Abstract
ABSTRACTMicrobial ecology has been transformed by the advent of high-throughput marker gene and metagenomic sequencing methods. These tools provide expansive descriptions of microbial communities, but the descriptions are framed in terms of molecular objects, such as 97% ribosomal operational taxonomic units (OTUs), rather than biological objects, such as species. A recent study by A. B. Chase and colleagues (mBio 8:e01809-17, 2017, https://doi.org/10.1128/mBio.01809-17) explores the so-called microdiversity within the Curtobacterium OTU, the most abundant OTU in a leaf litter community. Perhaps unsurprisingly, they find that some important ecologic traits, such as drought response, are coherent within the OTU, but that others vary significantly. Here we discuss their findings in relation to the more general issue of how molecular tools can be effectively used to study microbial ecology. We specifically note the need for investigators to choose the right molecular methods for their biological problem, as nature does not respect the limitations and conventions associated with our methods.
Highlights
When we try to make sense of microbial communities, we often conceive of a cast of coherent species playing roles determined by their phenotypes and traits
Known Curtobacterium strains contain 16S rRNA genes that are at least 97% similar; Curtobacterium strains have typically been grouped into a single object by previous operational taxonomic unit (OTU)-based analyses
In this study (1), the drought response of Curtobacterium was coherent across the Curtobacterium OTU, and amplicon sequencing of the 16S rRNA gene could be an effective tool for studying microbial drought response in leaf litter
Summary
When we try to make sense of microbial communities, we often conceive of a cast of coherent species playing roles determined by their phenotypes and traits. Chase and colleagues (1) combined shotgun metagenomics, wholegenome sequencing, and laboratory measurements of cultured isolates to probe the genetic and phenotypic diversity within the Curtobacterium OTU. The ability of each isolate to degrade cellulose and xylan, the most abundant complex carbohydrates in leaf litter, was directly tested by laboratory growth assays at two different temperatures.
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