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ISU ENVSCI690 Graduate Seminar Slides

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Slides for my guest lecture in a graduate seminar class.

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ISU ENVSCI690 Graduate Seminar Slides

  1. 1. Adina  Howe   Agricultural  and  Biosystems  Engineering   (slides  available  from  ww.germslab.org)     ENVIRONMENTAL   SCIENCE  RESEARCH   IN  THE  GERMS  LAB         Genomics and Environmental Research in Microbial Systems    
  2. 2. Who  am  I?   •  Mechanical  Engineer   •  Environmental  Engineer   •  Microbiologist   •  Bioinformatician   •  Big  data-­‐er   •  Teacher   •  Mentor   •  Trainer    
  3. 3. What  is  my  research  mission?   We  are  changing  the  environment  that   we  live  in.     To  preserve  environmental  integrity,   we  must  understand  and  manage  the   impacts  of  global  change.     Scientific  research  (and  data)  must   inform  our  decisions  and  policy.     GERMS  uses  innovative  scientific   methods  to  evaluate  and  understand   our  complex  and  changing  world.    
  4. 4. How  will  GERMS  do  this?       Put  simply,  our  vision  is  to…     Monitor,  evaluate,  and  manage  our  microbial   communities  and  their  services  in  the  environment.  
  5. 5. A  DEFINING-­‐THE-­‐   RELATIONSHIP  TALK   WITH  OUR  MICROBIAL   NEIGHBORS      
  6. 6. Can  we  live  without  them?   •  Assigned  reading  (Gilbert  and  Neufeld,   2014):      (many  questions  on  why  this  was   assigned)   •  Why  was  this  published?       •  Is  it  useful?   •  What  are  the  impacts/consequences  of   research?   •  Boundary  conditions   •  What  are  three  biggest  challenges  to  our   society,  for  the  world,  for  our  future,  for   the  state  of  Iowa?     •  What  can  understanding  microbiology  /   microbial  ecology  /  environmental  do  to   help?   ???  
  7. 7. Super  challenges  of  our  shared  future  
  8. 8. The  role  of  our  microbial  partners?  neighbors?   MICROBES IN ECOSYSTEMS NATURE AIR WATER SOIL MICROBIOMES HUMANS/ANIMAL ENGINEERED BIOREACTORS WASTEWATER
  9. 9. Understanding  community  dynamics  in  the   environment     • Who  is  there?   • What  are  they  doing?     • How  are  they  doing  it?     Kim  Lewis,  2010  
  10. 10. Sequencing  the  code  of  life     http://www.iflscience.com/chemistry/do-­‐try-­‐home   Who?   What?     How?  Why?   (Experimental   Design)  
  11. 11. Transforming technology? Stein,  Genome  Biology,  2010     E.  Coli  genome  4,500,000  bp  ($4.5M,  1992)   1990        1992        1994        1996        1998        2000        2003        2004        2006        2008        2010        2012              Year     0.1   1   10   100   1,000   10,000   100,000   1,000,000   DNA  Sequencing,  Mbp  per  $   10,000,000   100,000,000  
  12. 12. Rapidly decreasing costs with today’s sequencing technologies Stein,  Genome  Biology,  2010     Next  Generation  Sequencing   4,500,000  bp  (E.  Coli,  $200,  presently)   1990        1992        1994        1996        1998        2000        2003        2004        2006        2008        2010        2012              Year     0.1   1   10   100   1,000   10,000   100,000   1,000,000   DNA  Sequencing,  Mbp  per  $   10,000,000   100,000,000  
  13. 13. Effects  of  low  cost  sequencing…   First  free-­‐living  bacterium  sequenced    for   billions  of  dollars  and  years  of  analysis   Personal  genome  can  be   mapped  in  a  few  days  and   hundreds  to  few  thousand   dollars  
  14. 14. Postdoc  experience  with  data   2003-­‐2008  Cumulative  sequencing  in  PhD  =  2000  bp   2008-­‐2009  Postdoc  Year  1  =  50  Gbp   2009-­‐2010  Postdoc  Year  2  =  450  Gbp  
  15. 15. Computational  reconstruction  of  genes.   Titus  Brown  
  16. 16. IN  THE  NEWS:    80%  of  Americans  polled  support   WARNING:  This  product  contains   deoxyribonucleic  acid  (DNA).  The   Surgeon  General  has  determined  that   DNA  is  linked  to  a  variety  of  diseases  in   both  animals  and  humans.  In  some   configurations,  it  is  a  risk  factor  for   cancer  and  heart  disease.  Pregnant   women  are  at  very  high  risk  of  passing  on   DNA  to  their  children.   Washington  Post,  Jan,  2015  
  17. 17. Super  challenges  of  our  shared  future  
  18. 18. BACK  ON  TRACK…  
  19. 19. The shifting experimental continuum Single  Isolate     Pure  Culture   Enrichment   Mixed  Cultures   Natural  systems  
  20. 20. Something  old,  something  new,   something  borrowed,  something   blue   SOME  GERMS   RESEARCH  PROJECTS  
  21. 21. SOILS  (SOMETHING   OLD):         HOW  DOES  LAND  USE   CHANGE  SOIL   ECOSYSTEM  HEALTH?  
