How Research on Microbiomes is Changing Biology: A Discussion on the Concept of the Organism

Abstract

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems (digestive, immune, nervous, etc.) of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation-conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology.

The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality

“…And this includes the host genome too. Notice that the same cannot be said about the gravitational field, which would be the same irrespectively of whether there are organisms whose metabolism, development, or immunology it can affect (see also Stencel and Proszewska 2017;Suárez and Triviño 2019;Lloyd and Wade 2019;Suárez and Stencel, under review).…”

Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation

“…Unfortunately, the above understanding of organisms, which forms the basis for BDM incompatibility, is currently being questioned from many different angles, especially that of microbiomics, which shows—as we have presented throughout this paper—that many fundamental functions of organisms are performed by symbiotic microorganisms (see Pradeu 2010 , 2011 ; Gilbert et al 2012 ; Stencel and Proszewska 2017 ). The most radical example, presented in the previous section, is the case of vestimentiferans (tubeworms), which acquire sets of symbiotic bacteria from their environment on which they depend for their energy supply, and which, during the stage of metamorphosis, lose their functioning digestive tract altogether (Gibson et al 2010 ).…”

“…This approach to speciation is a consequence of the Modern Synthesis paradigm; organisms were understood by contemporary scientists in the classic way, specifically, as a group of cells, the product of successive divisions of an egg cell, which interact with one another to induce developmental pathways, and which, as a whole, constitute the organism. This is one of the most popular ways of conceptualising organisms (see Pradeu 2010 ; Gilbert et al 2012 ; Stencel and Proszewska 2017 ). Furthermore, this view of what constitutes an organism was maintained over the years as well by others, even by those who aimed to undermine the basic concepts of evolutionary biology, such as Dawkins ( 1982 , p. 263): ‘The organism has the following attributes.…”

A part‐dependent account of biological individuality: why holobionts are individuals and ecosystems simultaneously

“…Discerning what counts as a biological individual constitutes a central problem in the agenda of biologists (Pepper & Herron, 2008; Gilbert et al ., 2012; Rees, Bosch, & Douglas, 2018), and philosophers (Godfrey‐Smith, 2013; Clarke, 2013; Kovaka, 2015; Smith, 2017; Stencel & Proszewska, 2018; Suárez, 2018; Wilson & Barker, 2019; cf . Section II in Smith‐Ferguson & Beekman, 2019).…”