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.

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

“…Species require a combination of biotic and abiotic conditions to occupy a determined area and grow and reproduce during a certain period of time [18]. The entire set of conditions to keep its growth rate positive is known as niche [19][20][21].…”

A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria

“…Some HGT genes in the GECs of different ecological niches may thus help recipients to adapt to new habitats, and affects population diversification (Baquero et al . 2021 ). These results allow us to speculate that the GECs composed of strains in Lactobacillaceae family with high sugar utilization accelerated their adaptations to new niches.…”

On the Verge of a Catastrophic Collapse? The Need for a Multi-Ecosystem Approach to Microbiome Studies

“…A proper assessment of current health problems like new pandemics and the rise of autoimmune indications can thus only be effective by incorporation of all (microbial) ecosystems involved, not being limited to our human microbiome alone. For example, a full comprehension of zoonotic disease requires not only understanding of the human microbiome but also of the microbial ecosystem belonging to the vector from which the pathogenic microorganism is being transferred, as also suggested by the concept of microbiota coalescence ( Baquero et al, 2021 ). Analogously, health cannot be understood without a proper understanding of the ecosystem containing the old friends.…”