Phylogenetic conservatism of functional traits in microorganisms
Open Access
- 13 December 2012
- journal article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 7 (4), 830-838
- https://doi.org/10.1038/ismej.2012.160
Abstract
A central question in biology is how biodiversity influences ecosystem functioning. Underlying this is the relationship between organismal phylogeny and the presence of specific functional traits. The relationship is complicated by gene loss and convergent evolution, resulting in the polyphyletic distribution of many traits. In microorganisms, lateral gene transfer can further distort the linkage between phylogeny and the presence of specific functional traits. To identify the phylogenetic conservation of specific traits in microorganisms, we developed a new phylogenetic metric-consenTRAIT-to estimate the clade depth where organisms share a trait. We then analyzed the distribution of 89 functional traits across a broad range of Bacteria and Archaea using genotypic and phenotypic data. A total of 93% of the traits were significantly non-randomly distributed, which suggested that vertical inheritance was generally important for the phylogenetic dispersion of functional traits in microorganisms. Further, traits in microbes were associated with a continuum of trait depths (τD), ranging from a few deep to many shallow clades (average τD: 0.101-0.0011 rRNA sequence dissimilarity). Next, we demonstrated that the dispersion and the depth of clades that contain a trait is correlated with the trait's complexity. Specifically, complex traits encoded by many genes like photosynthesis and methanogenesis were found in a few deep clusters, whereas the ability to use simple carbon substrates was highly phylogenetically dispersed. On the basis of these results, we propose a framework for predicting the phylogenetic conservatism of functional traits depending on the complexity of the trait. This framework enables predicting how variation in microbial composition may affect microbially-mediated ecosystem processes as well as linking phylogenetic and trait-based patterns of biogeography.Keywords
This publication has 53 references indexed in Scilit:
- Rainfall-induced carbon dioxide pulses result from sequential resuscitation of phylogenetically clustered microbial groupsProceedings of the National Academy of Sciences of the United States of America, 2012
- Characterization ofProchlorococcusclades from iron-depleted oceanic regionsProceedings of the National Academy of Sciences of the United States of America, 2010
- adephylo: new tools for investigating the phylogenetic signal in biological traitsBioinformatics, 2010
- Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypesProceedings of the National Academy of Sciences of the United States of America, 2009
- Evolutionary history and the effect of biodiversity on plant productivityProceedings of the National Academy of Sciences of the United States of America, 2008
- A Rapid Bootstrap Algorithm for the RAxML Web ServersSystematic Biology, 2008
- Resistance, resilience, and redundancy in microbial communitiesProceedings of the National Academy of Sciences of the United States of America, 2008
- PATRIC: The VBI PathoSystems Resource Integration CenterNucleic Acids Research, 2006
- Annually reoccurring bacterial communities are predictable from ocean conditionsProceedings of the National Academy of Sciences of the United States of America, 2006
- Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptationProceedings of the National Academy of Sciences of the United States of America, 2006