Tag Archives: diversity

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)



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!