The Origin of Niches and Species in the Bacterial World

Abstract

Niches are spaces for the biological units of selection, from cells to complex communities. In a broad sense, "species" are biological units of individuation. Niches do not exist without individual organisms, and every organism has a niche. We use "niche" in the Hutchinsonian sense as an abstraction of a multidimensional environmental space characterized by a variety of conditions, both biotic and abiotic, whose quantitative ranges determine the positive or negative growth rates of the microbial individual, typically a species, but also parts of the communities of species contained in this space. Microbial organisms ("species") constantly diversify, and such diversification (radiation) depends on the possibility of opening up unexploited or insufficiently exploited niches. Niche exploitation frequently implies "niche construction," as the colonized niche evolves with time, giving rise to new potential subniches, thereby influencing the selection of a series of new variants in the progeny. The evolution of niches and organisms is the result of reciprocal interacting processes that form a single unified process. Centrifugal microbial diversification expands the limits of the species' niches while a centripetal or cohesive process occurs simultaneously, mediated by horizontal gene transfers and recombinatorial events, condensing all of the information recovered during the diversifying specialization into "novel organisms" (possible future species), thereby creating a more complex niche, where the selfishness of the new organism(s) establishes a "homeostatic power" limiting the niche's variation. Once the niche's full carrying capacity has been reached, reproductive isolation occurs, as no foreign organisms can outcompete the established population/community, thereby facilitating speciation. In the case of individualization-speciation of the microbiota, its contribution to the animal' gut structure is a type of "niche construction," the result of crosstalk between the niche (host) and microorganism(s). Lastly, there is a parallelism between the hierarchy of niches and that of microbial individuals. The increasing anthropogenic effects on the biosphere (such as globalization) might reduce the diversity of niches and bacterial individuals, with the potential emergence of highly transmissible multispecialists (which are eventually deleterious) resulting from the homogenization of the microbiosphere, a possibility that should be explored and prevented.

Keywords: bacterial niches; bacterial species; evolution; nichification; speciation.

FIGURE 1

Niches, diversification, and commonality of bacterial populations. Top: Two ancestor populations (red and blue triangles) that were adapted to their primitive, fundamental niches (broken lines); at the sides, the stair-like profiles represent the subdivision of the biotope by gradient formation. Different spaces in the gradient facilitate the diversification of the ancestor population in variants (colored rectangles), splitting the ancestor niche into new specific niches (adaptive radiation). Middle: Each of these specific variants further pixelates the biotope, taking advantage of sub-gradients, resulting in new rounds of diversification (red colored circles) and nichification (new adaptive radiation). Low: There is a limit to the diversification process, when neighbor variants start to exchange adaptive information, eventually producing an adaptive commonality and the emergence of a higher entity population (species?).

FIGURE 2

The process of conversion of biotopes in niches. The figure represents nine successive stages of nichification of a biotope, whose constituents are depicted by target-like circles, to represent gradients. First row: (left), a small bacterial population finds a selective combination of traits able to sustain its growth (brown circle); the limits are those of the current niche; the color intensity reflects the bacterial abundance; (middle), the population is expanding and converting in niche the neighboring regions of the biotope; (right), the combination of traits defining the niche is shifting to the right, so that the niche moves into the biotope space. Second row: (left), an extinction event has eliminated the pioneering colonizer population; however, from the outside environment, a new small population of the same organism enters the biotope, recognizes the conditions of the ancient niche, and reinstalls itself; (middle), the sequential variants of the pioneering population emerge. This variation allows for the expansion of the niche; (right), a new invader of the biotope (blue circle) produces a new niche. Third row: (left), sequential variation of the new population expands the blue niche; (middle), niches of the brown and blue populations start to converge; (right), this convergence facilitates genetic exchanges between brown and blue populations, creating a new pink population (species?) advancing the exploitation of the biotope’s carrying capacity, which is almost entirely converted in a niche.