Friday, February 1, 2019

February 2019 science journal article summary

Needle ice
Hello,

Here are some articles focused on genomics, but with a few others on deforestation, ecosystem services, and sustainable agriculture. The photo above of needle ice in my backyard is totally unrelated, but I'd never seen or even heard of it, and I found it super cool. Read about it on wikipedia!

Let me know if you need a copy of any of these articles. If you know someone who wants to sign up to receive these summaries, they can do so at http://bit.ly/sciencejon

DEFORESTATION:
Jokpe & Schoneveld 2018 is a close look at zero-deforestation commitments (ZDC) by 50 influential  corporate "power brokers."  They identify several problems with implementation gaps and externalities. In particular they note that a lack of traceability and transparency about where commodities are sourced from makes verification difficult (and most companies rely on asking their suppliers to honestly self-report deforestation). They also report that 3/4 of companies with ZDC don't require company wide commitments from suppliers (so those suppliers can just sell deforestation linked products to other companies who don't care). This one is long but worth reading for breakouts by sector and other useful info. Note that TNC in this article refers to transnational companies and not The Nature Conservancy. The problems and gaps identified are things we're hoping to address with the Accountability Framework (https://accountability-framework.org/), which should be formally launched this spring.

ECOSYSTEM SERVICES:
There are many methods and tools to assess ecosystem services. Neugarten et al. 2018 is a report reviewing 9 assessment tools (EST, PA-BAT, TESSA, ARIES, C$N, InVEST, MIMES, SolVES, and WW) and providing decision trees on how to pick the right one for a given need. This is a fantastic reference for anyone working with ecosystem services, and it covers both written guidance documents and modeling tools. They recommend you identify the analysis question or need and think hard about expertise and resources you have to do the analysis before selecting a tool.

GENOMICS / GENE EDITING / GENETIC ENGINEERING:
Photosynthesis in plants relies on an enzyme called RuBisCO, sometimes called 'the most incompetent enzyme in the world' due to its inefficiency and energy loss during respiration. South et al. 2019 present a new transgenic GMO tobacco plant which improves the efficiency of respiration. As a result, their best modified tobacco plants had 41% higher biomass (including 33% more leaf biomass but also larger stems). It's not clear how much of the biomass gain could be translated to improved yields for grains or other crops, but that's still a potentially huge step forward which should be further explored. Eisenhut & Weber 2019 is a nice very short (1.5 page) summary of the article, and you can also read a blog about it here which includes some nice diagrams: https://phys.org/news/2019-01-scientists-shortcut-photosynthetic-glitch-boost.html

Kofler et al. 2018 is an editorial on benefits and risks of altering the DNA of wild organisms via gene editing. They call for collective oversight to ensure careful thought is given to environmental, social, and ethical concerns, and especially to local community involvement in each decision to potentially release an edited organism (as well as international bodies like IUCN). They stress that "using this technology irresponsibly or not using it at all could prove damaging" - and give good examples of each.

Sprink et al. 2016 looks at regulation of gene editing, and the difference between a process based approach (where the key factor is how an organism was modified) vs a product based approach (where the outcome is the key factor regardless of the process used). They argue that the European approach is outdated and doesn't reflect the continuum of modern technology (including several different applications of gene editing). They also dive into a legal argument of why it should be changed, and how it compares to the US and other countries. They make a good argument that regulation should be based on a genetic trait and product rather than the process used to develop it. This one is complex and wonky but a good reference, especially box 1 with definitions of several gene editing approaches.

Halewood et al. 2018 is an overview of how CGIAR is looking to use crop genome sequencing to drive more crop diversity and find crop traits that can deliver better outcomes for people and nature. Most readers can safely skip information on specific molecular markers (e.g. Table 1) but should read page 372 which lists several applications of gene editing technology and genotyping.

Zhong 2019 looks at how soy genotype and rhizobium inoculation (of seed or soil) impact plant growth, soy nodulation (the nodules help them fix nitrogen via bacteria), and microbiome. They found that the microbiome of soy varies depending on the genotype of soy. In particular whether the genotype forms high or low numbers of root nodules. Low-nodulation soy had more co-occurrence of the taxonomic groups (a more connected network) than the high-nodulation soy (figure 4). Both genotypes had their microbiome network connections increased by inoculation. The efficacy of the inoculant  varies depending on plant genotype. See figure 1c / 1d for details. Low-nodule soy got a significant boost in nodulation from inoculation, but still had fewer nodules than high-nodule soy (for which nodulation was unaffected by inoculation). Both genotypes of soy got a roughly similar growth boost from inoculation. This means that to evaluate biological seed treatments / inoculation we have to look at the intersection of the inoculant, plant genetics, and baseline soil microbiome.


SUSTAINABLE AGRICULTURE:
Eichler Inwood et al. 2018 is a thoughtful review of several different frameworks to assess agricultural sustainability (in different contexts and scales). Table 4 is a nice summary of the 9 frameworks they cover, with Table 5 providing more details on how and where they work. None are ideal in every context. Thy conclude with recommendations about how to select a framework (see Table 6 for properties they should have), choose indicators, collect data etc.

REFERENCES:
Eichler Inwood, S. E., López-Ridaura, S., Kline, K. L., Gérard, B., Monsalue, A. G., Govaerts, B., & Dale, V. H. (2018). Assessing sustainability in agricultural landscapes: a review of approaches. Environmental Reviews, 26(3), 299–315. https://doi.org/10.1139/er-2017-0058

Eisenhut, M., & Weber, A. P. M. (2019). Improving crop yield. Science, 363(6422), 32–33. https://doi.org/10.1126/science.aav8979

Halewood, M., Lopez Noriega, I., Ellis, D., Roa, C., Rouard, M., & Sackville Hamilton, R. (2018). Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing. Biopreservation and Biobanking, 16(5), 368–376. https://doi.org/10.1089/bio.2018.0043

Jopke, P., & Schoneveld, G. C. (2018). Corporate commitments to zero deforestation: An evaluation of externality problems and implementation gaps. Occasional Paper 181. Bogor, Indonesia: CIFOR.

Kofler, N., Collins, J. P., Kuzma, J., Marris, E., Esvelt, K., Nelson, M. P., … Schmitz, O. J. (2018). Editing nature: Local roots of global governance: Science, 362(6414), 527–529. https://doi.org/10.1126/science.aat4612

Neugarten, R. A., Langhammer, P. F., Osipova, E., Bagstad, K. J., Bhagabati, N., Butchart, S. H. M., … Willcock, S. (2018). Tools for measuring, modelling, and valuing ecosystem services: guidance for Key Biodiversity Areas, natural World Heritage sites, and protected areas. (C. Groves, Ed.). Gland, Switzerland: IUCN. https://doi.org/10.2305/IUCN.CH.2018.PAG.28.en

South, P. F., Cavanagh, A. P., Liu, H. W., & Ort, D. R. (2019). Synthetic glycolate metabolism pathways stimulate crop growth and productivity in the field. Science, 363(6422), eaat9077. https://doi.org/10.1126/SCIENCE.AAT9077

Sprink, T., Eriksson, D., Schiemann, J., & Hartung, F. (2016). Regulatory hurdles for genome editing: process- vs. product-based approaches in different regulatory contexts. Plant Cell Reports, 35(7), 1493–1506. https://doi.org/10.1007/s00299-016-1990-2

Zhong, Y., Yang, Y., Liu, P., Xu, R., Rensing, C., Fu, X., & Liao, H. (2019). Genotype and rhizobium inoculation modulate the assembly of soybean rhizobacterial communities. Plant, Cell & Environment. https://doi.org/10.1111/pce.13519


Sincerely,

Jon

p.s. as a reminder, you can search all of the science articles written by TNC staff (that we know of) here http://www.conservationgateway.org/ConservationPlanning/ToolsData/sitepages/article-list.aspx
(as you publish please email science_pubs@tnc.org to help keep this resource current).
If you'd like to keep track of what I write as well as what I read, I always link to both my informal blog posts and my formal publications (plus these summaries) at http://sciencejon.blogspot.com/

Wednesday, January 2, 2019

January 2019 science journal article summary: best of 2018

Christmas cookie decorating party

Happy new year!

Resolved to try harder to keep with science? Why not start with some of the best papers from last year that you may have missed? This month I picked my favorite 15 articles that I reviewed in 2018, plus a few other resources. A few were published earlier, but I read them all last year. I picked some because of importance, others because they were interesting, and two plug my own work.

There is one new article I couldn't resist mentioning, which is about the Camboriú water fund that I worked on. Kroeger et al. 2019 talks about how the water fund was designed, including estimating the impact it would have on land use change and water quality. We were able to show that it provided a positive financial return on investment after 44 years (if you include some modest societal co-benefits like flood control and biodiversity). PDF available here until ~Feb 10 after which an unformatted PDF is available here.

