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

1. hanggliding.org

2. http://www.merrittcartographic.co.uk/earth_structure.html

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. Intertwined questions
DIVERSITY GEOGRAPHY EVOLUTION
FUNCTION
/ ROLE
(1)
(2)
(3)

5. Do microbial “species”
show spatial structure?

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. Burkholderia pseudomallei
(soil transmission)
– yes!
Pearson et al. (2009) BMC Biol

8. Do microbial communities
show spatial structure?

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. 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. 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. 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. 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. Relating phylogeny to
function

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. It works
surprisingly
well!
Langille et al. (2013) Nat Biotechnol

17. but…
Larsbrink et al. (2014) Nature

18. Growth on xyloglucans
Red: YES
Blue: NO
Green: MAYBE
Larsbrink et al. (2014) Nature
Dysgonomonas (termites!)

19. P. aeruginosa
P. fluorescens
P. putida
P. syringae
P. entomophila
P. stutzeri
P. mendocina
Holloway and Beiko, 2010

20. Function *mostly*
correlates with phylogeny
(but maybe not for the functions and roles you care about!)

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. 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. 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