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Microbial diversity and the “lower-limit” problem of biodiversity

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Abstract

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “biodiversity”: the issues of defining the units of biodiversity and of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity.

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Notes

  1. It is worth noting that this situation has changed significantly since the beginning of the 1990s. The relationship between diversity and ecosystems properties such as stability, decomposition or primary productivity has become a most fertile area of ecological investigation (e.g. Loreau et al. 2001; Naeem 2002; Petchey and Gaston 2006; Dornelas 2010).

  2. In this respect, O’Malley and Dupré (2007) and Morgan (2010) are rare exceptions.

  3. This is probably symptomatic of a more general lack of theoretical integration in ecology (see, for instance, Pickett et al. 2007; Scheiner and Willig 2011).

  4. These estimates should be taken with caution and are disputed (see Whitman et al. 1998; Lipp et al. 2008; Kallmeyer et al. 2012). In particular, estimates of the total biomass that these unicellular organisms represent differ significantly. Nevertheless, estimates of the total number of unicellular organisms on Earth are consistent in terms of orders of magnitude.

  5. For instance, if n is the total number of species of a given ecosystem E, and if p i is the relative abundance of species i (such that ∑p i  = 1), then the species richness of E is equal to n. Similarly, the Shannon-Wiener diversity measure of E is equal to exp(−∑p i log(p i )) and the Simpson diversity measure of E is 1/∑p 2 i . If one has phylogenetic or taxonomic information about the species of E such that it is possible to assess, for instance, pairwise distances between species depending on their characteristic features, then one can define measures that include these distances and account for the diversity of E in terms of features. For more details, see for instance (Magurran 2004).

  6. Indices that focus on species abundance and heterogeneity include the species richness index, the Shannon-Wiener diversity measure or the Simpson diversity measure (see note 5); indices that focus on species features and dissimilarities include the Weitzman index or the Nehring-Puppe index. For more details about these indices, see for instance Baumgärtner (2006b) or Magurran (2004).

  7. Viroids are viral particles that are usually smaller than viruses and that are composed of a short stretch of circular single-stranded RNA. Unlike viruses, viroids do not have any protein coat (e.g. Diener 1971; Dimmock et al. 2007). Satellites are viral agents composed of nucleic acid (DNA or RNA) that can only reproduce if their host cells are also co-infected with another specific virus called a helper-virus or master-virus. Satellites may represent evolutionary intermediates of viroids and viruses (e.g. Saunders and Stanley 1999; Dimmock et al. 2007). Virophages are viruses that infect other larger viruses. They are sometimes considered a sub-group of satellites, yet some argue for a distinct classification (e.g. La Scola et al. 2008). Plasmids are double-stranded, and often circular, DNA molecules that notably occur in bacteria and that can replicate independently of the chromosomal DNA (e.g. Lederberg 1952). Prions are often infectious agents that are not composed of nucleic acids but that consist of proteins considered to be in a misfolded form and that have been identified in different mammals and in yeast (e.g. Prusiner 1982). Interestingly, prions have recently been found to be capable of Darwinian evolution (Li et al. 2010). It is the development of sequencing techniques and of biochemical tools in the past decades that has led to a more thorough investigation of these numerous, minute, and organized entities that abound in the vicinity of known living entities at their sub-cellular scale. Because these discoveries have so far been mostly driven by the pathogenicity of the entities in question, it is reasonable to expect that many more such non-pathogenic sub-cellular entities will be identified in the near future.

  8. The International Committee on the Taxonomy of Viruses recognizes the existence of 2,475 virus species as of late 2011 (see http://www.ictvonline.org/virusTaxInfo.asp).

  9. This is the case both in the diachronic context of origins of life research that aims at explaining the historic transition from non-living matter to living matter, and in the synchronic context of microbial research that investigates the present frontier of life and non-life. In this paper, the focus is obviously on this second synchronic research context.

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Acknowledgments

I wish to thank Maureen O’Malley as well as four anonymous referees for extremely constructive comments that have led to substantial improvements. The manuscript also benefited from exchanges with Frédéric Bouchard, Steve Kembel, Dan Kneeshaw and Purificación López-García.

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    Christophe Malaterre

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Malaterre, C. Microbial diversity and the “lower-limit” problem of biodiversity. Biol Philos 28, 219–239 (2013). https://doi.org/10.1007/s10539-012-9356-9

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