18 Case Study #2 – Environment

Case study #2 – The Land is Sick

Disclaimer: This is a fictitious scenario created for the purposes of microbiome, health, disease, and environmental education. Any names, characters, places and incidents either are products of the author’s imagination or are used fictitiously. Any resemblance to actual events or locales or persons, living or dead, is entirely coincidental.

 

Part I – Background and Problem

Coffee production in South America has drastically decreased in the 2021-23 growing seasons. Specifically, the major farms in Columbia and Brazil which collectively contribute over half of each countries coffee (both specialty and commercial) production, have had severe crop failures. As a result, the price of a cup of coffee has noticeably increased, putting financial strain on suppliers and businesses.

 

Figure 1. Coffee exports by country 2019-20. Source: International Coffee Organization

 

Figure 2. A world map of countries by coffee production, 2019.

Interestingly, the few years prior to this decline, coffee production was at an all-time high, with more coffee in the market than demanded. This dropped the price of coffee, and in many cases original farmers were not fairly compensated.

The International Coffee Organization (ICO) has tasked a team of researchers to identify potential problems to South American coffee plant failure and provide quick and efficient resolution.

Article 1  – The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato

Article 2 – A review of three major fungal diseases of Coffea Arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya

Article 3 – Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei

Video 1 – The biggest threats to the coffee industry

Video 2 – #1 Specialty coffee and the price crisis | Producer Crossover 2019

Questions:

  1. As a scientific researcher, what are some factors you would take into consideration when addressing this problem?
  2. What type of environmental microbiomes could be implicated in coffee plant crop failure and why?
  3. Should other coffee farms in countries besides those in South America be worried about similar failure in their crops? Why or why not?

Attributions:

 

Case study #2 – The Land is Sick

Disclaimer: This is a fictitious scenario created for the purposes of microbiome, health, disease, and environmental education. Any names, characters, places and incidents either are products of the author’s imagination or are used fictitiously. Any resemblance to actual events or locales or persons, living or dead, is entirely coincidental.

 

Part II – Approach, Implementation, Reasoning

Upon initial inspection, the unhealthy coffee plants exhibited yellowing of leaves, appearance of red-brown lesions, abnormal shape, damaged coffee berries, and little new growth or production. Researchers decided to take samples of healthy and unhealthy leaves and berries, as well as soil and root samples.

 

Article 1 – Prokaryotic diversity in the rhizosphere of organic, intensive, and transitional coffee farms in Brazil

Article 2 – A metagenomics approach in the evaluation of the soil microbiome in coffee plantations under organic and conventional production in tropical agroecosystems

Video 1 – #2 Producer Crossover 2019

Video 2 – How countries farm and make coffee differently

 

Over the next year, other plantations in Columbia and Central American begin to experience similar declines in coffee plant health. Farmers were questioned about any changes in practices, and while there have been some adjustments do to the fluctuating coffee prices, traditional farming techniques have remained the same for the most part in smaller plantations. Larger plantations with intensive farming made more changes due to trader suggestions on improving yields including application of different fertilizers and hiring less experienced workers.

Questions:

  1. What type of analytical techniques do you think were or should be performed on the samples taken?
  2. How could the observed symptoms of the unhealthy plants be connected to an associated microbiome?
  3. How could human intervention exacerbate or ameliorate this situation?

Attributions:

 

 

Case study #2 – The Land is Sick

Disclaimer: This is a fictitious scenario created for the purposes of microbiome, health, disease, and environmental education. Any names, characters, places and incidents either are products of the author’s imagination or are used fictitiously. Any resemblance to actual events or locales or persons, living or dead, is entirely coincidental.

 

Part III – Discussion

Analysis of the negatively affected plantations’ soil showed a decline in plant growth promoting bacteria and mycorrhizae and an increase in bacterial and fungal pathogens like Pseudomonas syringae and Cercospora coffeicola.

Over the next few years (2022-24) coffee plants still struggle to grow in Central and South America. Other parts of the world, such as Vietnam and other Asian countries, are seeing a decline in crop health also, further contributing to global coffee market troubles. Many of these farms switched from shade-grown to intense sun-grown coffee to try to meet needs for demand. Larger corporations and roasters have purchased many of the smaller family farms to try to recoup losses and implement ‘new and improved’ growing strategies for increased production. This included switching to primarily sun-grown coffee, and application of large amounts of synthetic nitrogen fertilizer.

 

Shade grown coffee in Guatamala

Figure 1. Shade grown coffee in Guatemala

Figure 2. Sun-grown coffee plantation in Brazil

 

Video 1- #3 The future of the price crisis

Video 2 – How coffee destroys the environment

Article 1 – Root endophytes of coffee (Coffea Arabica): Variation across climatic gradients and relationships with functional traits

Article 2 – Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario

Article 3 – Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil

Questions:

  1. What factors could cause these changes in the soil microbiomes?
  2. Why do you think coffee plantations across the globe are beginning to fail as well?
  3. How does natural biodiversity benefit ecosystem health on both a micro and macro scale?

Attributions:

 

 

 

Case study #2 – The Land is Sick

Disclaimer: This is a fictitious scenario created for the purposes of microbiome, health, disease, and environmental education. Any names, characters, places and incidents either are products of the author’s imagination or are used fictitiously. Any resemblance to actual events or locales or persons, living or dead, is entirely coincidental.

