Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology

Abstract

Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR, microarray analysis and metagenomics to complex microbial populations. In the absence of suitable cultivation methods, it was not possible to obtain DNA samples from individual microorganisms. Recently, a method called multiple displacement amplification (MDA) has been used to circumvent these limitations by amplifying DNA from microbial communities in low-biomass environments, individual cells from uncultivated microbial species and active organisms obtained through stable isotope probing incubations. This review describes the development and applications of MDA, discusses its strengths and limitations and highlights the impact of MDA on the field of microbial ecology. Whole genome amplification via MDA has increased access to the genomic DNA of uncultivated microorganisms and low-biomass environments and represents a 'power tool' in the molecular toolbox of microbial ecologists.

Comparative study of viromes from freshwater samples of the Ile-Balkhash region of Kazakhstan captured through metagenomic analysis

“…Nucleic acids were isolated from the collected samples in the amount of 2.5-4 lg per 1 L water sample, which corresponds to the average number of isolated nucleic acids from the same volume [29]. Considering that rather small input amounts of ng are sufficient for sequencing of nucleic acid with Illumina HiSeq [30], in further studies it will be possible to reduce the volume of water samples in order to decrease the time and cost of isolation of nucleic acids.…”

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

“…There are numerous review articles describing the impact of genomics and metagenomics methods on microbial ecology (Xu 2006, Binga, Lasken et al 2008, Aziz, Breitbart et al 2010, Gilbert and Dupont 2011, Rittmann and Herwig 2012, Su, Lei et al 2012, Thompson, Field et al 2013, Reid 2014, Tseng and Tang 2014. There is also a plethora of papers that discuss the application of metagenomics in the field of biotechnology to discover novel enzymes, drug molecules, processes and applications (Lorenz, Liebeton et al 2002, Schloss and Handelsman 2003, Cowan, Meyer et al 2005 Eck Kennedy, Marchesi et al 2007, Brady, Simmons et al 2009, Steele, Jaeger et al 2009, Piel 2011, Iqbal, Feng et al 2012, de Castro, Sartori da Silva et al 2013, Hicks and Prather 2014.…”

Development of a "genome-proxy" microarray for profiling marine microbial communities, and its application to a time series in Monterey Bay, California

“…16S-or ITS-profiling of libraries has also been proxy for profiling of the communities themselves (e.g. Suzuki et al 2004, Martin-Cuadrado et al, 2007, Neufeld et al, 2008. End-sequencing of large-insert libraries has been used to describe the taxonomic and metabolic profile of the community (e.g.…”

“…Such large-insert libraries have been constructed from a number of habitats and extensively screened for clones of interest (e.g. Rondon et al, 2000, Béjà et al, 2002a, Zeidner et al, 2003, de la Torre et al, 2003, Treusch et al, 2004, Sabehi et al, 2005, Neufeld et al, 2008. 16S-or ITS-profiling of libraries has also been proxy for profiling of the communities themselves (e.g.…”