Fierer Lab

Exploring the structure and function of microbial communities

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Insights, rants, shameless self promotion, etc. from the Fierer lab and its affiliates.

Is RNA a useful measure of microbial activity?

By Noah Fierer Let’s say a microbial ecologist wants to identify which bacteria are active in a given environmental sample at a given point in time. For example, you may want to determine which bacteria are active in a desert soil after a large rainfall event. This is often done by comparing the representation of

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Intragenomic heterogeneity and its implications for ESVs

By Angela Oliverio and Noah Fierer In a recent blog post, we focused on the advantages and disadvantages of using exact sequence variants (ESVs) versus OTUs to cluster marker gene sequences for microbial community analyses. Just to recap – let’s say we sequenced a pool of 16S rRNA genes from a bacterial community found in

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Lumping versus splitting – is it time for microbial ecologists to abandon OTUs?

By Noah Fierer, Tess Brewer, & Mallory Choudoir Typically, when we analyze 16S rRNA gene data for bacterial and archaeal community analyses we start by clustering sequences into operational taxonomic units (OTUs), i.e. clustering sequences that fall into fixed similarity thresholds (with OTUs often, but not always, defined at the ≥97% sequence similarity level). A

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Ecosystem restoration: what do soil and feces have in common?

By: Noah Fierer Some of you may have seen this paper that came out recently in Nature Plants by Wubs et al. “Soil inoculation steers restoration of terrestrial ecosystems”. As a soil ecologist – this paper brings joy to my heart. It was great to read this paper as it demonstrates the likely importance of

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