  22. 22. Great  Prairie  (where  is  this?)  
  23. 23. Paired  Treatments  in  3  States  
  24. 24. Diverse  genes  present  in  soil  affecting  health,   nutrient  availability,  and  C/N/P  cycling   0 100 200 300 400 aminoacidmetabolism carbohydratemetabolism membranetransport signaltransduction translation folding,sortinganddegradation metabolismofcofactorsandvitamins energymetabolism transportandcatabolism lipidmetabolism transcription cellgrowthanddeath replicationandrepair xenobioticsbiodegradationandmetabolism nucleotidemetabolism glycanbiosynthesisandmetabolism metabolismofterpenoidsandpolyketides cellmotility TotalCount KO corn and prairie corn only prairie only Howe  et.  al,  PNAS,  2014   •  Incredible  soil  biodiversity  (only   able  to  sample  10%  with  our   significant  efforts  –  largest   published)   •  Many  functions  shared  between   corn  and  prairie  (red)   •  Prairie  soils  have  many  more   unique  functions     à How  important  are  these   unique  functions?   à Does  biodiversity  provide   stability?   à Can  we  recover  these   functions  after  land   conversion?        
  25. 25. GUTS  (SOMETHING   NEW):         HOW  DO  MICROBES  IN   OUR  BODIES  AFFECT   OUR  HEALTH?  
  26. 26. We  are  supraorganisms   26  
  27. 27. Gut microbiota interacts with genetics and environment to influence our health 27   Source:    Zhao,  2013   Obesity   Intestinal  inflammation   IBD  diseases   Diet  has  a  greater   potential  to  shape  the   structure  and  function  of   gut  than  host  genetics.   Direct  influence  on  health  state  
  28. 28. Two baseline diets (with a perturbation) Low-­‐fat  (LF)  baseline  diet   Milk-­‐fat  (MF)  baseline  diet   Age  (wk)   4   5   6   7   8   9   10   11   12   13   14   Diet  Switch   Washout  (Return  to  Baseline)     Baseline   28   LF / 10% Fat / Complex Carbs MF / 37% Fat / Simple Sugars MF LF MF LF
  29. 29. Two baseline diets (with a perturbation) Low-­‐fat  (LF)  baseline  diet   Milk-­‐fat  (MF)  baseline  diet   Age  (wk)   4   5   6   7   8   9   10   11   12   13   14   Diet  Switch   Washout  (Return  to  Baseline)     Baseline   29   LF / 10% Fat / Complex Carbs MF / 37% Fat / Simple Sugars MF LF MF LF Viruses  can:   •  Wipe  out  specific  populations  of   bacteria   •  Transfer  genes  (functions)  to  bacteria   •  Expand  or  destroy  “niches”  of  bacteria  
  30. 30. How  do  bacteria  and  viruses  respond  to  diet   changes?   • Bacteria   • Broadly,  bacteria  will  return  to  baseline  conditions   even  when  on  an  alternate  diet  (within  24  hours).   • Observed  under  both  diets   • Viruses   • When  grown  on  low  fat  diet,  response  was  similar   to  bacteria,  return  to  baseline  communities.   • Response  was  diet-­‐specific:    milk  fat  diet  mice   viruses  became  different  and  did  not  have  any   trends  towards  return  to  original  (in  this   experiment)    
  31. 31. WATER  (SOMETHING   BLUE):         CAN  WE  PROVIDE   BETTER  TOOLS  TO   MONITOR  WATER   QUALITY?  