I also wanted to once again plug a cool resource  to help you figure out which journal to submit a paper to: http://jane.biosemantics.org/  You enter the title and abstract of your paper and it gives you a list of appropriate journals. You may also want these tips on how to write an abstract to get found easily in Google and Google Scholar: https://authorservices.wiley.com/author-resources/Journal-Authors/Prepare/writing-for-seo.html and my blog on how to ensure all of your own research is viewable by others: http://sciencejon.blogspot.com/2018/03/tips-for-helping-people-to-find-your.html

Finally, my wife's comment on my book chapter on global agriculture land use trends (that there was no clear key take-away point) has stuck with me as a reminder of how important it is to get input from non-scientists on science writing. Here's a short blog where I tried to supplement the chapter: http://sciencejon.blogspot.com/2018/01/take-2-what-i-wish-id-put-in-my-recent.html

ARTICLES:
Carvin et al 2018 is a study I've been eagerly awaiting for years. It is a rigorous paired watershed study looking at the impact of a carefully targeted set of agricultural interventions, and is one of the first papers in the US to show we CAN improve water quality at a watershed scale (50 km2) through shifting ag. Initial work had found 9% of the area was contributing 40% of the phosphorous load, so the authors really targeted those heavy contributors. They found a 55% reduction in phosphorus runoff loads and suspended sediment event loads decreased by 52% for events during unfrozen soil conditions  into the Pecatonica River tributary during storm events. This is big news as these outcomes have been elusive. However, this watershed was picked as one of the most likely to respond well, and those seeking to replicate these results should also carefully select their watersheds. Contact Steve Richter at TNC for more info.

Cui et al 2018 reports on the results of an ambitious study that worked with 21 million farmers (!) of maize, rice, and wheat over 10 years. China currently has some of the least efficient farms in the world, presenting a huge need to improve. This study used a soil & crop management framework that resulted in ~11% improved yield while reducing N application by ~16% (and reactive N losses by ~25%), and GHGs by 14-22% depending on crop. The scale is impressive: altogether they influenced 37.7 million ha. Interestingly, extension staff impacted over 10 times the area per staff person (471 ha / person) compared to agribusiness partners (see Fig 2). Regardless, this is good news in showing that it's possible to achieve "win-win" outcomes at scale even with smallholders. On the other hand, nitrogen efficiency is so poor in China, that much larger changes are needed to bring them in line with world averages, let alone truly sustainable targets (highlighting that policy changes are likely needed as well). Fig 1 has a great breakdown of impacts by crop and region.

Almost everyone who works for or closely with The Nature Conservancy heard about the 2017 "Natural Climate Solutions" paper (Griscom et al. 2017, I reviewed it in November 2017). If you've been waiting for the sequel - good news! Fargione et al. 2018 just provided a similar analysis specifically for the United States. It's short, excellent, and worth reading, but if you're impatient skip to Figure 1. That summarizes the potential of each pathway and splits out how much is achievable at different carbon prices. They found a maximum potential of 1.2 Pg (aka 1200 million metric tons) CO2e / yr (21% of current US emissions and ~27% of 2005 emissions), and ~300 Tg (million metric tons) achievable at $10 / t CO2e (~5% of US emissions). The biggest low cost opportunities are in planting cover crops followed by forest management, avoided habitat conversion, and improved farm nutrient management. You can read more about it on TNC's web site at https://www.nature.org/en-us/explore/newsroom/natural-climate-solutions-study/ or at https://eurekalert.org/pub_releases/2018-11/cu-nsr111418.php

Fisher et al. 2018 ("Knowledge diffusion within a large conservation organization and beyond") looks at how people find information about innovations and share them, specifically the spread of Conservation by Design 2.0 (CbD 2.0). We review how earlier versions of CbD spread from TNC (looking at published science articles and expert interviews), then use tons of varied data to look at CbD 2.0. I wrote a blog about the paper here: http://sciencejon.blogspot.com/2018/03/share-good-news-paper-on-improving.html
and the full paper is at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0193716
but here's a summary of what we learned:
  1.  Sending repeated broadly-targeted communications (e.g. all-staff email / newsletters / etc.) that make it easy for recipients to find out more worked better than more narrowly focused communications (e.g. plenary talks, emails from executives).
  2. Expert interviews revealed several factors to promote diffusion: bringing in partners early to develop and test methods, committing up front to sustain support for the planning methods, having in-person workshops, using peer-review and shared learning, providing financial support, explaining how the methods address existing needs planners already have, and the existence of a support and learning network like the conservation coaches network (CCNET). 
  3. Organizations may wish to use internal data to identify staff likely to play a key role in diffusing so that they can encourage that process (the paper has details on how, with more forthcoming in an upcoming paper)
  4. Working with academics on publications represents a potential way to get the word out with relatively low effort for organizations (academics I have worked with in other contexts are often very interested in data no one else has access to, and have published cool papers from those data). 
  5. For scientists interested in this topic, we learned a lot about how to study knowledge diffusion, and share tips for researchers (e.g. thinking about image-blocking, legal and privacy constraints, distinguishing internal and external website visits, etc.).

Fisher & Kareiva 2019 (still in press) is a book chapter about sustainable agriculture that I write a few years ago. The first half is OK but is out of date and was written when I knew far less about agriculture. I'd skip to the 2nd half (start with the "Can Corporate Sustainability reporting be a force for improved agricultural practices?" section). There's some interesting content I haven't seen anywhere else on corporate sustainabiltiy and food labels. The chapter is available from: http://fish.freeshell.org/publications/FisherKareiva_CUP_2018_preformatted.pdf

Garnett et al. 2017 ("Grazed and Confused") is a very thoughtful review of the climate change / GHG impact of ruminants (largely cattle). Their first key findings is that even with good grazing ruminants still have high net GHG emissions. They also note sequestering soil carbon often has trade-offs with methane and nitrous oxide. Finally, as demand for animal protein rises sharply there is likely to be both land conversion and increasing GHGs as a result. These have all been reported widely in other studies, but it's a nice summary. On the one hand, it's hard to pull out quantitative results from this paper. On the other, it does a great job of covering the various arguments and counterpoints around cattle and carbon, and presenting the data in a value-neutral tone. Anyone interested in this topic should at least skim the 8-page summary.

Given how much research there is on trying to get crops to fix their own nitrogen, the finding by Griesmann et al. 2018 that many plants have lost the ability to fix N blew my mind. By comparing genomes of N-fixing plants to those that don't, they were able to find that ~3/4 of the species in their sample that didn't fix N had an ancestor that could! They suggest that the fact this ability has been lost multiple times reflects that plants spend a lot of energy to support N fixation, and that when N levels are adequate in the soil they eventually can lose the ability to fix it. In other words, as we try to engineer plants to fix their own N, it's worth reflecting on the costs that may have led plants in the past to reject this evolutionary path.
There's a blog on this one at http://www.sciencemag.org/news/2018/05/many-plants-need-bacterial-roommates-survive-so-why-do-some-kick-them-out

Hansen et al 2018 is a cool paper using empirical data to test how effective wetlands in the Minnesota River basin are at reducing nitrates in an ag landscape compared to cover crops and land retirement. They compared river water quality at ~200 sites under different flow conditions to high-resolution data on wetlands and land use to map correlations (they didn't get at true causation). They found wetlands were 5 times more effective per unit area at removing nitrates compared to cover crops and land retirement (although it's much harder to make a business case to a farmer around wetland creation). They also found wetlands strategically placed to intercept as much flow as possible were much more effective (see Fig 4 - the concept is obvious but the numbers are interesting). All these findings align well with prior work emphasizing the critical role of well-placed wetlands to improve water quality. If you read this paper watch out for the term "crop cover" (% of a given site area used to grow crops) as opposed to "cover crops" (presence of an additional crop on farmland that would otherwise be fallow for part of the year), as they're not super clear how they use the two terms.

Klein et al. 2007 is a fantastic reference examining dependence on animal pollination across 115 major crop species (ignoring crops like corn which are entirely wind-pollinated). I mainly use Appendix 2, which for each crop lists how much it benefits from animal pollination (from entirely dependent on animal pollinators like cocoa or squash, to receiving almost no benefit) as well as listing the type of pollinator, pointing to references, etc. While the appendix is my favorite part, they also note in the main paper that a) non-insect pollinators (e.g. birds and bats) are less well studied and b) as agriculture intensifies wild pollinators are likely to decline. This means thinking about pollinator habitat in and around farms can be important for some crops, and the appendix can identify which ones are most likely to see more benefit.

