Soil metabarcoding reveals the distinct microbial signature of a remnant forest patch at a local restoration initiative in the Ecuadorian Chocó

Abstract

The Tumbes-Chocó-Magdalena hotspot is a globally recognized center of endemism that is undergoing severe deforestation. While conservation and restoration efforts typically prioritize the recovery of aboveground macroscopic biodiversity, the response of soil microbial communities remains largely uncharacterized in this region. To address this data gap, we assessed soil bacterial communities in three land-use types (reference forest, early-stage restored parcel, and degraded land) within the "La Esperanza Forest" reserve in the Ecuadorian Chocó. Using 16S rRNA gene metabarcoding and robust compositional data analysis (e.g., ALDEx2, PERMANOVA), we evaluated shifts in taxonomic diversity and community structure. Sequencing revealed 1,208 genera and dominant genera (e.g., Bacillus , Paenibacillus ) that persisted across all habitats. However, despite the shared presence of these dominant taxa, the sampled land-use plots exhibited distinct structural differences in their microbial communities. Reference remnant forest's soils exhibited significantly higher community evenness and distinct multivariate partitioning driven by strongly associated structural taxa (e.g., Dinghuibacter , Phyllobacterium ). Conversely, degraded lands were significantly enriched in stress-associated bacteria, notably Rhodanobacter . Early-stage restored parcel soil clustered structurally closer to degraded soil than to the reference forest, indicating a pronounced spatial compositional similarity to disturbed soils rather than the reference state. Our findings from this localized study indicate that the fundamental microbial scaffolding of this remnant Chocó Forest soil hosts a distinct bacterial community structure, and that recovering soil microbial diversity in the adjacent old agricultural land may require extended timeframes and additional restoration approaches. We highlight remnant forest patches as critical reservoirs of belowground biodiversity and emphasize the necessity of integrating soil microbiology into continuous, long-term conservation monitoring frameworks.