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Interdisciplinary Microbiome Research - the National Microbiome Initiative and Agriculture Research on the Iss

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Presentation by Elizabeth Stulberg, Ph. D., USD

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Interdisciplinary Microbiome Research - the National Microbiome Initiative and Agriculture Research on the Iss

  1. 1. Interdisciplinary Microbiome Research: The National Microbiome Initiative and Agriculture Research on the ISS Dr. Elizabeth Stulberg United States Department of Agriculture Office of the Chief Scientist Omes and Omics: Exploring the Microbiome/Immunome and Diseases on the International Space Station U.S. National Lab Cleveland, OH October 25, 2016
  2. 2. Microbes are everywhere, and they are important!
  3. 3. White House Office of Science and Technology Policy – Science Division Microbiomes are integral to many Presidential priorities • Precision medicine • Energy • Agriculture • Climate change Dr. Jo Handelsman
  4. 4. What is already being done, and what is needed in the Federal Government? Chartered a “Fast Track Action Committee” • Convened 12 Federal departments and agencies. • Developed a survey to measure quantitative and qualitative metrics of microbiome science. • Published a report outlining Federal microbiome research and science. • Made actionable suggestions that could move microbiome science forward.
  5. 5. • Convened scientists at OSTP. • Issued a Request for Information in the Federal Register. What is already being done and what is needed in the private sector/academia?
  6. 6. Emerging themes cut across disciplines: Common questions across biological systems: • What is a healthy microbiome? • What is the nature of robustness? Technology is needed to: • Detect, measure, and model microbial communities • Develop computational tools to analyze vast datasets Human Resources: • Workforce training coupled with new human resources with data management skills.
  7. 7. What’s needed? Engage interdisciplinary groups. Develop platform techniques and technologies and distribute them. Engage a workforce with data management skills. Common questions across biological systems: • What is a healthy microbiome? • What is the nature of robustness? Technology is needed to: • Detect, measure, and model microbial communities • Develop computational tools to analyze vast datasets Human Resources: • Workforce training coupled with new human resources with data management skills.
  8. 8. The National Microbiome Initiative Goals of the Initiative • Interdisciplinary research on fundamental questions about diverse microbiomes. • Platform technologies for probing and changing microbiomes and data access. • New workforce through citizen science, public engagement, and educational opportunities.
  9. 9. What can the White House OSTP do? • Promote investments in microbiome research. • Facilitate interdisciplinary research
  10. 10. The National Microbiome Initiative Builds on prior work • U.S. Government invested more than $900 million from 2012- 2014 in microbiome research Facilitates new investments • $120 million of U.S. Government-supported research • $400 million in new commitments from non-Government groups.
  11. 11. The National Microbiome Initiative USDA’s commitments to the NMI include: • $15.9 million for FY 2017 to expand computational capacities through USDA’s Agriculture Research Service. • $8 million for FY 2017 in support for investigations through USDA’s National Institute of Food and Agriculture on the microbiomes of plants, livestock, fish, soil, air, and water as they influence food production systems.
  12. 12. Dr. Catherine Woteki The role of Chief Scientist is held by the Under Secretary for Research, Education, and Economics (REE) USDA Chief Scientist Office of the Chief Scientist • Ensures the Chief Scientist is the leading communicator of USDA Science nationally & internationally • Advises the Secretary & Departmental Leadership • Ensures a Department-wide culture of science-based decision making for science policy • Raises the visibility of USDA Science • Institutes, maintains, & enhances USDA’s Scientific Integrity Policy
  13. 13. The case for agriculture research in space • Astronauts will need to grow their own food on long-term space exploration missions. • Limited seed stocks mean fewer options when a cultivar is susceptible to disease. • Plants grown in space will need to use the fewest possible resources, such as water and fertilizer. • Not every part of a plant can be eaten…by a human Microbiome research is essential to this area of study Beneficial microorganisms can increase crop yields through: • Enhanced immunity
  14. 14. The case for agriculture research in space Microbiome research is essential to this area of study Beneficial microorganisms can increase crop yields through: • Enhanced immunity • Disease suppression • Astronauts will need to grow their own food on long-term space exploration missions. • Limited seed stocks mean fewer options when a cultivar is susceptible to disease. • Plants grown in space will need to use the fewest possible resources, such as water and chemical fertilizers. • Not every part of a plant can be eaten…by a human
  15. 15. The case for agriculture research in space Microbiome research is essential to this area of study Beneficial microorganisms can increase crop yields through: • Enhanced immunity • Disease suppression • Increased nutrient uptake • Astronauts will need to grow their own food on long-term space exploration missions. • Limited seed stocks mean fewer options when a cultivar is susceptible to disease. • Plants grown in space will need to use the fewest possible resources, such as water and chemical fertilizers. • Not every part of a plant can be eaten…by a human