Nevle & Bird 2008 is grim but fascinating. They find a connection between seemingly unrelated factors: global CO2 levels and pandemics among indigenous people in the Americas brought on by European contact. They link the population crash to a reduction in burning of forests for swidden agriculture, subsequent forest regrowth storing ~5-10 Gt carbon, and argue this is a likely contributor to a small measured reduction in global atmospheric CO2 at the same time. It's more of an interesting hypothesis with data which is consistent than real 'proof' but it's still a fascinating (if depressing) read.

Rasmussen et al. 2018 is a global review of whether or not agricultural intensification is good for both people and the environment. While they find income and food production generally go up, ecosystem services go down in most cases. The figures have great summaries of results by geography, by metric of ecosystem services or human well being, and by separating 'win-win' cases from 'lose-lose' and mixed results in different contexts. The specific case studies are very interesting and thought provoking. Surprisingly, increased inputs were more likely to lead to win-win outcomes, with crop changes as reduced fallow more likely to lead to lose-lose. This is a relatively understudied area (this paper summarizes 53 studies) given the importance of intensification strategies; the lack of evidence for consistent positive outcomes doesn't mean intensification CAN'T work, but shows more work (design and monitoring) is needed to ensure we succeed in our goals. See https://www.scidev.net/global/agriculture/news/intensified-farming-rarely-aids-wellbeing-environment.html for a blog on the subject.

Springmann et al. 2018 asks what it would take to sharply reduce the impact of global food production by 2050 (and stay within resource constraints) without simply offsetting impacts like GHGs through reforestation or other mitigation. They look at 3 options (diet change, tech and management, and  reducing food waste) across 5 aspects: GHGs, fresh water use, land use, nitrogen, and phosphorous. They key finding is that no one category of solution is enough, and that for GHGs in particular major diet change (towards mostly plant based foods) would have to be part of the solution. Figure 3 summarizes this set of scenarios nicely. With their medium ambition scenario, they find halving food loss and waste improves impact 6-16% (relative to 2050), improving tech and management reduces impact 3-30%, and modest diet change improves 5-29% (see Figure 2), or they could all be combined for a 25-45% reduction. Note that their findings are global averages, and some places will deviate considerably (e.g. they find nuts and seeds don't account for much overall water use, but in places like California they have a big water footprint). Check the methods for country-level data. You can read two articles about this study here: https://www.washingtonpost.com/health/2018/10/10/how-will-or-billion-people-eat-without-destroying-environment/ and here: https://www.theguardian.com/environment/2018/oct/10/huge-reduction-in-meat-eating-essential-to-avoid-climate-breakdown

For over a year now, TNC staff have been hearing about a science analysis asking whether it's possible for both people and nature to thrive (in a shared conservation vision). Tallis et al 2018 is the newly available science paper behind that analysis. It compares two 2050 global scenarios: business as usual (BAU), and one designed to improve human and environmental outcomes (Sustainability). The latter would result in 577 million ha more habitat than BAU, while limiting climate change, improving air quality, and more. It doesn't assume we can drastically change diets, and sticks with biophysical constraints, but it does recognize that there are major social, economic, and political barriers to making the sustainability scenario a reality. The discussion has several thoughtful limits and caveats, but it's still exciting to see what is at least possible, if not easy to achieve. You will have to read the supplemental material to get a good sense of the work, but the main paper is conveniently short. One final note is that they assume climate change won't impact ag much in either scenario, which is optimistic. You can read all about the paper and its findings here: https://www.nature.org/en-us/what-we-do/our-insights/perspectives/the-science-of-sustainability/?vu=r.v_twopaths

VanZanten et al. 2018 is a really thoughtful paper that takes a refreshing approach to looking at the environmental impact of animal foods in our diet. They note that while using arable land to feed livestock (rather than directly feeding humans) is inherently inefficient, there are some grasslands, food waste, and food by-products like distillers grains that humans can't eat. So to minimize land used to feed the world, ~10% of calories (& ~1/3 of protein needed) could come from animal foods. Fig 4 shows how animal consumption in different regions compares to the protein goal, and Fig 5 shows a similar breakdown for calories and other nutrients. They cover how different animals fit in (e.g. ruminants for grasslands, pigs for food waste, etc.), noted that GHGs are still higher in their scenario than an all-vegan diet, and cover several interesting caveats and twists. One thing they didn't mention - some of the underlying studies have a large role for milk, which people have trouble digesting in many places around the world. But is is a really well done paper and I highly recommend it.

Woodard & Verteramo-Chiu look at how much better the Federal Crop Insurance Program (FCIP) could perform if it used soil data to establish rates and coverage. In other words, how could FCIP incentivize soil health practices that would reduce risks and costs of the program, while avoiding perverse incentives (e.g. in the past crop insurance was not available to farmers using cover crops). It's a fairly wonky economics paper, but they make a good case for much errors and bias exist in the current program. The key finding is that farms with high-quality soils are generally overpaying, and low-quality farms are underpaying. See Fig 3 for an example of how strong the pricing erors are (up to a factor of 6). By accounting for soils data (and perhaps current practices), this program could be an important driver to get farmers to start rebuilding healthier soils to keep premiums low. They focus on top corn producing states where soil quality is relatively homogeneous; benefits of accounting for soil should be higher in regions with more varied soil. With predicted volatility from climate change, improving crop insurance will be increasingly important.

REFERENCES:
Carvin, R., Good, L. W., Fitzpatrick, F., Diehl, C., Songer, K., Meyer, K. J., … Richter, S. (2018). Testing a two-scale focused conservation strategy for reducing phosphorus and sediment loads from agricultural watersheds. Journal of Soil and Water Conservation, 73(3), 298–309. https://doi.org/10.2489/jswc.73.3.298

Cui, Z., Zhang, H., Chen, X., Zhang, C., Ma, W., Huang, C., … Dou, Z. (2018). Pursuing sustainable productivity with millions of smallholder farmers. Nature, 555, 363–366. https://doi.org/10.1038/nature25785

Fargione, J. E., Bassett, S., Boucher, T., Bridgham, S. D., Conant, R. T., Cook-patton, S. C., … Griscom, B. W. (2018). Natural climate solutions for the United States. Science Advances, 4(November).

Fisher, J. R. B. and Kareiva, P. (In Press, 2019). Using environmental metrics to promote sustainability and resilience in agriculture. In Gardner et al. (Eds), Agricultural Resilience: Perspectives from Ecology and Economics. Cambridge University Press. Manuscript accepted for publication.

Fisher, J. R. B., Montambault, J., Burford, K. P., Gopalakrishna, T., Masuda, Y. J., Reddy, S. M. W., … Salcedo, A. I. (2018). Knowledge diffusion within a large conservation organization and beyond. PLoS ONE, 13(3), 1–24. https://doi.org/10.1371/journal.pone.0193716

Garnett T., Godde C., Muller A., Röös E., Smith P., de Boer I.J.M., Ermgassen E., Herrero M., van Middelaar C., Schader C. and van Zanten H. (2017). Grazed and confused? Ruminating on cattle, grazing systems, methane, nitrous oxide, the soil carbon sequestration question. Food Climate Research Network, University of Oxford http://www.fcrn.org.uk

Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., … Cheng, S. (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science, 361(6398). https://doi.org/10.1126/science.aat1743

Hansen, A. T., Dolph, C. L., Foufoula-Georgiou, E., & Finlay, J. C. (2018). Contribution of wetlands to nitrate removal at the watershed scale. Nature Geoscience. https://doi.org/10.1038/s41561-017-0056-6

Klein, A.-M., Vaissière, B. E., Cane, J. H., Steffan-Dewenter, I., Cunningham, S. a, Kremen, C., & Tscharntke, T. (2007). Importance of pollinators in changing landscapes for world crops. Proceedings. Biological Sciences / The Royal Society, 274(1608), 303–313. https://doi.org/10.1098/rspb.2006.3721

Kroeger, T., Klemz, C., Boucher, T., Fisher, J. R. B., Acosta, E., Cavassani, A. T., … Dacol, K. (2019). Returns on investment in watershed conservation: Application of a best practices analytical framework to the Rio Camboriú Water Producer program, Santa Catarina, Brazil. Science of The Total Environment, 657, 1368–1381. https://doi.org/10.1016/j.scitotenv.2018.12.116

Nevle, R. J., & Bird, D. K. (2008). Effects of syn-pandemic fire reduction and reforestation in the tropical Americas on atmospheric CO2 during European conquest. Palaeogeography, Palaeoclimatology, Palaeoecology, 264(1–2), 25–38. https://doi.org/10.1016/j.palaeo.2008.03.008

