# The plant microbiota signature of the Anthropocene as a challenge for microbiome research

## TL;DR

The paper discusses how human activities are changing plant microbiomes, leading to loss of diversity and increased pathogens, which threatens ecosystem health.

## Contribution

The paper identifies a unique microbiome signature of the Anthropocene linked to human activities and its impact on plant microbiota.

## Key findings

- Human activities shift plant microbiota diversity and evenness, reducing host specificity.
- The Anthropocene signature includes increased r-strategic microbes, pathogens, and antimicrobial resistance genes.
- These changes are associated with dysbiosis and frequent pathogen outbreaks.

## Abstract

One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.

Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.

Video abstract

Video abstract

The online version contains supplementary material available at 10.1186/s40168-021-01224-5.