Reconstructing each cell's genome within complex microbial communitiesâ€”dream or reality?

Patrick Schwientek,Tanja Woyke,Christian Rinke,Scott Clingenpeel,Alicia Clum

doi:10.3389/fmicb.2014.00771

Abstract

As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.

Highlights

Our current inability to cultivate the bulk of bacteria and archaea in the laboratory combined with a strong drive to analyze microbial communities in situ, gave rise to a large array of cultivation-independent methods that have been used for the past 20 years
With the advent of metagenomics it became possible to examine the genetic content of microbial communities without needing any a priori knowledge of the genetic sequences present
Improved methods for the assembly and binning of metagenome sequences are emerging (Wrighton et al, 2012; Albertsen et al, 2013), linking potential functions to phylogeny still poses a major challenge for metagenomic approaches, especially in complex communities

Summary

Introduction

Our current inability to cultivate the bulk of bacteria and archaea in the laboratory combined with a strong drive to analyze microbial communities in situ, gave rise to a large array of cultivation-independent methods that have been used for the past 20 years. LIMITED GENOME ACCESS The fraction of single-cell genomes that can be recovered from a sample is highly variable (Figure 1A) due to technical challenges and biases at multiple steps of the process. The step of the process involves lysing the cells so that the genome amplification reagents will have access to the cell’s DNA.

Results

Conclusion