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
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
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
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
I’m in my fourth week here in the Taupo Volcanic Zone of New Zealand on my quest to understand what eukaryotic life –especially protists– can thrive in hotsprings. A quick refresher: protists are single-celled microbial eukaryotes and include many diverse lineages like amoebae, ciliates and flagellates. While bacteria and archaeal taxa have long been appreciated
The problem There – I did it. I made it through processing my raw amplicon (marker gene, 16S rRNA, 18S rRNA, or fungal ITS, etc.) DNA sequences. Now I have a table that tells me how many of each taxon (i.e. phylotype, OTU, etc.) are represented in each sample. This table is often referred to
By: Noah Fierer As the NFL season draws to a close, we can look back and try to figure out why some teams were winners (Go Broncos!) while others are perennial losers (sorry Cleveland). Undoubtedly one key to success is the ability of coaches and managers to select good players. Fortunately, for every prospective player
By: Noah Fierer Recently there was a call from a group of esteemed microbiologists and microbial ecologists for a ‘Unified Microbiome Intiative’. I won’t go into the details as you can read the articles here and here. I agree with most of what the authors are proposing. However, there are a few aspects of this
The most up-to-date lab group photo! Farewell to our former student/lab tech extraordinaire, Xavier. Welcome to our new grad students, Angela and Hannah!
By: Noah Fierer Microbial ecology has surprisingly few unifying concepts. It is difficult to identify ‘rules’ or paradigms that apply across the field of microbial ecology regardless of the taxonomic group or environment in question. Here is my short list and I realize I am probably missing quite a few obvious ones: Bacterial cell size