 

Part IV – Resolution

In 2030, most varieties of coffee are extinct, and only small amounts of coffee are produced on shade grown farms further from the equator. It appears that coffee plantations were severely impacted by increasing global temperatures, which altered ecosystem dynamics and promoted pathogen and pest invasion. Fungi, bacteria, and arthropods devastated already struggling coffee farms and with a major switch to sun-grown coffee, soil microbiomes were depleted and disease spread rapidly through monoculture crops. This switchover was prompted by an energy drink corporation, KAPOW!, which wanted to corner the caffeine market and boost production, though their expertise in growing coffee was lacking and the excessive use of synthetic fertilizers on already sun baked land which requires much more watering further doomed plantations. At least they now produce a cheap “coffee” flavored energy drink. It tastes terrible.

Article 1 – Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review

Article 2 – Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador

Article 3 – One health relationships between human, animal, and environmental microbiomes: A mini-review

Video 1 – Teaching coffee farmers about the birds and the bees

Questions:

  1. In what ways are environmental microbiomes impacted by changing environmental factors and how can this promote diseases within an ecosystem?
  2. How could various environmental microbiomes be utilized to improve sustainable practices and technology?
  3. How are environmental and human microbiomes interconnected?

Attributions:

References:

  1. Hindorf, H., & Omondi, C. O. (2011). A review of three major fungal diseases of Coffea arabica L. in the rainforests of Ethiopia and progress in breeding for resistance in Kenya. Journal of Advanced Research, 2(2), 109–120. https://doi.org/https://doi.org/10.1016/j.jare.2010.08.006
  2. Lamelas, A., Desgarennes, D., López-Lima, D., Villain, L., Alonso-Sánchez, A., Artacho, A., Latorre, A., Moya, A., & Carrión, G. (2020). The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato. Frontiers in Plant Science, 11. https://www.frontiersin.org/article/10.3389/fpls.2020.00136
  3. Duong, B., Marraccini, P., Maeght, J.-L., Vaast, P., Lebrun, M., & Duponnois, R. (2020). Coffee Microbiota and Its Potential Use in Sustainable Crop Management. A Review. Frontiers in Sustainable Food Systems, 4. https://www.frontiersin.org/article/10.3389/fsufs.2020.607935
  4. Fulthorpe, R., Martin, A. R., & Isaac, M. E. (2019). Root Endophytes of Coffee (Coffea arabica): Variation Across Climatic Gradients and Relationships with Functional Traits. Phytobiomes Journal, 4(1), 27–39. https://doi.org/10.1094/PBIOMES-04-19-0021-R
  5. dos Santos DG, Coelho CCdS, Ferreira ABR, Freitas-Silva O. Brazilian Coffee Production and the Future Microbiome and Mycotoxin Profile Considering the Climate Change Scenario. Microorganisms. 2021; 9(4):858. https://doi.org/10.3390/microorganisms9040858
  6. Caldwell AC, Silva LCF, da Silva CC, Ouverney CC (2015) Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil. PLoS ONE 10(6): e0106355. doi:10.1371/journal.pone.0106355
  7. Rodríguez, A. C.-, R. T.- Calzada, C. G.-D. la Peña, J. G. A.- Ávila, E. N.- Reyna, F. V.- Paniagua, C. D.- Velásquez, and C. A. M.- Herrera. “A Metagenomic Approach in the Evaluation of the Soil Microbiome in Coffee Plantations under Organic and Conventional Production in Tropical Agroecosystems”. Emirates Journal of Food and Agriculture, Vol. 32, no. 4, Apr. 2020, pp. 263-70, https://doi.org/10.9755/ejfa.2020.v32.i4.2092.
  8. Rao, M., Rice, R., Fleischer, R., & Muletz Wolz, C. (2020). Soil fungal communities differ between shaded and sun-intensive coffee plantations in El Salvador. PLOS ONE, 15, e0231875. https://doi.org/10.1371/journal.pone.0231875
  9. Mejía-Alvarado, F. S., Ghneim-Herrera, T., Góngora, C. E., Benavides, P., & Navarro-Escalante, L. (2021). Structure and Dynamics of the Gut Bacterial Community Across the Developmental Stages of the Coffee Berry Borer, Hypothenemus hampei. Frontiers in Microbiology, 12. https://www.frontiersin.org/article/10.3389/fmicb.2021.639868
  10. Veloso, T. G. R., da Silva, M. de C. S., Cardoso, W. S., Guarçoni, R. C., Kasuya, M. C. M., & Pereira, L. L. (2020). Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil. Scientific Reports, 10(1), 14692. https://doi.org/10.1038/s41598-020-71309-y
  11. Trinh, P., Zaneveld, J. R., Safranek, S., & Rabinowitz, P. M. (2018). One Health Relationships Between Human, Animal, and Environmental Microbiomes: A Mini-Review. Frontiers in Public Health, 6. https://www.frontiersin.org/article/10.3389/fpubh.2018.00235

 

 

 

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Microbiomes: Health and the Environment Copyright © 2022 by Dylan Parks is licensed under a Creative Commons Attribution 4.0 International License, except where otherwise noted.

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