Behind the scenes of the Maestre lab (VII): Fernando on how aridity impacts soil microbial communities in global drylands
We continue with the series of posts describing the “behind the scenes” of the research presented in the articles we publish (you can find the previous posts of this series here: I, II III, IV V and VI). In this case we will talk about a paper recently published in PNAS entitled “Increasing aridity reduces soil microbial diversity and abundance in global drylands”, led by Fernando. This article is also related to another paper just published in Nature Communications led by Manuel Delgado-Baquerizo (“Microbial diversity drives multifunctionality in terrestrial ecosystems”), which will be the subject of the next post of this series (to come soon).
Fernando Maestre in a laboratory of the Hawkesbury Institute of the Environment during the stay he made in this Australian research center in 2015.
These are the Q & A for Fernando:
What is this paper about?
This paper presents results from a standardized survey conducted across 80 dryland sites from all continents except Antarctica to assess how changes in aridity affect the composition, abundance and diversity of soil bacteria and fungi. It is part of the research we have conducted in the framework of the European Research Council-funded BIOCOM project.
What are the key messages of this article?
The key result we found is that the diversity and abundance of soil bacteria and fungi, measured using quantitative PCR and DNA-sequencing approaches (Illumina Miseq), respectively, is reduced as aridity increases in global drylands. A more detailed analysis of our data suggested that these results were mostly driven by the negative impacts of aridity on soil organic carbon content, which positively affected the abundance and diversity of both bacteria and fungi. We also found some changes in the relative abundance of major microbial groups. For example, aridity promoted shifts in the composition of soil bacteria, with increases in the relative abundance of Chloroflexi and α-Proteobacteria and decreases in Acidobacteria and Verrucomicrobia. Our results also revealed interesting findings about the microbial communities inhabiting dryland soils; contrary to what has been reported by previous continental and global-scale studies, soil pH was not a major driver of bacterial diversity, and soil fungal communities were dominated by Ascomycota.
How did you come up with the idea of conducting this study?
Soon after we established the global network of dryland sites and collaborators, I explored the possibility to obtain frozen soil samples from as many sites as possible to study soil microbial communities. Once we secured samples from a relatively large number of sites I quickly start thinking about how nice it would be to explore how they change along aridity gradients and to evaluate their relationships with multifunctionality. This was for me a logical follow up from other analyses we have done with the data gathered from this global dryland network (like exploring the relationships between plant species richness and multifunctionality, analyzing the effects of aridity on soil stoichiometry or evaluating how aridity and human impacts affect N cycling, among others, check our lab publications page for a full listing of all the publications derived from these data).
What have you enjoyed the most during the “life cycle” of this article (from its conception to its publication)?
I have certainly enjoyed all the stages involved in the life cycle of this article, but if I have to choose a couple of them these are certainly the analysis of the data and the writing of the manuscript, which I did (almost) entirely during a research stay at the Hawkesbury Institute of the Environment (HIE) I conducted between February and May 2015. During my time in Australia I had the chance to work with Prof. Brajesh Singh and his team, and I learned a lot about the possibilities that state-of-the-art DNA sequencing approaches can do for our research. I had also the time and quietness to spend lots of time playing with the data, reading papers and writing, something that I really enjoy doing and that unfortunately cannot do on a daily basis because of the multiple things I have to do to run the lab. I also spent lots of time with old friends and former lab members, such as David Eldridge, Manuel Delgado-Baquerizo, Raúl Ochoa-Hueso and Juan Piñeiro, and made new friends and collaborators. My time in Australia was certainly memorable from the personal point of view too, and both my family and I enjoyed our time there very much.
What have been the major difficulties you have encountered when conducting the research reflected in this article?
Certainly the most difficult thing has been trying to obtain frozen soil samples from the sites and transporting them to the lab in good conditions. Given that many sites are located in remote areas with difficult or no access to a freezer we were not able to obtain frozen soils from all the 224 sites we originally surveyed. And for those places where we managed to get frozen samples we had to organize the logistics very carefully to ensure that we received the samples in good conditions for extracting their DNA upon their receipt in the lab.
How has been your experience publishing this article in PNAS?
This has been the first article I got accepted in PNAS (I have submitted in the past other manuscripts, but none of them were accepted), and my experience with the journal has been really good in this case. Our manuscript was quickly sent to review, the reviews came in in less than a month (and were very constructive) and once we sent our revised manuscript it was definitively accepted 10 days later if I do not remember badly. And the article was published really quickly. Overall I am very satisfied with the publishing experience of this article, albeit I must say that the submission of the revised manuscript took me quite a few hours and a couple of headaches to fit all the supplementary materials we had into the limits imposed by the journal.
Any other issues/comments about this work you would like to highlight?
Just that I had lots of fun (and learned a lot) working with our international team of collaborators, and particularly with Manuel Delgado-Baquerizo, who has made fundamental contributions to this work. And I would also like to acknowledge the work of everyone involved in this study, from the international team of collaborators that conducted vegetation and soil surveys at their sites to everyone at the group of Prof. Singh, who provided us access to the sequencing facilities of the HIE, the knowledge on bioinformatics needed to process the data and were great hosts during my stay at the HIE. I would like to particularly acknowledge the technicians of the lab (Victoria, Dolo, Daniel and Bea), whose work behind the scenes is key for successfully completing a very complex study like this one.