# Soil Bacteriome Shifts along a Cultivation Gradient in Southwestern Spanish Wetlands

## TL;DR

This study shows how rice farming over decades changes soil bacteria in Spanish wetlands, with major shifts in bacterial types and soil chemistry happening quickly, within 25 years.

## Contribution

The study provides new insights into how long-term rice cultivation rapidly transforms soil bacterial communities and their functions in wetland ecosystems.

## Key findings

- Cultivated soils showed increased Chloroflexota and decreased Actinomycetota and Planctomycetota with longer cultivation.
- Denitrification potential rose in rice paddies, linked to Chloroflexota, while natural wetlands had more diverse nitrogen pathways.
- Key bacterial groups like Anaerolineae and Nocardioides were enriched in rice soils, while others like Euzebya and Rubrobacter were more common in natural wetlands.

## Abstract

Understanding how long-term agricultural practices affect soil bacteriome is essential for sustainable land management. In the Guadalquivir Marshes of southwestern Spain, which encompass both Doñana National Park and one of Europe’s most productive rice cultivation areas, decades of rice farming have transformed natural wetlands into artificial agroecosystems. Although bacterial degradation in cultivated soils has been previously suggested, comparative analyses between rice paddies and adjacent natural wetlands remain scarce.

Here, we characterized the soil bacteriome across a cultivation gradient by comparing undisturbed natural marshes, within Doñana National Park, with rice fields cultivated for 25 years (Cantarita) and 80 years (Mínima 2). Using full 16S rRNA gene via long-read metabarcoding and standardized soil physicochemical assays, we analysed taxonomic composition, environmental associations, and predicted functional profiles.

Our results reveal a progressive restructuring of bacterial communities with increased cultivation time, notably a significant enrichment of Chloroflexota (especially Anaerolineae) and a decline in Actinomycetota and Planctomycetota in paddy soils. Functional predictions indicated a higher potential for denitrification in cultivated soils—likely involving Chloroflexota taxa—compared to more diverse nitrogen pathways in natural sites. These shifts were strongly associated with changes in pH, electrical conductivity, calcium carbonate, and nitrate levels. Remarkably, most bacterial differences were already evident within the first 25 years of cultivation, underscoring the rapid ecological impact of intensive rice cultivation.

Notably, we identified specific bacterial groups (Anaerolineae and Nocardioides in paddy soils; Euzebya, Rubrobacter, and Planctomycetota in natural wetlands), whose enrichment was associated with soil type. This approach highlights the value of integrating bacterial-based assessments into sustainable wetland management strategies.

The online version contains supplementary material available at 10.1007/s00248-025-02660-8.