  32. 32. How  do  we  monitor  water  quality  now?  
  33. 33. How  do  we  monitor  water  quality  now?   Data Type Example Cost per sample / Frequency of sampling Precision / Water quality information Challenges Water properties chemical analysis of water quality narrow range of information about services in ecosystem Traditional integrity indicators presence of coliform bacteria detection methods lack specificitity and are often imprecise Phytoplankton community characterization cyanotoxin detection through fractionation of ammonia detection of toxicity may not reveal source Microbial community characterization (16S rRNA) abundance of genes present and assoiated with all cyanobacteria characterization of microbial community structure may not reveal gene function; data volume large for public understanding Proposed MAVeRiC genes (DNA) abundance of genes present associated with specific source of pollution identifying relevant genes of interest to water quality; DNA reveals genes present but not necessarily actively expressed Proposed MAVeRiC genes (RNA) abundance of genes expressed and present associated with specific source pollution identifying relevant genes of interest to water quality
  34. 34. Scalable,  quantitative  tools  to  monitor  microbial   responses  in  complex  environments         Estimating  risks  from   pathogens   Biotic  integrity  of  a  healthy   water  system   Sources  of  non  point   pollution   Role  of  waters  in  stabilizing   climate  change   Microbial  genetic  biomarkers  can  capture…  
  35. 35.     !! ! B D 24 Samples (216 targets per sample) Nutrients Toxicity Diversity (Broad and specific) !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! !!! CA Lake%1 Lake%2% … Lake%132 Total%Biodiversity%Indexes % Bacteria(+(Archaeea 10 8 … 2 Bacteria1specific 2 0 10 Archaea1specific Fungal1specific Specific%Biodiversity%Indexes Cyanobacteria1specific 2 8 … 9 Mycrocystis(sp.1specific 8 2 … 9 Cylindrospermopsis(sp.1specific 4 2 … 0 Nutrient%Indexes % Nitrogen(fixation(index 2 4 … 7 Denitrification(index 3 3 … 5 Phosphorus(cycling(index 10 10 … 5 Carbon(cycling(index 5 7 … 4 Cyanobacteria(nitrogen(fixation 4 6 … 8 Phosphate1solubilizing(rhizobacteria 4 2 … 0 Toxicity%Indexes % Microcystis(gene(presence 8 9 … 4 Microcystis(gene(activity 7 9 … 5 B I O D I V E R S I T Y F U N C T I O N Project  with  John  Downing,  Chris  Filstrup,  and  Fan  Yang  
  36. 36. Color  test  for  Ebola  virus  à  color  test  for   environmental  contaminants?   http://www.kurzweilai.net/synthetic-­‐biology-­‐ on-­‐ordinary-­‐paper-­‐a-­‐new-­‐operating-­‐system  
  37. 37. Color  test  for  environmental  contaminants?   http://www.kurzweilai.net/synthetic-­‐biology-­‐ on-­‐ordinary-­‐paper-­‐a-­‐new-­‐operating-­‐system  
  38. 38. Three  things  to  take  home:   1.  Microbes  are  not  simple,  and  today’s  emerging   (emerged?)  technology  is  allowing  to  access  their   complexity.   2.  There  is  incredible  microbial  diversity  (millions)  –   and  these  are  systems/resources  that  we  need  to   monitor,  understand,  and  manage.   3.  Environmental  science  is  an  inter-­‐disciplinary   science,  microbial  data  (but  not  alone)  is  a  huge   opportunity  to  address  our  questions.  
  39. 39. Thank  you!    QUESTIONS?   • Collaborators:   •  Kirsten  Hofmockel&  Fan  Yang    (ISU,  EEOB)     •  John  Downing  &  Chris  Filstrup  (ISU,  EEOB)   •  Daina  Ringus  &    Gene  Chang  (University  of  Chicago)   •  Folker  Meyer  &  Sarah  Owens  (Argonne  National  Laboratory)   • GERMS  Lab   Jin  Choi   Ryan  Williams   Recruiting  NOW!  

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