Fierer Lab

Exploring the structure and function of microbial communities

A plea for help – hot topics in soil ecology?

By: Noah Fierer

In early June, I’ll be attending the biennial meeting of the Soil Ecology Society in Colorado Springs. Despite being the home of Focus on the Family and one of the more conservative cities in the U.S. (the yin to Boulder’s yang) – it is a scenic place. More importantly the Soil Ecology Society meetings are great and this one is not to be missed. I’ve been going to these meetings since I was an innocent young graduate student and they are always worth attending, for the following reasons:

  • good science
  • not too big, not too small (typically around 150 attendees)
  • nice mix of people at different career stages
  • open bars
  • friendly people (if you study dirt, it is easy to stay grounded)

I’m not just writing this blog post to rave about this meeting. Rather, consider this post a plea for help. I’ve been tasked with giving a brief ‘overview’ talk on the current state of soil ecology. Thus, I am asking for your input on what you think are the big unanswered and exciting questions being asked in the field of soil ecology. In other words, what topics are going to be driving exciting and novel work in the field of soil ecology over the next few years?

Here is a partial list to get the ball rolling (admittedly incomplete – I’m just throwing some ideas out there):

1) What determines soil C availability? A lot of the organic carbon stored in soil is old and not readily accessible to microorganisms. What are the mechanisms responsible for ‘protecting’ soil organic carbon from mineralization and how will global change factors (including elevated temperatures) alter soil C availability over time?

2) How are soil organisms interacting, either directly or indirectly? When we study belowground biota, we typically study groups of organisms in isolation. The microbiologists study bacteria or archaea, the mycologists study fungi, and the nematologists study nematodes, etc.. In reality, all of these soil organisms are interacting in important ways and these interactions are often missed in current investigations of belowground diversity.

3) What causes the priming effect? When labile substrates are added to soil, the mineralization of more recalcitrant substrates will often increase for reasons that are unclear (see here, here, and here, among many other papers on this topic). Is it a biotic process, an abiotic process, or a combination of both? How widespread is the priming effect and how important to overall rates of soil carbon storage?

4) What are viruses doing in soil? We know that viruses are abundant in soil and enormously diverse (with most of the viruses remaining undescribed). Do these viruses play a critical role in structuring soil biota and do they influence soil biogeochemical processes? – who knows. Soil viruses are the ‘known unknowns’.


I’d appreciate any input on other questions/topics to add. I don’t want this list to encapsulate only my narrow and biased worldview – I want input from all of you soil ecologists out there (a.k.a. soil microbial ecologists, terrestrial biogeochemists, ecosystem ecologists, soil zoologists, mycologists, etc..). Tell me what you think will be the new and exciting research directions in the field of soil ecology. Feel free to add your ideas to the comments section or just email me directly (noahfierer(at) All ideas considered.




9 thoughts on “A plea for help – hot topics in soil ecology?

  1. We need to know how and how fast soil organisms move around. The answers to these questions are likely to span broad spatial, temporal and phylogenetic scales. It’s going to take more effort than simply obtaining correlative data on what is currently in the soil at a location or locations. We need experiments to determine what organisms are arriving at any particular time, how they are arriving, and how “the environment selects.” This is true for both micro- and meso-biota.

  2. Hey Noah
    Whats happening biologically in the vadose zone? Probably low activity but there is plenty of vadose zone. Is this the buffer between the topsoil and groundwater?
    cheers Louis

    • Hi Louis, I have the same question. I think that vadose zone may hold rare microorganisms (from extinct era or from a near past) and a lot of genetic information to succession studies. Here in Brazil the sequencing is so expensive that majority of researches can afford just to study the first 10 cm of soil, where the DNA is easily available due high abundance of microorganisms.

  3. I say the impact of soil biota on soil processes, especially C & N cycling, is an exciting area of further research. We know that soil biota, especially macro fauna and the microbial community composition, can drastically change the rates of cycling from what we would predict given a certain climate and soil type. However, I think we are far away from actually being able to predict the interaction between soil community, abiotic context, and the resulting speed and nature of nutrient cycling. I think making these sorts of predictions will require a much more detailed understanding of how soil organisms interact (your second point!) and measuring how these interactions moderate the flow of nutrients between pools.

  4. Which aspects of microbial community composition structure are likely to increase predictive power of soil C cycling and storage estimates? We’ve sequenced a lot of microbial communities in soil but its not clear if these studies will improve our understanding of how soil functions. Which approaches will push us forward: Diversity metrics? Microbial functional groups? Microbial function in the context of historical contingencies? Microbial allocation strategies?

    • I would second this comment, but expanded beyond C cycling, to the absolute necessity to definitively link soil microbial community phylogenetic composition with soil function, fertility, and health. This would take us leaps and bounds towards a universal definition of these terms and developing effective and site-specific management strategies.

  5. Plant-soil microbe feedbacks. What is the impact of the soil microbial community on plant growth/disease resistance, and what is the impact of the plant on the soil microbiome, both short term and long term?

  6. immense species/population level diversity already at the rhizosphere scale and still neither we fully understand the drivers of this diversity nor we understand the functional meaning of it, if there’s any…

  7. What is the best way to scale microbial processes from the lab to the soil horizon to the ecosystem? How can we identify the most important processes without destroying the context in which they occur? This dilemma seems especially important in biogeochemical hotspots like the rhizosphere, zones of alternating redox, peats, permafrost, etc. The significance of microbial processes like priming will be appreciated when they influence macroscopic processes and properties, but bridging the gap between reductionist experiments and emergent ecosystem phenomena seems like a topic we still need to tackle.

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