Microbiomes in light of traits:

microbiomes—are intricately linked to hu-man health and critical ecosystem services. New technologies allow the rapid charac-terization of hundreds of samples at a time and provide a sweeping perspective on mi-crobiome patterns. However, a systematic un-derstanding of what determines microbiome diversity and composition and its implica-tions for system functioning is still lacking. A focus on the phenotypic characteristics of microorganisms—their traits—offers a path for interpreting the growing amount of mi-crobiome data. Indeed, a variety of trait-based approaches have been proposed for plants and diversity-process relationships, and ecosystem responses to environmental change. Although there is a growing emphasis on microbial traits, the concept has not been fully appreciated in microbiology. However, a trait focus formicroorganismsmay present an even larger research opportunity than for macro-organisms. Not only do microorganisms play a central role in nutrient and energy cycling in most systems, but the techniques used to char-acterizemicrobiomes usually provide extensive molecular and phylogenetic information. ADVANCES: One major difference between macro- and microorganisms is the potential lated to the history of the vertically descended parts of the genome. If true, then the taxonomic composition of a microbiome might reveal little about the health or functioning of a system. We first review key aspects of microbial traits and then recent studies that document the distribution of microbial traits onto the tree of life. A synthesis of these stud-ies reveals that, despite the promiscuity of HGT, microbial traits appear to be phylogenetically con-served, or not distributed randomly across the tree of life. Further, microbial traits ap-pear to be conserved in a hierarchical fash-ion, possibly linked to their biochemical and genetic complexity. For instance, traits such as pH and salinity preference are rel-atively deeply conserved, such that taxa with-in deep clades tend to share the trait. In contrast, other traits like the ability to use simple carbon substrates or to take up or-ganic phosphorus are shallowly conserved, and taxa share these traits only within small, shallow clades