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Metagenomics and the niche concept

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Abstract

The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.

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Acknowledgments

I am grateful to Dr. Pieter van Dillewijn, Professor Chris Thomas and an anonymous reviewer for helpful comments on earlier stages of the manuscript. This paper was written during a Sabbatical stay at the Estación Experimental del Zaidín (CSIC), Granada, Spain, granted to DEM by the Ministry of Education of Spain.

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Authors and Affiliations

  1. Laboratorio de Ecología, Area de Producción Orgánica, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ciudad Universitaria, Av. Valparaiso s/n, Córdoba, CP 5000, CC 508, Argentina

    Diana Marco

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Correspondence to Diana Marco.

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Diana Marco is a member of the Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET).

Appendix

Appendix

Some terms used in the metagenomics field

Contig:

the result of joining an overlapping collection of sequences or clones.

Coverage (or depth):

the average number of times that a nucleotide is represented by a high-quality base in a collection of random raw sequence.

Metagenomic library:

a library made of cloned DNA from an environmental sample.

Raw sequence:

individual unassembled sequence reads, produced by sequencing of clones containing DNA inserts.

Scaffold:

the result of connecting contigs by linking information, such as paired-end reads from plasmids, paired-end reads from BACs, known mRNAs, or other sources. The contigs in a scaffold are ordered and oriented with respect to one another.

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Marco, D. Metagenomics and the niche concept. Theory Biosci. 127, 241–247 (2008). https://doi.org/10.1007/s12064-008-0028-x

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