Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

Microbial communities typically contain many rare taxa that make up the majority of the observed membership, yet the contribution of this microbial "rare biosphere" to community dynamics is unclear. Using 16S rRNA amplicon sequencing of 3,237 samples from 42 time series of microbial communities from nine different ecosystems (air; marine; lake; stream; adult human skin, tongue, and gut; infant gut; and brewery wastewater treatment), we introduce a new method to detect typically rare microbial taxa that occasionally become very abundant (conditionally rare taxa [CRT]) and then quantify their contributions to temporal shifts in community structure. We discovered that CRT made up 1.5 to 28% of the community…

• UD
  U.S. Department of Energy

  Awards: AC02-06CH11357, DE-AC02, 06CH11357, DE-AC02-06CH11357, DE-AC02-
• GA
  Gordon and Betty Moore Foundation
• LS
  Life Sciences Research Foundation