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hanggliding.org
http://www.merrittcartographic.co.uk/earth_structure.html
‘‘the lower the organization of the body is, the more generally it is
distributed.”
Augustin Pyramus de Candolle (1821)
tr...
Intertwined questions
DIVERSITY GEOGRAPHY EVOLUTION
FUNCTION
/ ROLE
(1)
(2)
(3)
Do microbial “species”
show spatial structure?
van Gremberghe et al. (2011) PLoS ONE
Microcystis
(freshwater)
– no!
Parsimony network of
trimmed ITS sequences
Europe
Asi...
Burkholderia pseudomallei
(soil transmission)
– yes!
Pearson et al. (2009) BMC Biol
Do microbial communities
show spatial structure?
Qualitative β-diversity
= presence / absence of different groups
Quantitative β-diversity
= relative abundance of differen...
Arctic soil microbes – no!
Data from Chu et al. (2010) Environ Microbiol
Retrieved from Earth Microbiome Project
Visualiza...
Bray-Curtis clustering of Arctic samples (http://www.ncbi.nlm.nih.gov/pubmed/20561020), colored by pH
Data from Chu et al....
Martiny et al. (2008) Env Micro
“Due to the large population size and relatively short generation
time, cells may evolve f...
Hypersaline communities –
maybe?
Martiny et al. (2011) PNAS
Community similarity varied
with distance only WITHIN marshes,...
Relating phylogeny to
function
PICRUSt
(Morgan) Langille et al. (2013) Nat Biotechnol
Sequenced genomes
(known function)
Reference phylogeny
(known funct...
It works
surprisingly
well!
Langille et al. (2013) Nat Biotechnol
but…
Larsbrink et al. (2014) Nature
Growth on xyloglucans
Red: YES
Blue: NO
Green: MAYBE
Larsbrink et al. (2014) Nature
Dysgonomonas (termites!)
P. aeruginosa
P. fluorescens
P. putida
P. syringae
P. entomophila
P. stutzeri
P. mendocina
Holloway and Beiko, 2010
Function *mostly*
correlates with phylogeny
(but maybe not for the functions and roles you care about!)
Rethinking beta diversity
Boon, Meehan et al. (2013) FEMS Microbiol Rev
(a) Marker-gene phylogeny
(b) Functional gene dist...
Questions
• Do bacteria have biogeography? It depends on the
dispersal mechanism
• Is phylogeny predictive of function? Ye...
Acknowledgments
Community evolution / LGT
• Morgan Langille
• Conor Meehan
• Dennis Wong
• Donovan Parks
• Eva Boon
• Cath...
Beiko biogeography
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Beiko biogeography

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Presentation at "Understanding biodiversity dynamics using diverse data sources" conference, Canberra, April 2014

Publicada em: Tecnologia, Carreiras
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Beiko biogeography

  1. 1. hanggliding.org
  2. 2. http://www.merrittcartographic.co.uk/earth_structure.html
  3. 3. ‘‘the lower the organization of the body is, the more generally it is distributed.” Augustin Pyramus de Candolle (1821) tr. Kurt Sprengel ‘‘everything is everywhere: but the environment selects” Lourens Baas-Becking (1934) ‘‘He [Martinus Beijernick] proposed that most ‘germs’ were cosmopolitan, and that their presence or absence could be predicted and practically produced by creating specific environmental conditions, rather than being subject to the historical contingency of simply being in a particular place at a particular time.” Maureen O’Malley (2007) Nat Rev Micro
  4. 4. Intertwined questions DIVERSITY GEOGRAPHY EVOLUTION FUNCTION / ROLE (1) (2) (3)
  5. 5. Do microbial “species” show spatial structure?
  6. 6. van Gremberghe et al. (2011) PLoS ONE Microcystis (freshwater) – no! Parsimony network of trimmed ITS sequences Europe Asia Oceania Africa South America North America Mantel r = 0.131
  7. 7. Burkholderia pseudomallei (soil transmission) – yes! Pearson et al. (2009) BMC Biol
  8. 8. Do microbial communities show spatial structure?
  9. 9. Qualitative β-diversity = presence / absence of different groups Quantitative β-diversity = relative abundance of different groups Phylogenetic β-diversity = either of the above, but related groups contribute less to diversity Pairwise -diversity Outcome: 0 = identical 1 = maximally different
  10. 10. Arctic soil microbes – no! Data from Chu et al. (2010) Environ Microbiol Retrieved from Earth Microbiome Project Visualization / Analysis in GenGIS Bray-Curtisdistance Longitude difference between sites R2 = 0.001 p = 0.25 Mantel test of Bray-Curtis dissimilarity between pairs of sites (genus level), vs. difference in longitude between sites
  11. 11. Bray-Curtis clustering of Arctic samples (http://www.ncbi.nlm.nih.gov/pubmed/20561020), colored by pH Data from Chu et al. (2010) Environ Microbiol Retrieved from Earth Microbiome Project Visualization / Analysis in GenGIS The environment selects
  12. 12. Martiny et al. (2008) Env Micro “Due to the large population size and relatively short generation time, cells may evolve faster than ocean currents can mix them and this may maintain local microdiversity.” Prochlorococcus (marine) – slightly! Relationship between community similarity and dispersal time was only significant at a very fine taxonomic threshold e.g. “sub-sub-sub-subspecies”
  13. 13. Hypersaline communities – maybe? Martiny et al. (2011) PNAS Community similarity varied with distance only WITHIN marshes, not regionally or continentally (1) Local, spatially structured environmental variable? (2) Restricted movement within marshes / colonization effects?
  14. 14. Relating phylogeny to function
  15. 15. PICRUSt (Morgan) Langille et al. (2013) Nat Biotechnol Sequenced genomes (known function) Reference phylogeny (known function + unknown function) - AND - Taxonomic samples = FUNCTIONAL PREDICTIONS
  16. 16. It works surprisingly well! Langille et al. (2013) Nat Biotechnol
  17. 17. but… Larsbrink et al. (2014) Nature
  18. 18. Growth on xyloglucans Red: YES Blue: NO Green: MAYBE Larsbrink et al. (2014) Nature Dysgonomonas (termites!)
  19. 19. P. aeruginosa P. fluorescens P. putida P. syringae P. entomophila P. stutzeri P. mendocina Holloway and Beiko, 2010
  20. 20. Function *mostly* correlates with phylogeny (but maybe not for the functions and roles you care about!)
  21. 21. Rethinking beta diversity Boon, Meehan et al. (2013) FEMS Microbiol Rev (a) Marker-gene phylogeny (b) Functional gene distribution (PICRUSt!) (c) Co-occurrence patterns (d) Functional gene phylogeny
  22. 22. Questions • Do bacteria have biogeography? It depends on the dispersal mechanism • Is phylogeny predictive of function? Yes and no • LGT and other modes of convergence can drastically diminish the predictive value of phylogeny • Strain-level information can be critical! • Do *genes* have biogeography, or do they follow Baas- Becking as well? • Interactions between dispersal-limited species? • Limiting factors on LGT including co-localization of donor and recipient
  23. 23. Acknowledgments Community evolution / LGT • Morgan Langille • Conor Meehan • Dennis Wong • Donovan Parks • Eva Boon • Catherine Holloway PICRUSt • Jesse Zaneveld • Rob Knight • Curtis Huttenhower • Greg Caporaso • Dan Knights • Daniel MacDonald • Josh Reyes • Jose Clemente

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