Rasmussen, L. V., Coolsaet, B., Martin, A., Mertz, O., Pascual, U., Corbera, E., … Ryan, C. M. (2018). Social-ecological outcomes of agricultural intensification. Nature Sustainability, 1(6), 275–282. https://doi.org/10.1038/s41893-018-0070-8

Springmann, M., Clark, M., Mason-D’Croz, D., Wiebe, K., Bodirsky, B. L., Lassaletta, L., … Willett, W. (2018). Options for keeping the food system within environmental limits. Nature. https://doi.org/10.1038/s41586-018-0594-0

Tallis, H. M., Hawthorne, P. L., Polasky, S., Reid, J., Beck, M. W., Brauman, K., … McPeek, B. (2018). An attainable global vision for conservation and human well-being. Frontiers in Ecology and the Environment, 1–8. https://doi.org/10.1002/fee.1965

Van Zanten, H. H. E., Herrero, M., Hal, O. Van, Röös, E., Muller, A., Garnett, T., … De Boer, I. J. M. (2018). Defining a land boundary for sustainable livestock consumption. Global Change Biology, (April). https://doi.org/10.1111/gcb.14321

Woodard, J. D., & Verteramo-Chiu, L. J. (2017). Efficiency impacts of utilizing soil data in the pricing of the federal crop insurance program. American Journal of Agricultural Economics, 99(3), 757–772. https://doi.org/10.1093/ajae/aaw099

Monday, December 3, 2018

December 2018 science journal article summary

Cool insect eggs (Harlequin bug)

Greetings,

Here are some articles focused on pest control (the photo above is of harlequin bug eggs on kale), food safety, climate change, evidence, and even beer! Let me know if you need a copy of any of them. If you know someone who wants to sign up to receive these summaries, they can do so at http://bit.ly/sciencejon


CLIMATE CHANGE / NATURAL CLIMATE SOLUTIONS:
Almost everyone who works for or closely with The Nature Conservancy heard about the 2017 "Natural Climate Solutions" paper (Griscom et al. 2017, I reviewed it in November 2017). If you've been waiting for the sequel - good news! Fargione et al. 2018 just provided a similar analysis specifically for the United States. It's short, excellent, and worth reading, but if you're impatient skip to Figure 1. That summarizes the potential of each pathway and splits out how much is achievable at different carbon prices. They found a maximum potential of 1.2 Pg (aka 1200 million metric tons) CO2e / yr (21% of current US emissions and ~27% of 2005 emissions), and ~300 Tg (million metric tons) achievable at $10 / t CO2e (~5% of US emissions). The biggest low cost opportunities are in planting cover crops followed by forest management, avoided habitat conversion, and improved farm nutrient management. You can read more about it on TNC's web site at https://www.nature.org/en-us/explore/newsroom/natural-climate-solutions-study/ or at https://eurekalert.org/pub_releases/2018-11/cu-nsr111418.php

ORGANIC AGRICULTURE / FOOD SAFETY:
This is an interesting study on how consumption of organic vs. conventional foods affects cancer risk. They did find the people who ate the most organic food had 24% less cancer compared to the people who ate the least (even after controlling for quite a few lifestyle and diet variables, see Model 3 in Table 2). Unfortunately, they didn't test for pesticide residue (to confirm the hypothesis that pesticide was driving these results), there was a short follow-up time, they used a single unvalidated diet assessment, and there are enough odd findings (e.g. finding processed meat intake doesn't intake cancer risk) to make me suspect they didn't discover a causative relationship. I also don't understand how their model could find the organic diet has such a strong impact on cancer but then find that people eating a high quality diet AND lots of organic food didn't have reduced risk relative to those eating a low quality diet and little organic food (and supplemental table 6 looks like there IS a reduced risk although perhaps the confidence interval is too high to state it definitively). In short, this was an interesting paper but I don't think it is strong evidence for the conclusions they present. You can read a blog about this one at https://www.nytimes.com/2018/10/23/well/eat/can-eating-organic-food-lower-your-cancer-risk.html


EVIDENCE & DECISION MAKING:
To be effective in conservation, we need reliable evidence about the impact of different actions and strategies. This lets us focus on the strategies that will best help us reach our goals. Game et al. 2018 (led by TNC's Eddie Game) has timely guidance for how scientists should assess the quality of evidence (across multiple disciplines). They recommend beginning with a results chain to map out causal associations between actions, intermediate results, and outcomes, and then looking for the evidence of each link. They also note that in conservation a broader approach is needed than in other disciplines like medicine. The key point is the set of four principles they use to assess the strength of evidence. They are: variety (multiple types of evidence available), consistency (the evidence has consistent findings), credibility (the evidence comes from trusted sources), and applicability (the evidence matches the context of the issue being evaluated). You can read a blog about the paper at https://sustainabilitycommunity.nature.com/channels/1385-behind-the-paper/posts/38893-required-rethink-on-what-is-evidence

Bennett et al. 2018 is an attempt to make value of information (VOI) theory more practical. While still theoretical, they show how to apply VOI theory across multiple "management units." In each unit, the model compares two choices: acting with existing imperfect information, or doing more monitoring to support decision making. The revised model is a step forward, and I also enjoyed the discussion of limitations. For example, they mention that their model is risk neutral, which is often not the case with real decision makers.


CLIMATE CHANGE & BEER:
As we approach a major holiday season in the U.S., many people celebrate with alcohol. Xie et al. 2018 has a dire warning from the ghost of Christmas future: climate change may reduce barley yields (3-17%) and beer supply while driving up prices. Essentially they predict worsening drought and extreme heat will reduce barley production, and that during extreme years barley for beer will be reduced in favor of livestock feed and direct consumption. See Figure 3 for a nice summary of patterns of barley use by country now and under climate change. Some important limits: they don't predict future demand for beer (likely to increase), and they don't look at adaptation (e.g. making more beer w/ rice and corn as some major brewers do already, improved seed genetics, etc.). These caveats reinforce my skepticism of some predictions such as the price of beer in Ireland almost doubling (it's hard to imagine that could happen without a strong adaptive response). Nonetheless, most science predicting future food demand and supply focuses more on staples than luxuries, and this is an interesting twist.


REFERENCES:
Baudry, J., Ke, A., Touvier, M., Allès, B., Seconda, L., Latino-Martel, P., … Kesse-Guyot, E. (2018). Association of Frequency of Organic Food Consumption with Cancer Risk: Findings From the NutriNet-Santé Prospective Cohort Study. JAMA Internal Medicine. https://doi.org/10.1001/jamainternmed.2018.4357

Bennett, J. R., Maxwell, S. L., Martin, A. E., Chadès, I., Fahrig, L., & Gilbert, B. (2018). When to monitor and when to act: Value of information theory for multiple management units and limited budgets. Journal of Applied Ecology, 55(January), 2102–2113. https://doi.org/10.1111/1365-2664.13132

Deutsch, C. A., Tewksbury, J. J., Tigchelaar, M., Battisti, D. S., Merrill, S. C., Huey, R. B., & Naylor, R. L. (2018). Increase in crop losses to insect pests in a warming climate Downloaded from. Science, 361(August), 31. https://doi.org/10.1126/science.aat3466

Fargione, J. E., Bassett, S., Boucher, T., Bridgham, S. D., Conant, R. T., Cook-patton, S. C., … Griscom, B. W. (2018). Natural climate solutions for the United States. Science Advances, 4(November).

Game, E. T., Tallis, H., Olander, L., Alexander, S. M., Busch, J., Cartwright, N., … Sutherland, W. J. (2018). Cross-discipline evidence principles for sustainability policy. Nature Sustainability, 1(9), 452–454. https://doi.org/10.1038/s41893-018-0141-x

Karp, D. S., Chaplin-Kramer, R., Meehan, T., Martin, E., DeClerck, F., Grab, H., … Zou, Y. (2018). Crop pests and predators exhibit inconsistent responses to surrounding landscape composition. Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1800042115

Waterfield, G., & Zilberman, D. (2012). Pest Management in Food Systems: An Economic Perspective. Annual Review of Environment and Resources, 37, 223–247. https://doi.org/10.1146/annurev-environ-040911-105628

Xie, W., Xiong, W., Pan, J., Ali, T., Cui, Q., Guan, D., … Davis, S. J. (2018). Decreases in global beer supply due to extreme drought and heat. Nature Plants. https://doi.org/10.1038/s41477-018-0263-1



Sincerely,

Jon

p.s. as a reminder, you can search all of the science articles written by TNC staff (that we know of) here http://www.conservationgateway.org/ConservationPlanning/ToolsData/sitepages/article-list.aspx
(as you publish please email science_pubs@tnc.org to help keep this resource current).
If you'd like to keep track of what I write as well as what I read, I always link to both my informal blog posts and my formal publications (plus these summaries) at http://sciencejon.blogspot.com/

Thursday, November 1, 2018

November 2018 science journal article summary

Hi there,

Here are some mixed articles focused on general conservation, global agriculture, no-till farming, and remote sensing. Let me know if you need a copy of any of them. If you know someone who wants to sign up to receive these summaries, they can do so at http://eepurl.com/diB0nr

Also for anyone attending TNC's Global Science Gathering in Houston - let me know if you'd like to join for a side meeting for scientists working on sustainable agriculture.

