# A Concept Using α‐Niche Evolution Within Bacterial Communities to Direct β‐Niche Evolution of Focal Species

## TL;DR

The paper proposes a new concept for steering bacterial evolution by linking resource use (α-niche) and environmental adaptation (β-niche) through microbial community interactions.

## Contribution

A novel framework for directing bacterial evolution by leveraging interspecies interactions to influence β-niche traits via α-niche evolution.

## Key findings

- Bacterial evolution can be steered through α-niche evolution that indirectly influences β-niche traits.
- Biotic interactions in microbial communities can be harnessed to control evolutionary outcomes.
- The concept offers potential applications in reducing antibiotic resistance and enhancing bioremediation.

## Abstract

The process of bacterial adaptation has a profound impact on human wellbeing and health, but our toolkit to modify evolution is limited. Here, we present a concept of how steering adaptation can be achieved by integration of bacterial evolution and microbial ecology. The fundamental question is how specific species bloom after community perturbation and subsequently evolve. We consider two kinds of traits—α‐niche traits involved in partitioning resources (e.g., broadened resource consumption) and β‐niche traits driven by changes in the abiotic environment (e.g., pH adaptation or resistance after antibiotic treatment). We suggest that the evolution of the second trait can be directed indirectly via the evolution of the first trait, exploiting specific interspecies interactions. Thus, understanding how these traits interact in co‐evolving communities may offer unprecedented opportunities to deflect trait evolution. Summarising current knowledge, emphasising open questions and highlighting conceptual ideas, we hope to stimulate new studies that are needed to move this field forward.

There is a great need for approaches to control how species evolve in response to environmental changes, particularly in complex microbiomes. The feasibility is often met with scepticism due to the multitude of open questions and high dimensionality of community eco‐evolutionary dynamics. Attempts to direct evolution in microbiomes may seem elusive, but our synthesis of the field delivers promising ways to overcome these problems. We start our work by summarising how microbiomes impact evolutionary change over ecological timescales before building a concept that rationalises ecological and evolutionary approaches. We state how this combined approach will generate new and exciting knowledge that will have a multifaceted impact from healthcare to environmental bioremediation. The concept describes how evolution can be directed by biotic interactions that modify ecological opportunities. We detail how and when evolution to exploit a novel resource, the evolution of α‐niches, mediates the evolution of a trait needed to mitigate abiotic environmental change, the evolution of β‐niches, and how this plays out in the context of a community. A worked example visualises how applying the concept can create opportunities that minimise the evolution of antibiotic resistance, and another example visualises how this could be exploited for bioremediation. We then summarise how biotic interactions impact evolutionary rates more generally before proposing the focus of future research; this highlights new avenues to illuminate the ‘black box’ of the ecological niches of microbes, and suggests experimental designs that shift the eco‐evolutionary standard.