Biogeography of microorganisms
No borders. No limits. No fear.
hanggliding.org
Rob BeikoFaculty of Computer Science
Dalhousie University
‘‘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
van Gremberghe et al. (2011) PLoS ONE
Microcystis (freshwater) – no!
Parsimony network oftrimmed ITS sequences
EuropeAsiaOceaniaAfricaSouth AmericaNorth America
Mantel r = 0.131
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 β-diversity
Outcome: 0 = identical1 = maximally different
Arctic soil microbes – no!
Data from Chu et al. (2010) Environ MicrobiolRetrieved from Earth Microbiome ProjectVisualization / Analysis in GenGIS
Bray
-Cur
tis d
istan
ce
Longitude difference between sites
R2 = 0.001p = 0.25
Mantel test of Bray-Curtis dissimilaritybetween pairs of sites (genus level), vs. difference in longitude between sites
Bray-Curtis clustering of Arctic samples (http://www.ncbi.nlm.nih.gov/pubmed/20561020), colored by pH
Data from Chu et al. (2010) Environ MicrobiolRetrieved from Earth Microbiome ProjectVisualization / Analysis in GenGIS
The environment selects
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 themand this may maintain local microdiversity.”
Prochlorococcus (marine) – slightly!
Relationship between community similarity and dispersal time wasonly significant at a very fine taxonomic threshold e.g. “sub-sub-sub-subspecies”
Hypersaline communities – maybe?
Martiny et al. (2011) PNAS
Community similarity variedwith distance only WITHIN marshes,not regionally or continentally
(1) Local, spatially structured environmental variable?(2) Restricted movement within marshes / colonizationeffects?
PICRUSt
(Morgan) Langille et al. (2013) Nat Biotechnol
Sequenced genomes(known function)
Reference phylogeny(known function +unknown function)
- AND -Taxonomic samples
= FUNCTIONALPREDICTIONS
Growth on xyloglucans
Red: YESBlue: NOGreen: MAYBE
Larsbrink et al. (2014) NatureDysgonomonas (termites!)
P. aeruginosaP. fluorescensP. putidaP. syringaeP. entomophilaP. stutzeriP. 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 distribution
(PICRUSt!)
(c) Co-occurrence patterns (d) Functional gene phylogeny
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
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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