Microbial single-cell omics: the crux of the matter

Anne-Kristin Kaster,Morgan S Sobol

doi:10.1007/s00253-020-10844-0

Anne-Kristin Kaster, Morgan S Sobol

Open Access

https://doi.org/10.1007/s00253-020-10844-0

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Abstract

Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.Key points• Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways.• Disadvantages of metagenome-assembled genomes are overcome by single-cell omics.• Functional analysis of single cells explores the heterogeneity of gene expression.• Technical challenges still limit this field, thus prompting new method developments.

Highlights

Microbial dark matter (MDM)Prokaryotic microorganisms harbor an enormous potential for biotechnological applications, such as novel natural product discovery, bioenergy production, and bioremediation of harmful anthropogenic-introduced substances (Singh et al 2014; Katz and Baltz 2016; Kumar and Kumar 2017; Mullis et al 2019; Stincone and Brandelli 2020)
Large structural variants (SVs) such as genome rearrangements, gene insertions, duplications, or losses which can vary in highly homologous cells due to mutations, horizontal gene transfer (HGT), and recombination cannot be analyzed and mobile genomic elements such as plasmids or transposable elements cannot be accurately binned (Fraser et al 2007; Vergin et al 2007; MartinezGarcia et al 2012b; Shapiro et al 2012; Dam et al 2020)
Long-read sequencing technologies such as Pacific Biosciences’ (PacBio) single-molecule real-time (SMRT) sequencing and Oxford Nanopore Technologies’ (ONT) nanopore sequencing have improved the detection and study of large SVs that lead to heterozygosity on the strain level (Amarasinghe et al 2020; Ho et al 2020)

Summary

Introduction

Microbial dark matter (MDM)Prokaryotic microorganisms harbor an enormous potential for biotechnological applications, such as novel natural product discovery, bioenergy production, and bioremediation of harmful anthropogenic-introduced substances (Singh et al 2014; Katz and Baltz 2016; Kumar and Kumar 2017; Mullis et al 2019; Stincone and Brandelli 2020). The workflow involves (a) sampling and preservation, (b) non-specific staining of microbial populations, (c) cell sorting, (d) cell lysis, (e, f) whole genome amplification (WGA), (g) screening for SAGs of interest, and (h, i) sequencing and analysis (Fig. 1).

Results

Conclusion