of Soils! Just hop on Twitter and look up posts tagged with #IYS2015 – every day new photographs and articles are being posted. There has been a plethora of great pieces on the importance of soil, including ten things everyone should know about soil, Resources from the FAO (including the infographic below), the Soils Atlas, and another cool infographic form Mother Nature Network. There was a recent New York Times piece on no-till farming practices and how they benefit soils here, and the Guardian recently published a piece on how we depend on soils here. With more articles being published as the year progresses and various conferences and meetings taking place, there are plenty of ways to join in with the discussion.

The International Year of Soils is in full swing, with activities ranging from those geared towards professional soil scientists and soil ecologists to public outreach campaigns. To learn more about activities that are happening in your area check out the FAO calendar of events here. Do you have an interest in learning more about soils in an online course? Check out this free online course from Lancaster University here. Have an interest in reaching out to younger audiences? Check out the colouring book, children’s book, and card game from the Global Soil Biodiversity Initiative here.

FAO-Infographic-IYS2015-fs2-en (1)

What can you do for the soil?
Racking your brain for some concrete actions you can take to be more considerate of the soils beneath your feet? Taking small steps to be more mindful about your food consumption and food waste practices are good places to start. Compost food wastes to create nutrient rich compost to use in your garden beds – more information from the FAO here. Purchase locally-sourced food, and support local farmers and community supported agriculture groups (CSAs- more information here) to reduce the carbon footprint of your meals. Grow your own food – whether you live in an urban or rural environment a variety of gardening options are available: try growing fresh herbs in the windowsill or a large pot of cherry tomatoes on your apartment balcony. Educate yourself about the soils in your area and foods that grow best given your climate conditions here. Use that compost pile you have been building up to fertilize your garden, and you will have come full circle.

Get your friends, family, and children involved, because we all need food to survive and sustain ourselves. Take some time to appreciate the soils that fulfil such a fundamental requirement of our existence. Think about the little steps you can take to improve the soils in your area, or reduce your carbon footprint to help lead to a healthier planet.

Relena Ribbons is a FONASO Ph.D. fellow at Bangor University and the University of Copenhagen researching tree species effects on soils and nutrient cycling. She loves gardening. Find her on Twitter: @relenaribbons, on her website, or drop her an email: rribbons@gmail.com.

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.


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.


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

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

#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!