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Title: Capturing the genetic makeup of the active microbiome in situ

Abstract

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Authors:
 [1];  [2];  [1]
+ Show Author Affiliations
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. Univ. of Vienna (Austria). Dept. of Microbial Ecology and Ecosystem Science. Division of Microbial Ecology
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); European Research Council (ERC)
OSTI Identifier:
1436339
Grant/Contract Number:  
AC02-05CH11231; 294343
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 11; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; environmental microbiology; microbial ecology

Citation Formats

Singer, Esther, Wagner, Michael, and Woyke, Tanja. Capturing the genetic makeup of the active microbiome in situ. United States: N. p., 2017. Web. doi:10.1038/ismej.2017.59.
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Singer, Esther, Wagner, Michael, & Woyke, Tanja. Capturing the genetic makeup of the active microbiome in situ. United States. https://doi.org/10.1038/ismej.2017.59
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Singer, Esther, Wagner, Michael, and Woyke, Tanja. Fri . "Capturing the genetic makeup of the active microbiome in situ". United States. https://doi.org/10.1038/ismej.2017.59. https://www.osti.gov/servlets/purl/1436339.
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@article{osti_1436339,
title = {Capturing the genetic makeup of the active microbiome in situ},
author = {Singer, Esther and Wagner, Michael and Woyke, Tanja},
abstractNote = {More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.},
doi = {10.1038/ismej.2017.59},
journal = {The ISME Journal},
number = ,
volume = 11,
place = {United States},
year = {Fri Jun 02 00:00:00 EDT 2017},
month = {Fri Jun 02 00:00:00 EDT 2017}
}
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