CONSERVATION (GENERAL):
For over a year now, TNC staff have been hearing about a science analysis asking whether it's possible for both people and nature to thrive (in a shared conservation vision). Tallis et al 2018 is the newly available science paper behind that analysis. It compares two 2050 global scenarios: business as usual (BAU), and one designed to improve human and environmental outcomes (Sustainability). The latter would result in 577 million ha more habitat than BAU, while limiting climate change, improving air quality, and more. It doesn't assume we can drastically change diets, and sticks with biophysical constraints, but it does recognize that there are major social, economic, and political barriers to making the sustainability scenario a reality. The discussion has several thoughtful limits and caveats, but it's still exciting to see what is at least possible, if not easy to achieve. You will have to read the supplemental material to get a good sense of the work, but the main paper is conveniently short. One final note is that they assume climate change won't impact ag much in either scenario, which is optimistic. You can read all about the paper and its findings here: https://www.nature.org/en-us/what-we-do/our-insights/perspectives/the-science-of-sustainability/?vu=r.v_twopaths

The Nature Conservancy has recently shifted priorities away from land protection in general, to focusing on larger areas (to reduce fragmentation and improve resilience). Armsworth et al. 2018 asks how that focus affects the ecological return on investment (ROI). They found that larger areas are the most efficient way to improve connectivity and reduce fragmentation, offering 2-3 times the ecological return compared to small sites (TNC can buy properties that are 10x the size for just 5x the cost). However, smaller areas offer 5-8 times the ecological ROI for the number of species protected. Optimizing for species persistence rather than simply presence again favors larger areas (although the authors caution that this finding may be an artefact). These findings aren't surprising, but they are an important reminder that protecting some small areas will likely be important to protect endemic species.

GLOBAL AGRICULTURE:
Springman et al. 2018 asks what it would take to sharply reduce the impact of global food production by 2050 (and stay within resource constraints) without simply offsetting impacts like GHGs through reforestation or other mitigation. They look at 3 options (diet change, tech and management, and  reducing food waste) across 5 aspects: GHGs, fresh water use, land use, nitrogen, and phosphorous. They key finding is that no one category of solution is enough, and that for GHGs in particular major diet change (towards mostly plant based foods) would have to be part of the solution. Figure 3 summarizes this set of scenarios nicely. With their medium ambition scenario, they find halving food loss and waste improves impact 6-16% (relative to 2050), improving tech and management reduces impact 3-30%, and modest diet change improves 5-29% (see Figure 2), or they could all be combined for a 25-45% reduction. Note that their findings are global averages, and some places will deviate considerably (e.g. they find nuts and seeds don't account for much overall water use, but in places like California they have a big water footprint). Check the methods for country-level data. You can read two articles about this study here: https://www.washingtonpost.com/health/2018/10/10/how-will-or-billion-people-eat-without-destroying-environment/ and here: https://www.theguardian.com/environment/2018/oct/10/huge-reduction-in-meat-eating-essential-to-avoid-climate-breakdown

Pretty et al. 2018 has good news - they show improvements in global implementation of several forms of sustainable agricultural practices. They focus on practices that they see as representing "redesign" of agriculture as part of sustainable intensification or "SI" (offering yield and environmental benefits). This includes integrated pest management (IPM), conservation agriculture / soil health practices, and several others. They find some form of "SI" practices on 29% of global farms covering 9% of global agricultural land (crop and pasture). This shows progress is being made (although much remains to do). However, one caveat is not apparent in the paper: they define these practices as inherently intensifying or yield-promoting, but do NOT filter on farms where actual increases in yield have been measured. That's important as each of these practices has the potential to boost or reduce yield depending on how it's implemented, so it's unlikely that all of these farms actually represent true sustainable intensification. The lead author told me in a message that in developing nations would always be "win-win," and in more industrialized countries environmental benefits improved but yields could go up or down or stay the same.

Williams et al. 2018 is another paper on the land sparing vs. land sharing debate, focusing on carbon stocks. They use a mix of interviews and field data to model relationships between agricultural yield and above ground carbon, and then do a bit of modeling. They found that as crop yields go up, above ground carbon goes down (as expected). Nonetheless, across the landscapes they looked at, land sparing led to the most C stocks compared to land sharing or intermediate strategies. There are a few caveats which they helpfully admit to. First, results could vary for other environmental outcomes like water quality. They didn't look at social impacts (from either farms or ecosystem services from habitat). They don't look at methane or nitrous oxide, so for intense systems with inefficient fertilizer use the C benefit would be reduced. Finally, land sparing will not happen on its own - making farms more profitable gives them incentive to clear more habitat unless there are countervailing factors (e.g. zoning, taxes or penalties for clearing, incentives, etc.). You can read a blog about this one at https://www.npr.org/sections/thesalt/2018/08/03/634344754/which-vision-of-farming-is-better-for-the-planet

AGRICULTURE / NO-TILL:
Two recent papers (both Daryanto et al. 2017) find that no-till (NT) farming can increase the loss of nutrients under some conditions. They found that NT often increases loss of nitrate (NO3-) - generally there is similar or less runoff, but more leaching. But results vary across soil textures, climate, and crop management.

For phosphorous (P), overall NT led to lower nutrients ending up in aquatic ecosystems, and less  particulate P export (except during wet years). But it increased dissolved P loss. There are lots of caveats and conditions on the results (e.g. no-till most effectively reduced particulate P from 0-3% slope, but on 4-9% slopes it actually increased P load), so it's worth reading the papers in full. A key finding of both papers is that NT has to be combined with other practices to be effective in reducing nutrient loss, that it doesn't work as well in dryland regions, and that NT benefits decrease over time so they  recommend occasional tillage (once every ~10 years) despite likely tradeoffs in soil carbon. TNC’s Carrie Vollmer-Sanders has seen similar results for P. She recommends a focus on fertilizer placement (subsurface when possible), periodic tillage (every ~10 years), and strip tillage when it’s dry enough. There's a paper about the P results here: https://www.cornandsoybeandigest.com/fertilizer/no-till-benefits-challenged

REMOTE SENSING:
Seifert et al. 2018 has two parts: a remote sensing method to detect cover crops, and an analysis of their impact on crop yields. For remote sensing, "accuracy" is complicated but their method correctly identified whether or not cover crops were present 92% of the time, which is 68% better than expected by chance alone. They relied on readily available data, so this method should be applicable elsewhere. The second piece is that they found cover crops are grown on poor performing field (presumably in an effort to improve soils as they tended to be on poor soils). After a year of cover cropping corn yields went up on average by 0.65%, and soy by 0.35%, but read the results on p6 as there's a lot of variation (from long term cover crops reducing yields, or only improving after several years, etc., varying by state and crop). Hopefully making it easier to detect cover crops will improve our ability to understand their impacts.

If you've ever done remote sensing work in the tropics, you've noticed that you often want imagery when plants are growing, aka the rainy season when clouds limit available imagery. Pedraza et al. 2018 (from several TNC colleagues and their partners) uses radar data (ALOS PALSAR, which can see through clouds) to look for farm-level deforestation in Colombia. It worked reasonably well, mostly between 62% and 100% accurate: see table 4, focusing on user and producer accuracy as overally accuracy is skewed by the high proportion of nonforest. They found that accuracy was lower in dry forests and mountainous terrain, although they improved it by integrating some optical data. It's a useful paper for anyone looking at integrating radar data for tropical remote sensing.

