# Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings

## TL;DR

This study shows that soil microbial functions in restored agricultural areas show persistent changes, especially in phosphorus metabolism, suggesting the need for targeted restoration strategies.

## Contribution

The study reveals that functional composition, not just diversity, reflects persistent agricultural impacts and suggests alternative states in restored soils.

## Key findings

- Functional composition differs between remnant and restored soils, especially with elevated phosphorus.
- Remnant soils support more phosphorus metabolism functions despite lower available phosphorus.
- Agricultural legacies may lead to alternative states requiring targeted interventions for full recovery.

## Abstract

Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa‐function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post‐agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.

Soil microbial functions are key indicators of ecosystem recovery but can be obscured by taxonomic redundancy. Using shotgun metagenomics, we show that while overall functional diversity remains stable across land conditions, functional composition shifts persist in restored soils, particularly in relation to phosphorus metabolism. These findings suggest that agricultural legacies may maintain alternative states, and targeted interventions addressing soil microbiomes or abiotic legacies may be needed to fully restore ecosystem function.