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Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

Abstract

Technological advances are enabling the sequencing of environmental DNA and RNA at increasing depth and with decreasing costs. Metagenomic and transcriptomic analysis of soil microbial communities and the assembly of 'population genomes' from soil DNA are therefore now feasible. Although the value of such 'omic' approaches is limited by the associated technical and bioinformatic difficulties, even if these obstacles were eliminated and 'perfect' metagenomes and metatranscriptomes were available, important conceptual challenges remain. This Opinion article considers these conceptual challenges in the context of the current use of omics in soil microbiology, but the main arguments presented are also relevant to the application of omics to marine, freshwater, gut or other environments.

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Figure 1: Metagenomic and metatranscriptomic analyses of soil samples.
Figure 2: Distinction between 'gene-centric' and 'genome-centric' metagenomics.
Figure 3: Changes in microbial metagenomes and metatranscriptomes following a change in temperature.

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Acknowledgements

The author is indebted to M. Firestone for invaluable constructive criticism of this article and to the Leverhulme Trust for the award of a Leverhulme Trust Research Fellowship.

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Correspondence to James I. Prosser.

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PowerPoint slides

Glossary

cDNA

Double-stranded DNA with a sequence that is complementary to that of the specific mRNA template from which it is synthesized in a reaction catalysed by reverse transcriptase.

Denaturing gradient gel electrophoresis

(DGGE). A gel electrophoresis-based method in which gradients in denaturing conditions (such as temperature, urea concentration or formamide concentration) are used to separate DNA fragments with different mobilities.

Extracellular polymeric material

Material secreted by microbial cells that mainly consists of polysaccharides and proteins; it is also known as extracellular polymeric substance (EPS). This may be released into the growth medium but it often remains attached to the cells and contributes to the formation and function of biofilms.

Genome closure

This process (also known as genome finishing) creates a complete genome by sequencing the gaps that remain when sequenced genome fragments are assembled into overlapping sequences known as contigs.

Maximum specific growth rate

The highest specific growth rate that is attainable under the prevailing environmental conditions with non-limiting substrate concentration and no inhibition of growth.

Neutral theory

A theory that assumes that all phylotypes within a microbial community follow the same rules, regardless of differences in phenotypic properties. The relative abundances of phylotypes and community composition are then determined by random birth, death, speciation and migration.

Nitrifier

Microorganisms that perform the process of nitrification, which is the sequential oxidation of reduced forms of nitrogen (usually in ammonia) to nitrite and then nitrate. In the soil, this process is carried out mainly by archaeal and bacterial ammonia oxidizers and by bacterial nitrite oxidizers.

Oligotrophy

Oligotrophic microorganisms are those that are adapted to exploit substrates present in low concentrations. The term is used to describe organisms that dominate natural habitats in which nutrients are scarce.

Phylotypes

A bacterial or archaeal phylotype is an evolutionarily related group of organisms. When communities are characterized in terms of 16S rRNA or functional gene sequences, phylotypes are defined as those sharing a particular level of sequence identity. Typically, for the 16S rRNA gene, this is 97% or 99% sequence identity, which reflects traditional classification criteria for microbial species.

Saturation constant

The concentration of a growth-limiting substrate at which the specific growth rate of a microbial population is half the maximum specific growth rate.

Seed bank

A term taken from plant ecology, which refers to the total number and diversity of seeds in the soil, including all ungerminated, viable seeds. By analogy, it can also be used to refer to all viable microorganisms within the soil, including those that are rare, inactive or dormant, and therefore constitutes the total richness of the soil microbial community.

Specific growth rate

In the context of a microbial population, this is the rate of increase in biomass relative to, or specific to, the current biomass. It has units of reciprocal time and is constant during exponential growth.

Tortuosity

A measure of the ability of fluid to flow through porous media. A soil with high tortuosity is one in which there is greater resistance to fluid flow owing to a more complex porous structure and greater path lengths.

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Prosser, J. Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology. Nat Rev Microbiol 13, 439–446 (2015). https://doi.org/10.1038/nrmicro3468

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