Long-term maize-Desmodium intercropping shifts structure and composition of soil microbiome with stronger impact on fungal communities

Abstract

Purpose Push–pull is an intercropping technology that is rapidly spreading among smallholder farmers in Sub-Saharan Africa. The technology intercrops cereals with Desmodium to fight off stem borers, eliminate parasitic weeds, and improve soil fertility and yields of cereals. The above-ground components of push–pull cropping have been well investigated. However, the impact of the technology on the soil microbiome and the subsequent role of the microbiome on diverse ecosystem benefits are unknown. Here we describe the soil microbiome associated with maize—Desmodium intercropping in push–pull farming in comparison to long-term maize monoculture. Methods Soil samples were collected from long-term maize—Desmodium intercropping and maize monoculture plots at the international centre for insect physiology and ecology (ICIPE), Mbita, Kenya. Total DNA was extracted before16S rDNA and ITS sequencing and subsequent analysis on QIIME2 and R. Results Maize—Desmodium intercropping caused a strong divergence in the fungal microbiome, which was more diverse and species rich than monoculture plots. Fungal groups enriched in intercropping plots are linked to important ecosystem services, belonging to functional groups such as mycorrhiza, endophytes, saprophytes, decomposers and bioprotective fungi. Fewer fungal genera were enriched in monoculture plots, some of which were associated with plant pathogenesis and opportunistic infection in humans. In contrast, the impact of intercropping on soil bacterial communities was weak with few differences between intercropping and monoculture. Conclusion Maize—Desmodium intercropping diversifies fungal microbiomes and favors taxa associated with important ecosystem services including plant health, productivity and food safety.

A comparative study on the impact of fiveDesmodiumspecies on soil microbiome reveals enrichment of selected bacterial and fungal taxa

“…In a separate study, the frequency of occurrence of a mycotoxin-producing fungus Aspergillus flavus was lower in push-pull than maize monoculture plots (Maxwell et al, 2017). These findings are in line with our previous study where we show that push-pull farming and Desmodium intercropping in cereal farming impact diversity of fungal communities more than bacteria (Mwakilili et al, 2021), manipulation of fungal communities in the soil to promote competitive beneficial filamentous fungi has been established as a method to manage mycotoxins in cereals (Sarrocco et al, 2019). In a similar vein, another study demonstrated that maize growing on soil from long-term push-pull plots produced higher amounts of secondary metabolites and experienced lesser herbivory than maize growing on soil from corresponding maize monoculture plots (Mutyambai et al, 2019).…”

“…plots harboured a substantial percentage of the significantly abundant taxa; these are D. uncinatum, D. incanum and D. intortum (Figure 7.) As in our previous long-term study on maize-Desmodium intercropping soils (Mwakilili et al, 2021) where we investigated impact of push-pull technology that employs perennial Desmodium spp. intercrops, soils diverged more in fungal than bacterial communities.…”

“…In a previous study we characterised the difference in soil microbial composition, structure and diversity in long term push-pull plots compared to maize monoculture (Mwakilili et al, 2021). Several other studies reporting on benefits of push-pull technology that are clearly linked to soil microbial communities suggest a deeper role than currently known.…”

Plants control the structure of mycorrhizal and pathogenic fungal communities in soil in a 50-year maize monoculture experiment

“…Paraglomus, was identified in crop rotation. Mwakilili et al (2021) demonstrated that the genus Glomus was enriched in maize monoculture plots. The abundance of Glomeromycota fungi was significantly negatively correlated with soil pH which was lower in monoculture.…”

The push-pull intercrop Desmodium does not repel, but intercepts and kills pests

“…This begs the question of why Desmodium releases these volatiles constitutively. Push-pull maize- Desmodium intercropping causes substantial shifts in below-ground ecosystems, including increased soil microbe diversification, increased soil nitrogen and carbon, increased plant defense through plant-soil feedback, and suppression of parasitic weeds and pathogenic microbes 22,23 . We therefore verified if the ‘constitutive’ release of volatiles was, in fact, induced or enhanced by soil-borne interactions.…”