REFERENCES:
Armsworth, P. R., Jackson, H. B., Cho, S. H., Clark, M., Fargione, J. E., Iacona, G. D., … Sutton, N. A. (2018). Is conservation right to go big? Protected area size and conservation return-on-investment. Biological Conservation, 225(November 2017), 229–236. https://doi.org/10.1016/j.biocon.2018.07.005

Daryanto, S., Wang, L., & Jacinthe, P.-A. (2017). Impacts of no-tillage management on nitrate loss from corn, soybean and wheat cultivation: A meta-analysis. Scientific Reports, 7(1), 12117. https://doi.org/10.1038/s41598-017-12383-7

Daryanto, S., Wang, L., & Jacinthe, P. A. (2017). Meta-analysis of phosphorus loss from no-till soils. Journal of Environmental Quality, 46(5), 1028–1037. https://doi.org/10.2134/jeq2017.03.0121

Pedraza, C., Clerici, N., Forero, C., Melo, A., Navarrete, D., Lizcano, D., … Galindo, G. (2018). Zero Deforestation Agreement Assessment at Farm Level in Colombia Using ALOS PALSAR. Remote Sensing, 10(9), 1464. https://doi.org/10.3390/rs10091464

Pretty, J., Benton, T. G., Bharucha, Z. P., Dicks, L. V, Flora, C. B., Godfray, H. C. J., … Wratten, S. (2018). Global assessment of agricultural system redesign for sustainable intensification. Nature Sustainability, 1(8), 441–446. https://doi.org/10.1038/s41893-018-0114-0

Seifert, C. A., Azzari, G., & Lobell, D. B. (2018). Satellite detection of cover crops and their effects on crop yield in the Midwestern United States. Environmental Research Letters, 13(6). https://doi.org/10.1088/1748-9326/aac4c8

Springmann, M., Clark, M., Mason-D’Croz, D., Wiebe, K., Bodirsky, B. L., Lassaletta, L., … Willett, W. (2018). Options for keeping the food system within environmental limits. Nature. https://doi.org/10.1038/s41586-018-0594-0

Tallis, H. M., Hawthorne, P. L., Polasky, S., Reid, J., Beck, M. W., Brauman, K., … McPeek, B. (2018). An attainable global vision for conservation and human well-being. Frontiers in Ecology and the Environment, 1–8. https://doi.org/10.1002/fee.1965

Williams, D. R., Phalan, B., Feniuk, C., Green, R. E., Williams, D. R., Phalan, B., … Balmford, A. (2018). Carbon Storage and Land-Use Strategies in Agricultural Landscapes across Three Continents. Current Biology, 28(15), 2500–2505. https://doi.org/10.1016/j.cub.2018.05.087


Sincerely,

Jon

p.s. as a reminder, you can search all of the science articles written by TNC staff (that we know of) here http://www.conservationgateway.org/ConservationPlanning/ToolsData/sitepages/article-list.aspx
(as you publish please email science_pubs@tnc.org to help keep this resource current).
If you'd like to keep track of what I write as well as what I read, I always link to both my informal blog posts and my formal publications (plus these summaries) at http://sciencejon.blogspot.com/

Monday, October 1, 2018

October 2018 science journal article roundup

Greetings,

Here is a short set of articles on potato cultivation, groundwater, and cattle and rangelands.

If you know someone who wants to sign up to receive these summaries, they can do so at http://eepurl.com/diB0nr

POTATO CULTIVATION:
Drakopolous et al. 2016 found that reduced tillage for potatoes led to 13% lower yields (smaller tubers) but also led to higher quality and nitrogen efficiency. The quality boost wasn't enough to offset yield loss and result in net economic benefit from reduced tillage.

Myrick 2016 is a masters thesis investigating adoption (and abandonment) of a potato variety resistant to late blight (C-88) in Yunnan, China. They found smaller farmers and those closer to cities were less likely to grow it, although they noted access to seed is very limited so decisions may largely be driven by which varieties extension agents promote. The appendix has some interesting (and at times, conflicting) data on farmer perceptions.

GROUNDWATER:
Jasechko et al. 2017 makes two important points about groundwater. The first is that between 42-85% of groundwater in the upper 1 km of the ground is over 12,000 years old, as is more than half the water pumped from deeper than 250m (highlighting challenges with pumping out "fossil" water which will be very slow to recharge). The other is that while the water is very old,  half of the wells showed contamination with tritium (a radioactive isotope mostly present in the environment from nuclear weapons and testing, showing relatively recent contamination). In other words, groundwater which took millennia to recharge and get clean is being contaminated more rapidly.
You can read a blog about this one: http://www.bbc.com/news/science-environment-39715738

RANGELANDS / CATTLE / REMOTE SENSING:
Reeves and Baggett 2014 developed a relatively simple way to assess rangeland degradation using remote sensing. Essentially they compare rangelands to reference conditions (all rangelands within similar ecological classifications), and found relatively little degradation (with degradation trends almost undetectable). They list several reasons for this in the discussion, but from other work in this space I've read it seems that estimating grassland productivity and degradation remotely is fundamentally challenging and limited (especially without field data to calibrate on), and NDVI is not an ideal tool for grasslands for several reasons. Caution could be taken before assuming relatively simple remote sensing estimates of grassland condition are accurate and actionable.

Reeves et al. 2017 predicts how climate change will affect cattle in the western U.S., considering forage (quantity, interannual variability, and vegetation types) and hear stress. They expect more forage in the north, less woody plants and more grass (in general), more variation in forage quantity year to year, and more heat sress (starting 2020-2030), which taken together means more vulnerability of cattle in most places (especially in the Southwest). In northern areas, the impacts of heat stress are expected to offset the benefits of more forage (with some exceptions). The two top maps in Figure 3 has a good summary of net impacts on cattle by 2060 and 2100, with yellow to red indicating negative effects, and green to blue indicating positive ones.

REFERENCES:
Drakopoulos, D., Scholberg, J. M. S., Lantinga, E. A., & Tittonell, P. A. (2016). Influence of reduced tillage and fertilization regime on crop performance and nitrogen utilization of organic potato. Organic Agriculture, 6(2), 75–87. https://doi.org/10.1007/s13165-015-0110-x

Jasechko, S., Perrone, D., Befus, K. M., Bayani Cardenas, M., Ferguson, G., Gleeson, T., … Kirchner, J. W. (2017). Global aquifers dominated by fossil groundwaters but wells vulnerable to modern contamination. Nature Geoscience, (April), 1–6. https://doi.org/10.1038/ngeo2943

Myrick, S. N. B. (2016). An Economic Impact Assessment of Cooperation-88 Potato Variety in the Yunnan Province of China. Virginia Polytechnic Institute and State University.

Reeves, M. C., & Baggett, L. S. (2014). A remote sensing protocol for identifying rangelands with degraded productive capacity. Ecological Indicators, 43, 172–182. https://doi.org/10.1016/j.ecolind.2014.02.009

Reeves, M. C., Bagne, K. E., & Tanaka, J. (2017). Potential Climate Change Impacts on Four Biophysical Indicators of Cattle Production from Western US Rangelands. Rangeland Ecology and Management, 70(5), 529–539. https://doi.org/10.1016/j.rama.2017.02.005


Sincerely,

Jon

p.s. as a reminder, you can search all of the science articles written by TNC staff (that we know of) here http://www.conservationgateway.org/ConservationPlanning/ToolsData/sitepages/article-list.aspx

Monday, September 3, 2018

September 2018 science journal article roundup



Aloha,

This is the 50th of these science summaries, and somehow I am still not caught up with all the interesting papers I have! For that occasion, I'm tackling a number of papers that didn't group nicely but still looked relevant. So there are papers on GMOs, fertilization and nitrogen fixation, food security, and Chinese ag.


GMOs:
You've probably heard the debate about whether or not to label genetically engineered / modified food. On the one hand, consumers argue that food should be transparent about its origins to enable consumers to choose. The counterargument has been that since there isn't good evidence that GMOs can harm human health, it could result in consumers thinking it's being labeled b/c it's dangerous. But Kolodinsky and Lusk (2018) have some surprising good news - after GMO labels became mandatory in Vermont, consumer concern / opposition to GMOs actually went down (while in other states there was a non-significant small increase)! Figure 1 shows this graphically. However, after looking at Table 1 I'm less convinced as they have data for five points in time, and concern in the most recent data is about the same as the earliest data. So the finding could be an artifact of how they did their regression, but it's still a promising possibility worth looking into to better understand how these kinds of
labels may affect consumer beliefs.

Cheke 2018 is a commentary on how the use of pest control traits by GM crops can have unintended side-effects, just as traditional chemical pesticide use can. He presents brief interesting case studies, and essentially argues that we need long-term monitoring data to understand how novel forms of pest control impact target pests, non-target pests, and natural predators of pests. To be clear, this isn't an anti-GM paper, it just notes that switching from aerial sprays to toxins within the plant may have unintended consequences. See Zhang et al. 2018 under Chinese Agriculture below for more detail on Bt cotton as a case study.


