RT Journal Article
SR Electronic
T1 Understanding How Microbiomes Influence The Systems They Inhabit: moving from a correlative to a causal research framework
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 065128
DO 10.1101/065128
A1 E.K. Hall
A1 E.S Bernhardt
A1 R.L. Bier
A1 M.A. Bradford
A1 C.M. Boot
A1 J.B. Cotner
A1 P.A. del Giorgio
A1 S.E. Evans
A1 E. B Graham
A1 S.E. Jones
A1 J.T. Lennon
A1 K.J. Locey
A1 D. Nemergut
A1 B.B. Osborne
A1 J.D. Rocca
A1 J.S. Schimel
A1 M.P. Waldrop
A1 M.W. Wallenstein
YR 2018
UL http://biorxiv.org/content/early/2018/01/01/065128.abstract
AB Translating the ever-increasing wealth of information on microbiomes (environment, host, or built environment) to advance the understanding of system-level processes is proving to be an exceptional research challenge. One reason for this challenge is that relationships between characteristics of microbiomes and the system-level processes they influence are often evaluated in the absence of a robust conceptual framework and reported without elucidating the underlying causal mechanisms. The reliance on correlative approaches limits the potential to expand the inference of a single relationship to additional systems and advance the field. In this perspective piece we propose that research focused on how microbiomes influence the systems they inhabit should work within a common framework and target known microbial processes that contribute to the system-level process of interest. Here we identify three distinct categories of microbiome characteristics (microbial processes, microbial community properties, and microbial membership) and propose a framework to empirically link each of these categories to each other and the broader system level processes they affect. We posit that it is particularly important to distinguish microbial community properties that can be predicted from constituent taxa (community aggregated traits, CATs) from those properties that are currently unable to be predicted from constituent taxa (emergent properties, EPs). We discuss how a series of existing methods in microbial ecology can be applied to more explicitly elucidate properties within each of these categories and connect these three categories of microbial characteristics with each other. We view this proposed framework, gleaned from a breadth of research on environmental microbiomes and ecosystem processes, as a promising pathway with the potential to advance microbiome science across a broad range of disciplines.