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.

Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation

“…While gene abundance (DNA) data give a good insight into the functional potential of a community, transcriptional (RNA) data provide a direct measurement of function and thus enable the understanding of a community's role in ecosystem function (Aguiar-Pulido et al, 2016;Singer et al, 2017;Hassa et al, 2018). Transcriptional data have been found to include gene sequences that are not present in corresponding gene abundance data (Shi et al, 2011).…”

Metabolic dependencies govern microbial syntrophies during methanogenesis in an anaerobic digestion ecosystem

“…However, a crucial limitation of studies based solely on metagenomic surveys is the lack of direct evidence for the activity of individual microbes. Therefore, other -omics approaches and advanced molecular tools, such as transcriptomics, proteomics, metabolomics, and stable isotope labelling were gradually introduced to analyze the microbial activity during the methanogenic process [14][15][16][17].…”

Microbial conservation in the Anthropocene

“…This is particularly important if one considers that niche partitioning, complex interaction networks and functional redundancy are key characteristics of most microbial ecosystems (Allison and Martiny, 2008). This could be achieved using a combination of metagenomic/metatranscriptomic sequencing (Birrer et al, 2017) and by incorporating recent developments in stable isotope analysis (for instance, H 18 2 O and or D 2 O assays; Aanderud and Lennon, 2011;Berry et al, 2015;Kopf et al, 2015) or biorthogonal noncanonical amino acid tagging (Hatzenpichler et al, 2016) that facilitate differentiation of active from nonactive cells prior to meta-omic analyses (Singer et al, 2017). Stress-response curves could then be generated for each microbial function or pathway (instead of taxa), and the derived EC 10 s or EC 50 s used to generate functional sensitivity distributions (FSD).…”