FOOD SECURITY:
Hasegawa et al. 2018 is an analysis of how climate mitigation may impact food security. They find that climate mitigation may cause more hunger than the direct effects of climate change. Livestock in particular would be more expensive (given higher GHG emissions and land use). The primary drivers would be food price increases driven by: tax on GHG emissions, higher land rents if ag expansion is slowed, and land competition by biofuel. However, this outcome isn't inevitable if policy is crafted more carefully. For example, a tax focused on animal products could drive a shift to producing more food consumable directly by humans, and revenue could be used for food aid. The key questions are thinking about who will bear the costs of implementation, and how it may affect food prices and thus food security for poor people in particular.


AGRICULTURE / NITROGEN FIXATION / FERTILIZER:
Van Deynze et al 2018 has been getting lots of press. The authors describe a landrace (local cultivar) of maize in Mexico that can fix its own nitrogen via microbes that hang out in aerial roots covered in goopy sugary mucilage. The authors did isotope tracing to verify that N was coming from the air and entering the aerial roots. Since corn uses tons of fertilizer, having it make its own sounds pretty exciting. In this case, it allows corn to be grown in nitrogen-depleted fields in Mexico, with ~30-80% of needed nitrogen coming from the air (varying by field and growth stage, but often ~50%). Unfortunately, this type of N-fixation is not as efficient as how legumes do it, and N-fixing maize is not brand new (Steve Wood sent me this paper from 1975 on the topic: http://www.pnas.org/content/72/6/2389.short). But (as Steve also pointed out) this is a pretty understudied area and there's a lot we don't know about the potential, which if nothing else shows the value in promoting crop diversity
so we don't lose potentially useful varities like this!
See https://news.wisc.edu/corn-that-acquires-its-own-nitrogen-identified-reducing-need-for-fertilizer/ for a blog post on this research.

Given how much research there is on trying to get crops to fix their own nitrogen, the finding by Griesmann et al. 2018 that many plants have lost the ability to fix N blew my mind. By comparing genomes of N-fixing plants to those that don't, they were able to find that ~3/4 of the species in their sample that didn't fix N had an ancestor that could! They suggest that the fact this ability has been lost multiple times reflects that plants spend a lot of energy to support N fixation, and that when N levels are adequate in the soil they eventually can lose the ability to fix it. In other words, as we try to engineer plants to fix their own N, it's worth reflecting on the costs that may have led plants in the past to reject this evolutionary path.
There's a blog on this one at http://www.sciencemag.org/news/2018/05/many-plants-need-bacterial-roommates-survive-so-why-do-some-kick-them-out

Chen et al. 2018 takes a different approach to improving fertilizer use in ag. They provide a review of possible ways to improve the environmental impacts of making chemical nitrogenous fertilizer. Currently the Haber-Bosch process relies on methane, so getting hydrogen from water instead could have many benefits if the higher energy cost can be overcome. This is a pretty technical paper but the first page is an overview that is much more accessible and introduces the possibilities.


CHINESE AGRICULTURE:
Zuo et al 2018 is a nice dense analysis of how Chinese agriculture has changed over the past ~20 years, focusing on crop yield and five environmental indicators (irrigation water, excess N, excess P, land use, and GHGs). While total crop calories produced increased by 66% (with only 1% more net land use), and environmental intensity (impact per calorie) went down, the total environmental impact still worsened quite a bit. This is a common challenge in sustainable intensification - it's often relatively easy to boost yields, but challenging to reduce actual impacts to the environment at the same time. The authors also note that urbanization has pushed cropland to more marginal and water-scarce areas, and future shifts in cropland may pose further challenges. This is worth reading in its entirety for anyone working in Chinese ag, but Table 1 summarizes the changes well, and Figure 3 is an intriguing map with potential priority areas to focus on different indicators.

Zhang et al. 2018 is a look at the impacts of planting Bt cotton (genetically engineered to produce the Bt toxin) in China on three major pests, and how that relates to farm management and nearby land use. The good news is that the use of Bt cotton decreased spraying for bollworm, which in turn allowed natural predators of aphids to recover (which reduced aphid population). Unfortunately, the reduced spraying also allowed mirid bugs to increase. Figure 3 shows how the infestations and spraying changed over time as Bt cotton was rolled out. These trade-offs show the need to think holistically about pest control. Farms in landscapes with more non-farm land use (urban, water, forest, grass, 'unused') had less aphids and mirid bugs (but bollworms were unaffected, and other research has found diverse land use may promote mirid bugs). Finally, farmers were found to spray for aphids and bollwords at non-damaging levels, which represents a missed opportunity to increase their profits (via reduced
costs) and improve their sustainability.


REFERENCES:
Cheke, R. A. (2018). New pests for old as GMOs bring on substitute pests. Proceedings of the National Academy of Sciences, 201811261. https://doi.org/10.1073/pnas.1811261115

Chen, J. G., Crooks, R. M., Seefeldt, L. C., Bren, K. L., Bullock, R. M., Darensbourg, M. Y., … Schrock, R. R. (2018). Beyond fossil fuel–driven nitrogen transformations. Science, 360(6391), eaar6611. https://doi.org/10.1126/science.aar6611

Griesmann, M., Chang, Y., Liu, X., Song, Y., Haberer, G., Crook, M. B., … Cheng, S. (2018). Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis. Science, 361(6398). https://doi.org/10.1126/science.aat1743

Hasegawa, T., Fujimori, S., Havlík, P., Valin, H., Bodirsky, B. L., Doelman, J. C., … Witzke, P. (2018). Risk of increased food insecurity under stringent global climate change mitigation policy. Nature Climate Change, 8(8), 699–703. https://doi.org/10.1038/s41558-018-0230-x

Kolodinsky, J., & Lusk, J. L. (2018). Mandatory Labels can Improve Attitudes toward Genetically Engineered Food. Science Advances, In press(June), 1–6. https://doi.org/10.1126/sciadv.aaq1413

Van Deynze, A., Zamora, P., Delaux, P., Heitmann, C., Jayaraman, D., Rajasekar, S., … Bennett, A. B. (2018). Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota. PLOS Biology, 16(8), e2006352. https://doi.org/10.1371/journal.pbio.2006352

Zhang, W., Lu, Y., Werf, W. Van Der, Huang, J., Wu, F., Zhou, K., & Deng, X. (2018). Multidecadal, county-level analysis of the effects of land use, Bt cotton, and weather on cotton pests in China. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1721436115

Zuo, L., Zhang, Z., Carlson, K. M., MacDonald, G. K., Brauman, K. A., Liu, Y., … West, P. C. (2018). Progress towards sustainable intensification in China challenged by land-use change. Nature Sustainability, 1(6), 304–313. https://doi.org/10.1038/s41893-018-0076-2

Wednesday, August 1, 2018

August 2018 Science Journal Roundup

Hello,

It's grilling season (at least in the US), and lately I've been getting lots of articles about animal protein and sustainability. Some are on the impact of animal foods and how much we can sustainably consume, and others are on the details of livestock management and production. There's also one paper finding that agricultural intensification has rarely led to positive outcomes for both humans and the environment.

Incidentally, the photo above is of a new plant-based sausage that's good enough to be selling out within hours whenever they're stocked!

ANIMAL FOODS / DIET:
VanZanten et al. 2018 is a really thoughtful paper that takes a refreshing approach to looking at the environmental impact of animal foods in our diet. They note that while using arable land to feed livestock (rather than directly feeding humans) is inherently inefficient, there are some grasslands, food waste, and food by-products like distillers grains that humans can't eat. So to minimize land used to feed the world, ~10% of calories (& ~1/3 of protein needed) could come from animal foods. Fig 4 shows how animal consumption in different regions compares to the protein goal, and Fig 5 shows a similar breakdown for calories and other nutrients. They cover how different animals fit in (e.g. ruminants for grasslands, pigs for food waste, etc.), noted that GHGs are still higher in their scenario than an all-vegan diet, and cover several interesting caveats and twists. One thing they didn't mention - some of the underlying studies have a large role for milk, which people have trouble digesting in many places around the world. But is is a really well done paper and I highly recommend it.

Mottet et al. 2017 also looks at how much animal food relies on food humans can't eat, although it's more optimistic about the impact of livestock than most similar studies. They make several interesting points like the utility of livestock as draught animals and providing manure for crops, as well as estimating that globally only 2.8-3.2 kg of human edible feed is needed to produce 1 kg of meat (2.8 for ruminants like cows, 3.2 for monogastrics like chicken and pigs). Those numbers are lower than what's usually cited but I don't think I've seen it calculated only for the human edible fraction of feed.

Poore and Nemecek is a useful comprehensive global reference on the impact of different foods and diets (and how consumers and producers can reduce those impacts) but it's dense and somewhat hard to read and unpack. They note several opportunities to improve on the production side, but also that animal foods are much higher impact than similar plant foods, arguing consumer diet choice is a key part of sustainability. They call for better systems to measure and communicate about sustainability to consumers. Two things to watch out for: when they say even the lowest impact animal foods are higher impact than plant substitutes, they exclude tree nuts, and in the figures with tons of little charts and graphs note that the scale of the axes changes often.

