The unseen world: environmental microbial sequencing and identification methods for ecologists

Authors

Naupaka Zimmerman, Stanford University & University of Arizona
Jacques Izard, The Forsyth Institute & Harvard School of Dental MedicineFollow
Christian Klatt, University of Agricultural Sciences
Jizhong Zhou, University of Oklahoma & Lawrence Berkeley National & Tsinghua University
Emma Aronson, University of California, RiversideFollow

Date of this Version

12-4-2014

Citation

The Ecological Society of America

Comments

Front Ecol Environ 2014; 12(4): 224–231, doi:10.1890/130055

Abstract

Archaea, bacteria, microeukaryotes, and the viruses that infect them (collectively “microorganisms”) are foundational components of all ecosystems, inhabiting almost every imaginable environment and comprising the majority of the planet’s organismal and evolutionary diversity. Microorganisms play integral roles in ecosystem functioning; are important in the biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorus (P), and various metals (eg Barnard et al. 2005); and may be vital to ecosystem responses to large-scale climatic change (Mackelprang et al. 2011). Rarely found alone, microorganisms often form complex communities that are dynamic in space and time (Martiny et al. 2006). For these and other reasons, ecologists and environmental scientists have become increasingly interested in understanding microbial dynamics in ecosystems. Ecological studies of microbes in the environment generally focus on determining which organisms are present and what functional roles they are playing or could play. Rapid advances in molecular and bioinformatic approaches over the past decade have dramatically reduced the difficulty and cost of addressing such questions (Figure 1; WebTable 1). Yet the range of methodologies currently in use and the rapid pace of their ongoing development can be daunting for researchers unaccustomed to these technologies.