The Unseen World: Environmental Microbial Sequencing and Identification Methods for Ecologists

Authors

Naupaka Zimmerman, Stanford University and University of Arizona
Jacques Izard, Forsyth Institute and Harvard School of Dental MedicineFollow
Christian Klatt, University of Agricultural Sciences
Jizhong Zhou, University of Oklahoma
Emma Aronson, University of California, RiversideFollow

ORCID IDs

Izard https://orcid.org/0000-0002-5904-5436

Document Type

Article

Date of this Version

12-4-2014

Citation

Frontiers in Ecology and Environment (2014) 12(4): 224–231

doi: 10.1890/130055

Comments

License: CC BY

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. Rarely found alone, microorganisms often form complex communities that are dynamic in space and time. 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. 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.