Dataset COABES-Benthic prokaryotic and fungal communities in streams

1. The expansion of oil palm plantations and cattle grazing lands has a detrimental impact on freshwater ecosystems, causing ecological degradation and biodiversity loss in the tropics. Particularly overlooked in this context are the effects on the aquatic microbial community.
2. We assessed the benthic aquatic microbial community of streams in grazing lands, oil palm plantations (with and without riparian buffers), and rainforests using metabarcoding to analyze prokaryotic amplicon sequence variants (ASVs) and fungal operational taxonomic units (OTUs).
3. We observed significantly higher microbial richness in streams in rainforests compared to grazing lands and oil palm plantations lacking buffers, but not compared to oil palm plantations with riparian buffers. Groups commonly found in fecal matter were found in streams in grazing land, streams in the plantations lacking buffers showed less abundance of wood decomposers, and these two land uses had more primary producers. Prokaryote richness and diversity were associated positively with riparian buffers and negatively with temperature, light, and grazing lands, while fungi richness responded positively to the proximity of forests and the protected area.
4. The negative effects of agriculture on the stream microbial richness, diversity, and community composition were partially mitigated by the conservation of riparian buffers in the oil palm plantations and probably, the proximity to forests (source of spores).
5. Our findings demonstrate the potential role of metabarcoding on stream benthos for monitoring agricultural lands and underline the importance of riparian buffers in mitigating, to some extent, biodiversity loss in agriculture streams.