Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil

Abstract

Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.

Keywords: Agroecosystems; Crop microbiome; Legacy effect; Monoculture; Temporal community development.

Fig. 1

Soil A bacteria/archaea community and B fungal community differentiation in response to different crop species, across different crop cycles, and whether there were actively growing plants in these soils (cultivated vs. uncultivated). Weighted UniFrac distance was used for bacteria/archaea and Bray–Curtis distance was used for fungi

Fig. 2

Cyclical changes in community richness and composition of bacteria/archaea A–B and fungi C–D over three cultivation cycles. The dotted lines mark the median and show the relationship between the cultivated and uncultivated soils as the communities develop overtime. The letters above the boxes indicate significance groups

Fig. 3

Normalized response (effect size) of bacteria/archaea compared to fungi in regard to their A community richness and B community composition (based on Aitchison distance) over three continuous cropping cycles. The response of each cultivated and uncultivated cycles is compared to the baseline prior to the first planting (i.e., cycle 1, uncultivated). The marks inside the circles indicate standard deviation

Fig. 4

Significant shifts in A bacterial/archaeal ASVs and B fungal OTUs from the first uncultivated cycle (prior to any planting) compared to the last cycle (cultivated). The shifts of the individual ASV/OTUs are measured in Log2 Fold change where positive values indicate increase in abundance and negative values indicate decrease in abundance. The individual ASV or OTU are represented by dots displayed on a single line. Each line represents a genus, grouped into their respective phyla