Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems

Microbiome - Tập 5 - Trang 1-23 - 2017
Joanne B. Emerson1,2, Rachel I. Adams3, Clarisse M. Betancourt Román4,5, Brandon Brooks3,6, David A. Coil7, Katherine Dahlhausen7, Holly H. Ganz7, Erica M. Hartmann4,8, Tiffany Hsu9,10, Nicholas B. Justice11, Ivan G. Paulino-Lima12, Julia C. Luongo13, Despoina S. Lymperopoulou3, Cinta Gomez-Silvan11,14, Brooke Rothschild-Mancinelli15, Melike Balk16, Curtis Huttenhower9,10, Andreas Nocker17, Parag Vaishampayan18, Lynn J. Rothschild19
1Department of Microbiology, The Ohio State University, Columbus, USA
2Current Address: Department of Plant Pathology, University of California, Davis, USA
3Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, USA
4Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, USA
5Institute of Ecology and Evolution, University of Oregon, Eugene, USA
6Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, USA
7Genome Center, University of California, Davis, Davis, USA
8Department of Civil and Environmental Engineering, Northwestern University, Evanston, USA
9Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, USA
10The Broad Institute of MIT and Harvard, Cambridge, USA
11Lawrence Berkeley National Lab, Berkeley, USA
12Universities Space Research Association, NASA Ames Research Center, Moffett Field, USA
13Department of Mechanical Engineering, University of Colorado at Boulder, Boulder, USA
14Department of Environmental Science, Policy, and Management, University of California, Berkeley, USA
15Division of Biological Sciences, The University of Edinburgh, Edinburgh, UK
16Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
17IWW Water Centre, Mülheim an der Ruhr, Germany
18Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
19Planetary Sciences and Astrobiology, NASA Ames Research Center, Moffett Field, USA

Tóm tắt

While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.

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Microbiome

Tập 5

1-23

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