Author Archives: franciskadevries

Deadline for applications for our sequencing meta-analysis workshop is extended till 17 April!

We have extended the deadline for our workshop below with one week, until April the 17th! Also, we are now also welcoming applications from people who don’t have relevant sequencing data but can contribute in another meaningful way, or from people who do have sequencing data and would like to be involved but can’t attend in person. We are looking into possibilities of streaming the talks and videoconferencing remote contributors.

 

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

The BES special interest group Plants, Soils, Ecosystems is 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

-Mattias de Hollander, Netherlands Institute of Ecology, the Netherlands

 

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 17th 5pm. Applicants will be notified whether they have been selected for the workshop by April the 24th. For questions email Franciska de Vries: franciska.devries@manchester.ac.uk

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

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IMPORTANT!

We are also for data contributions and distance involvement in this project! If you think you have relevant data and would like to be involved, please email franciska.devries@manchester.ac.uk

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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

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!

Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage

– added by Franciska de Vries

This paper, by Colin Averill and colleagues, came out as a Letter in Nature almost two weeks ago. It immediately excited me, as the title suggests that in this paper, the authors are revealing the mechanism through which mycorrhizal fungi increase soil carbon storage. Groundbreaking!

I started to read. What the authors did in this paper was compose a global dataset, consisting of observations of soil organic C, N, and clay content (to a depth of one meter) across a range of vegetation types and biomes. They then assigned values of mean annual temperature (MAT), mean annual precipitation (MAP), and net primary productivity (NPP) to each site, using previously published climate interpolations and satellite-based observations. Finally, they assigned a mycorrhizal status to each of the vegetation types, which could be either arbuscular (AM) or ericoid and ecto-mycorrhizal (EEM).

Mycorrhizal status of each site was assigned based on the dominant vegetation present, and knowledge of its mycorrhizal status. Understorey vegetation (in forests) was ignored, and where no vegetation data was present, they used the vegetation description. So, for example, the vegetation description “grassland” was classified as the AM, whereas “mixed coniferous forest” was classified as EEM.

This dataset was then used to explain soil C storage, using soil N and mycorrhizal status as explanatory variables, while at the same time accounting for variation in climate and other soil properties.

Using mixed effects models, the authors found that in ecosystems dominated by EEM fungi, 1.7 times more C was stored per unit N than in AM ecosystems.

For the first time, this study shows that C global cycling does not only depend on abiotic factors like temperature and moisture, but also on soil mycorrhizal status, highlighting the importance of biotic factors in addition to abiotic factors for soil C storage. This finding supports the results from a modelling study by Orwin et al. (2011), who showed that competition for organic N between EEM and decomposer fungi increases soil C storage.

Averill and colleagues conclude that ‘mycorrhizal functional traits are as important a control over decomposition and soil C storage as are soil chemical properties and the physical protection of soil organic matter’, and that ‘the identity and functional traits of soil microbes exert a control over the terrestrial C cycle’.

So, a pretty exciting paper, but does it really do what it promises? When I read the title, I expected a paper reporting on (a range of) mechanistic experiments to prove that mycorrhizal fungi drive soil C storage. But, rather than a mechanistic study, it is an observational study that uses a powerful data set and an advanced modeling approach to show that there is a relationship between mycorrhizal status and soil C storage. However strong their finding is, and although it holds across a range of ecosystems and biomes, their study does not allow for testing a hypothesis and elucidating a mechanism. As Mark Bradford elegantly says in his News and Views article about the paper: “The authors propose, in line with a previous hypothesis, that these richer carbon stores result from competition for nitrogen between EM fungi and free­living soil microorganisms that feed on organic matter” and: “Pinpointing which mechanism explains Averill and colleagues’ results will require more data and involve challenges common to all large observational data sets, including unobserved variables and spurious cor­ relations”.

I couldn’t agree more.

However powerful the data set in this paper is, there are several issues that would have to be addressed to come up with a conclusive answer of how and whether mycorrhizal fungi drive soil C storage. First of all, important soil properties that can explain both soil C content and mycorrhizal status, such as soil moisture or pH, haven’t been included in the models. Second, certain vegetation types, such as heathland, which is known to be dominated by ericoid mycorrhizal fungi, are missing. Third, the assigned mycorrhizal type might be occurring under a certain vegetation type because of the quality of the C inputs into the soil, which might itself drive soil C storage; something that the authors do acknowledge in the paper. Finally, Mark Bradford calculated, in his News and Views article, that only when the soil contains more that 3 kg N per square meter, C stores in EEM dominated systems exceeds that of AM dominated systems by 1.3 times.

But, despite these nuances that will need addressing in future studies, this is an important study that proposes an important hypothesis, namely that mycorrhizal type is of pivotal importance in driving soil C storage. By formulating this testable hypothesis and identifying a global relationship between soil biota and soil C storage, this study significantly advances the field of plant-soil interactions. It also highlights that disruptions of links between vegetation and mycorrhizal fungi, as a result of global change, might have far-reaching implications for soil C stocks and thus for the climate mitigation potential of soils.

So, I am curious what other people think about this paper! Do you agree or disagree with my views? How do you think we could go about testing the hypotheses proposed in this paper? Or is this enough evidence already? What do you think about the statistical methods used? Feel free to comment – the aim of this journal club is to stimulate discussion – through replies here, but also on Twitter. If you respond on Twitter, please use the hashtag #psejclub.

 

With thanks to all members of the Soil and Ecosystem Ecology group of The University of Manchester for inspiring discussions.

Full reference: Averill, C., B. L. Turner, and A. C. Finzi. 2014. Mycorrhiza-mediated competition between plants and decomposers drives soil carbon storage. Nature advance online publication.