  16. 16. The case for agriculture research in space Beneficial microorganisms can increase crop yields through: • Enhanced immunity • Disease suppression • Increased nutrient uptake • Drought tolerance Microorganisms can digest material that humans cannot. Microbiome research is essential to this area of study • Astronauts will need to grow their own food on long-term space exploration missions. • Limited seed stocks mean fewer options when a cultivar is susceptible to disease. • Plants grown in space will need to use the fewest possible resources, such as water and chemical fertilizers. • Not every part of a plant can be eaten…by a human
  17. 17. • Fungal and bacterial microorganisms each stimulate the immune systems of cucumber plants. • Together, their protection against the fungal pathogen, Fusarium, enhanced the plants’ resistance. Case Study 1: Enhanced immune function. Beneficial microorganisms increase plant growth and yield.
  18. 18. Beneficial microorganisms increase plant growth and yield. Case Study 2: Disease suppression. % Disease symptoms of sugar beet seedlings grown in: S – Suppressive soil. C – Conducive soil. CS – Conducive soil with 10% suppressive soil by weight. S50 – Suppressive soil treated at 50 C. S80 – Suppressive soil treated at 80 C. Rhizoctonia solani fungus
  19. 19. Case Study 2: Disease suppression. • As with most disease-suppressive soil, the suppression developed after an ongoing outbreak. • Identified key bacterial taxa and genes involved in suppression of a fungal root pathogen, Rhizoctonia solani. • Metagenomic sequencing revealed the importance of the relative abundance of several taxa, not specific species. Beneficial microorganisms increase plant growth and yield.
  20. 20. • Rhizobia, the nitrogen-fixers, are the poster microbes for nutrient uptake. • Non-symbiotic bacteria can also fix nitrogen and can be used by non- leguminous crops. • Phosphorus is also a limiting element for plant growth. Case Study 3: Increased nutrient uptake. Beneficial microorganisms increase plant growth and yield.
  21. 21. • Rhizobia, the nitrogen-fixers, are the poster microbes for nutrient uptake. • Non-symbiotic bacteria can also fix nitrogen and can be used by non- leguminous crops. • Phosphorus is also a limiting element for plant growth. • Symbiotic mycorrhizal fungi supply phosphorus in exchange for sugars. Case Study 3: Increased nutrient uptake. Beneficial microorganisms increase plant growth and yield.
  22. 22. Case Study 3: Increased nutrient uptake. Beneficial microorganisms increase plant growth and yield. • Cassava plants are never non-mycorrhizal in the field (plants grown in sterile soil are 10-20 times smaller). • Different mycorrhizal fungi species have variable effects on cassava growth. • In vitro-produced Rhizophagus irregularis tested on two cassava fields in Colombia was found to effectively increase yields at both sites in an economically viable manner.
  23. 23. Case Study 4: Drought tolerance Beneficial microorganisms increase plant growth and yield. • Collected endophytic fungi from coastal dune grass (salt adapted), and panic grass (heat adapted). • Commercial rice plants not adapted to salt, drought, heat, or cold stress were inoculated. • The inoculated rice used less water and set more seeds than the control when exposed to salt, drought, or cold (5-20 C).
  24. 24. Not every part of a plant can be eaten… What to do with excess plant material?
  25. 25. Not every part of a plant can be eaten… What to do with excess plant material? A cow’s rumen is a bioreactor.
  26. 26. The cow’s rumen takes cellulose and: • Produces methane and short-chain volatile fatty acids • Has very low energy costs • Operates with high biomass density (~15% w/v) • Maintains an active, stable microbial community Not every part of a plant can be eaten… What to do with excess plant material? A cow’s rumen is a bioreactor.
  27. 27. USDA ARS’s Paul Weimer studies the microbiomes of dairy cows in Madison, Wisconsin How stable is the cow’s gut microbiome?
  28. 28. • Take two cows – each has a different rumen microbial composition. • Take 95% of the rumen contents out, and switch them. • After two days, the cows’ microbiomes looks like the donors’. • After two weeks, the microbiomes have reverted to the hosts’. Very stable. • Fun fact: A cow’s microbiome will continue to ferment cellulose and lignin in an external container for up to 2.5 years – just add switchgrass and bicarbonate. How stable is the cow’s gut microbiome?
  29. 29. • Rumens can handle fiber, they make energy in the form of methane and SCFs, and the process, in the cow, takes about 8 hours. • Typical biodigesters don’t handle fiber, they make methane, and it takes weeks. • Contents of a biodigester are constantly mixing; a rumen’s contents stay in discrete layers. Rumen Biodigester Fiber, Starch, Sugars, Protein Starch, Sugars, Protein, Fats Methane, Short-Chain Fatty Acids Methane Discrete layers Constant mixing 8 hours Weeks It is unknown whether this process is gravity-dependent.
  30. 30. • The National Microbiome Initiative aims to promote and facilitate interdisciplinary microbiome research. • Interdisciplinary, agricultural microbiome research has benefits for food production and dealing with food by-products/waste. Summary • Each of these topics are important for future missions in space. • USDA research touches on each of them.

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