Hannah picking biochar

Hannah picking biochar

In our our ongoing video series, “What are you doing today?“, undergraduate research assistant Hannah Sanders explains why she’s using dental tools to pick biochar chunks clean of soil.


30in30: Week two

Wow! This is much harder than I thought. Mostly, that’s because I thought I would have more time to myself during this trip to France. Turns out that I’m spending more time in the lab than I expected. That’s great because it is time doing actual science as opposed to the usual science management that I do back home. But, it doesn’t free up much time to do that reading that I committed myself to. I’m also not taking time to read or work in the evenings or weekend, the way I might normally do when as home.

That being said, here is my catch-up on reading for week two:

8. (June 13) Paustian et al. (2016) Climate-smart soils. Nature  532:49–57. doi:10.1038/nature17174. Key to determining how large is the potential for soil GHG mitigation is distinguishing between what is technically feasible and what might be achieved given economic, social and policy constraints. In addition, there is large uncertainty in measuring the potential as well as the permanence of that sequestration. It is not a panacea, but can be a win-win contributor because of positive knock-on effects for sustainable agriculture.

9. (June 13) Finn et al. (2017) Microbial energy and matter transformation in agricultural soils. Soil Biol Biochem. 111:176-192. doi:10.1016/j.soilbio.2017.04.010. Was really hoping this paper would focus more on energy. I am increasingly intrigued by the notion that carbon cycling in soil organic matter is just the proxy for energy fluxes through the heterotrophic decomposition system and that “stability” or resistance to decomposition can be expressed as an energy barrier. Instead, the paper did not cite great work by Henry Janzen on this topic, focused a lot on the physical environment and the microbial community structure. To each their own, I guess.


30in30: Week one

Instead of separate blog posts for each paper, I’ll try to get these out on a weekly basis. Since most of this reading will be happening while I’m visiting INRA and the CEREGE in France, I may not actually be reading one paper daily. Instead, I’ll indicate what day I read each paper, and at the end of the month I hope to have reached the target 30 papers.

So, how did end up choosing my first reading of the project? A very common and conventional way: whatever shiny objects happened to catch my attention today. In this case, it was the newest issues of Nature Geoscience and Nature Ecol Evol.

1. (June 1) Boye et al. (2017) Thermodynamically controlled preservation of organic carbon in floodplains. Nature Geoscience 10:415–419. doi:10.1038/ngeo2940. Organic carbon decomposition in anoxic soils is presumed to depend on the energetics of available electron acceptors. However, this article also founds that the energetics of the organic carbon substrate itself can determine whether or not it is decomposed.

2. (June 2) Judson (2017) The energy expansions of evolution. Nature Ecology & Evolution 1:0138. doi:10.1038/s41559-017-0138. Separating the history of life on Earth into five energetics epochs: geochemistry, sunlight, oxygen, flesh and fire.

Catching up from the long weekend and travels…

3. (June 6) Sharples et al. (2017) What proportion of riverine nutrients reaches the open ocean? Global Biogeochem. Cycles, 31, 39–58, doi:10.1002/2016GB005483. Was hoping this would be about how much of the nutrients in the stream actually make it to the ocean, but instead it was about how nutrient that arrives at the shelf/estuary makes it to the open ocean.

4. (June 6) Ren et al. (2017) 21st-century rise in anthropogenic nitrogen deposition on a remote coral reef. Science, 356(6339): 749-752. doi:10.1126/science.aal3869. Examining N isotopes from a remote South China Sea coral, authors suggest that anthropogenic atmospheric deposition of N supplies nearly one quarter of the annual N input to the surface ocean in this region.