Godfray et al. 2018 is a nice summary of recent and predicted trends in meat consumption, plus impacts on human health and the environment. They conclude with thoughts about possible ways to shift diets to counteract the growth in demand for animal foods (with Denmark's saturated fat tax one real world example). There's no big new message here, but lots of good tidbits sprinkled throughout and it covers quite a few related topics. I found two figures especially interesting - 1c shows the potential impact of a carbon tax on the price and consumption of different animal foods, and 3a shows the current and projected 2050 allocation of ag GHGs by food type (both plant and animal).
 

AGRICULTURAL INTENSIFICATION:
Rasmussen et al. 2018 is a global review of whether or not agricultural intensification is good for both people and the environment. While they find income and food production generally go up, ecosystem services go down in most cases. The figures have great summaries of results by geography, by metric of ecosystem services or human well being, and by separating 'win-win' cases from 'lose-lose' and mixed results in different contexts. The specific case studies are very interesting and thought provoking. Surprisingly, increased inputs were more likely to lead to win-win outcomes, with crop changes as reduced fallow more likely to lead to lose-lose. This is a relatively understudied area (this paper summarizes 53 studies) given the importance of intensification strategies; the lack of evidence for consistent positive outcomes doesn't mean intensification CAN'T work, but shows more work (design and monitoring) is needed to ensure we succeed in our goals. See https://www.scidev.net/global/agriculture/news/intensified-farming-rarely-aids-wellbeing-environment.html for a blog on the subject.


LIVESTOCK PRODUCTION:
Smith et al. 2017 tackle an important question - how much of corn grown in the US is used for livestock, and where is it sourced from? It sounds simple, but is complex since lots of corn is used for ethanol but the leftovers ("distiller's grains") are still used for feed. Figure 3 is a fascinating map series showing where corn is grown to supply ethanol refineries, broiler chickens, hogs, and beef, and it gives you a sense of the supply chain complexity around corn. The authors find that only 59% of US corn is used by these four sectors, which makes me fairly certain that they're missing some livestock (e.g. this probably omits dairy and perhaps some poultry since typically ethanol + livestock are reported as using >80% of US corn). That 59% is made up of 25% for ethanol, 14% for beef, 12% for pork, and 8% for broilers. I need to dig into the data to verify but I'd guess poultry overall should be considerably higher. Regardless, this is a super interesting paper with some novel findings.

Van Boeckel et al. 2017 looks at the role of antimicrobials in livestock production, and argues for reductions (whether through a policy capping levels used, reducing overall production of livestock and animal foods, or charging a fee on antimicrobials sold for use by nonhumans). They explore all three options and conclude that a mixture could be an effective way to reduce usage of antiomicrobials by livestock by up to 80%.

Pelletier 2008 answers a question I've been hearing a lot lately - where are the biggest opportunities to improve the impact of poultry production? He finds that it's all about the feed - on average across multiple dimensions (energy, GHGs, water pollution, etc.) ~90% of impact comes from feed and ~10% from on-farm management (mostly heating and ventilation). Note that this study is limited to the US, and that they assumed all poultry litter had a net positive impact by displacing the use of synthetic fertilizer (which may not be valid everywhere). He finds that the animal fraction of poultry feed (especially poultry fat, poultry trimmings, and fishmeal) have much higher impact than the plant portion of the diet, indicating that unless the animal-based feed would otherwise be wasted, overall impact could be improved by shifting to a higher percentage of plant foods.

If you've ever been to a hog farm, you likely noticed the smell. In addition to being unpleasant, it can cause air quality problems affecting both human health and GHGs. Maurer et al. 2017 was a pilot study to see if biochar could help. It didn't work very well. They found that the highest dose of biochar reduced ammonia emissions moderately but increased methane emission, with H2S (rotten egg smell) and N2O unaffected (and with lower doses having no significant effect).

York et al. 2017 is an interesting look at two ways to reduce GHGs in smallholder dairy farms in India - anaerobic digesters and controlling Foot and Mouth Disease. The government has been paying to install digesters and vaccinate cows, but the authors argue that digesters are actually INCREASING emissions, while the simpler vaccination approach reduces emissions ~4-13%. The authors make a lot of assumptions I can't speak to the validity of, but the underlying ideas seem to be that the digesters leak, and that since the manure is managed as a solid anyway the avoidable emissions are relatively low to begin with. They note that where manure is managed as a liquid (e.g. in North India) digesters would make more sense. To me this is a good reminder that low-tech cheap solutions like avoiding waste and lost productivity should be looked at before jumping to more pricy high-tech solutions. Fun fact - my parents told me I had foot and mouth disease as a baby, but apparently it's a different virus than the one livestock gets.

Crespi and Saitone 2018 is a bit esoteric - they look at the vertical integration of livestock in the US, comparing the beef industry to poultry and swine in particular. They dive into the specifics of different relationships between actors along the livestock supply chains, and why cattle haven't been as vertically integrated as other animals (longer life cycle, low relative cost of forage vs. farmed feed, spatial distribution of grazing lands vs. feedlots). They also note that the four largest beef packers in the US are moving away from integrated models. The primary relevance to conservation is that vertical integration makes it easier to drive changes in production through the entire supply chain (e.g. promoting conservation practices in growing feed or grazing).


REFERENCES:
Crespi, J. M., & Saitone, T. L. (2018). Are Cattle Markets the Last Frontier? Vertical Coordination in Animal-Based Procurement Markets. Annual Review of Resource Economics, (June), 1–21.

Godfray, H. C. J., Aveyard, P., Garnett, T., Hall, J. W., Key, T. J., Lorimer, J., … Jebb, S. A. (2018). Meat consumption, health, and the environment. Science, 361(243). https://doi.org/10.1126/science.aam5324

Maurer, D., Koziel, J., Kalus, K., Andersen, D., & Opalinski, S. (2017). Pilot-Scale Testing of Non-Activated Biochar for Swine Manure Treatment and Mitigation of Ammonia, Hydrogen Sulfide, Odorous Volatile Organic Compounds (VOCs), and Greenhouse Gas Emissions. Sustainability, 9(6), 929. https://doi.org/10.3390/su9060929

Mottet, A., de Haan, C., Falcucci, A., Tempio, G., Opio, C., & Gerber, P. (2017). Livestock: On our plates or eating at our table? A new analysis of the feed/food debate. Global Food Security, 14, 1–8. https://doi.org/10.1016/j.gfs.2017.01.001

Pelletier, N. (2008). Environmental performance in the US broiler poultry sector: Life cycle energy use and greenhouse gas, ozone depleting, acidifying and eutrophying emissions. Agricultural Systems, 98(2), 67–73. https://doi.org/10.1016/j.agsy.2008.03.007

Poore, J., & Nemecek, T. (2018). Reducing food’s environmental impacts through producers and consumers. Science, 992(6392), 987–992.

Rasmussen, L. V., Coolsaet, B., Martin, A., Mertz, O., Pascual, U., Corbera, E., … Ryan, C. M. (2018). Social-ecological outcomes of agricultural intensification. Nature Sustainability, 1(6), 275–282. https://doi.org/10.1038/s41893-018-0070-8

Smith, T. M., Goodkind, A. L., Kim, T., Pelton, R. E. O., Suh, K., & Schmitt, J. (2017). Subnational mobility and consumption-based environmental accounting of US corn in animal protein and ethanol supply chains. Proceedings of the National Academy of Sciences, 201703793. https://doi.org/10.1073/pnas.1703793114

Van Boeckel, T. P., Glennon, E. E., Chen, D., Gilbert, M., Robinson, T. P., Grenfell, B. T., … Laxminarayan, R. (2017). Reducing antimicrobial use in food animals. Science, 357(6358), 1350–1352. https://doi.org/10.1126/science.aao1495

Van Zanten, H. H. E., Herrero, M., Hal, O. Van, Röös, E., Muller, A., Garnett, T., … De Boer, I. J. M. (2018). Defining a land boundary for sustainable livestock consumption. Global Change Biology, (April). https://doi.org/10.1111/gcb.14321

York, L., He, C., & Rymer, C. (2017). A comparison of policies to reduce the methane emission intensity of smallholder dairy production in India. Agriculture, Ecosystems and Environment Environment, 246, 78–85. https://doi.org/10.1016/j.agee.2017.05.032


Sincerely,

Jon

p.s. as a reminder, you can search all of the science articles written by TNC staff (that we know of) here http://bit.ly/TNC_articles