5. (June 6) Torres-Sallan et al. (2017) Clay illuviation provides a long-term sink for C sequestration in subsoils. Scientific Reports. 7:45635. doi:10.1038/srep45635. “…within the top 30 cm of the soil profiles, and a significant proportion (84% ± 9.5) of this topsoil SOC was located within large and small macroaggregates. A smaller proportion (16.1 ± 9.1%) of the SOC in the top 30 cm was associated with the microaggregates and silt plus clay.” But what do they propose the macroaggregates are made off if not microaggregates, silt and clay? This type of analysis and reporting has always bothered me.

6. (June 7) I read a bunch of papers directly relevant to the project I am currently working on in France. I focused mostly on the methods sections, so I’m not sure these “count” so I’ll bundle them all together. They are a series of papers applying transverse/tangential flow fractionation (TFF) and other similar techniques to isolate and/or characterize nanoparticles from soil or stream samples. Dabrin et al. (2013) Colloidal and truly dissolve metal(oid) fractionation in sediment pore waters using tangential flow filtration. Applied Geochemistry, 31:25-34. doi:10.1016/j.apgeochem.2012.12.002; Jiang et al. (2015) Phosphorous containing water dispersible nanoparticles in arable soil. Journal of Environmental Quality, 44:1772–1781. doi:10.2134/jeq2015.02.0085; Tang et al. (2009) Size fractionation and characterization of nanocolloidal particles in soils. Environ. Geochem. Health, 31:1-10. doi:10.1007/s10653-008-9131-7.

7. (June 8) Sebag (2016) Dynamics of soil organic matter based on new Rock-Eval indices. Geoderma, 284:185-203. doi:10.1016/j.geoderma.2016.08.025. “Feller et al. (2010) also question why this technique is not currently used in soil science” – maybe because the instruments are rare and very expensive? Or maybe because the indices are still being developed and interpreted?

30in30: Where to start?

30in30: Where to start?

The first challenge to my 30in30 research reading project is deciding what to read, which leads directly to deciding where to start in the literature that I’ve accumulated. Modern technology has allowed me to very easily accumulate a massive backlog of papers, chapters and books to read. I use Feedly to track journal table of contents for around 35 journals. There, I’ve flagged easily over a hundred articles for “Read later”. I also currently have around 40 open tabs in my browser pointing to various articles. And, I also have a folder on my desktop called “Papers to Read” containing 334 files.

I collect or flag papers that are directly relevant to the research we do, but I also flag papers of broader interests. And when your interests span soil science, biogeochemistry, environmental science, R coding and data science, etc. – that’s a lot of papers. Some papers get flagged for teaching purposes as well. I’m a sucker for a nice color figure in a synthesis paper that I can use in class – either having students read it themselves, or for me to integrate into a lecture. Clearly, my ability to collect papers of interest far exceeds my ability, time, energy, focus, discipline, etc. to actually read them.

This is a well-recognized phenomenon that has been written about: Scientific literature: Information overload (Landhuis, 2016, Nature 535:457–458 (21 July 2016) doi:10.1038/nj7612-457a) and How to tame the flood of literature (Gibney, 2014, Nature 513:129–130 (04 September 2014) doi:10.1038/513129a), for instance.

So where should I start? Chronological in order of when I collected the article, forward or reverse? Chronological order of the articles themselves? Shortest articles first? Topically? … I suspect some kind of triage will be necessary because I can actually get started. Ideally, the 30in30 exercise will allow me to focus in on what to read for different purposes.

30in30 for summer research reading

Mashing up ESPN’s 30 for 30 and the Twitter #365papers hashtag, I’ve decided to come up with my own research reading project: 30in30. I’m heading to Aix-en-Provence for the month of June to work at the European Center for Research and Teaching in Geosciences and the Environment (CEREGE). During that time, I’m committing myself to reading one paper per day – hence the 30in30. This will make only a small dent in the huge pile of papers that I’ve accumulated in my “To Read” folder, in open tabs in my browser, or flagged in Feedly. Hopefully, it will set a good habit in motion that will stick for longer than my trip to CEREGE. Watch this space. I’ll be posting my reflections on the papers and the process starting June 1.