The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

Abstract

Many bacteria and fungi in the plant rhizosphere and endosphere are beneficial to plant nutrient acquisition, health, and growth. Although playing essential roles in ecosystem functioning, our knowledge about the effects of multiple cropping regimes on the plant microbiome and their interactions is still limited. Here, we designed a pot experiment simulating different cropping regimes. For this purpose, wheat and faba bean plants were grown under controlled greenhouse conditions in monocultures and in two intercropping regimes: row and mixed intercropping. Bacterial and fungal communities in bulk and rhizosphere soils as well as in the roots and aerial plant parts were analyzed using large-scale metabarcoding. We detected differences in microbial richness and diversity between the cropping regimes. Generally, observed effects were attributed to differences between mixed and row intercropping or mixed intercropping and monoculture. Bacterial and fungal diversity were significantly higher in bulk soil samples of wheat and faba bean grown in mixed compared to row intercropping. Moreover, microbial communities varied between crop species and plant compartments resulting in different responses of these communities toward cropping regimes. Leaf endophytes were not affected by cropping regime but bacterial and fungal community structures in bulk and rhizosphere soil as well as fungal community structures in roots. We further recorded highly complex changes in microbial interactions. The number of negative inter-domain correlations between fungi and bacteria decreased in bulk and rhizosphere soil in intercropping regimes compared to monocultures due to beneficial effects. In addition, we observed plant species-dependent differences indicating that intra- and interspecific competition between plants had different effects on the plant species and thus on their associated microbial communities. To our knowledge, this is the first study investigating microbial communities in different plant compartments with respect to multiple cropping regimes using large-scale metabarcoding. Although a simple design simulating different cropping regimes was used, obtained results contribute to the understanding how cropping regimes affect bacterial and fungal communities and their interactions in different plant compartments. Nonetheless, we need field experiments to properly quantify observed effects in natural ecosystems.

Influence of plant genotype and soil on the wheat rhizosphere microbiome: Evidences for a core microbiome across eight African and European soils

“…However, the taxa richness was significantly affected by agricultural practices only in the Italian soils. These results are very similar to the findings of Hartman et al (2018) [9] that observed more effects of conventional vs organic practices on wheat microbiome structure (9-10% of the variance) than on diversity but also with other studies in various cropping systems [11,21]. The IT2 soil sampled from an organic farming field presented a higher taxa richness (56% higher) than IT1.…”

“…Following the advent of next generation sequencing, several studies characterized the rhizospheric wheat microbiome and investigated the influence of the compartment (rhizoplane vs endosphere), crop management or wheat genotypes on the diversity and structure of these complex microbial communities [6][7][8][9]. However, a great majority of these studies focused only on bacterial diversity (16S rRNA gene) and more rarely on fungal diversity (ITS) [10][11][12]. To our knowledge, no integrative assessment of the wheat rhizospheric microbiome including also the diversity of protists (i.e.…”

Diet and diet‐associated bacteria shape early microbiome development in Yellowtail Kingfish (Seriola lalandi)

“…16S rRNA gene reads were processed according to Granzow et al (2017). In brief, sequence data were initially quality-filtered and trimmed using TRIMMOMATIC version 0.36 truncating reads if the quality dropped below 15 in a sliding window of 4 bp (Bolger et al, 2014).…”

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

“…Part of G × E interactions that is linked to specific environmental factors such as soil type, climatic conditions, crop management, or microbial communities can be utilized in breeding for local adaptation (Annicchiarico, Bellah, & Chiari, ; Busby et al, ). Likewise, breeding more diverse cropping systems (e.g., mixed cropping, intercropping, undersowing) that harbour and maintain greater microbial diversity (Chave, Tchamitchian, & Ozier‐Lafontaine, ; Granzow et al, ; Lori, Symnaczik, Mäder, De Deyn, & Gattinger, ; Wang, Zheng, et al, ) will foster selection for beneficial plant microbe interaction.…”

“…In one of the first studies, Panke-Buisse, Poole, Goodrich, Ley, and Kao-Kniffin (2014) showed that Arabidopsis-associated root microbiomes that were selected for the plant trait (Annicchiarico, Bellah, & Chiari, 2005;Busby et al, 2017). Likewise, breeding more diverse cropping systems (e.g., mixed cropping, intercropping, undersowing) that harbour and maintain greater microbial diversity (Chave, Tchamitchian, & Ozier-Lafontaine, 2014;Granzow et al, 2017;Lori, Symnaczik, Mäder, De Deyn, & Gattinger, 2017;Wang, Zheng, et al, 2017) will foster selection for beneficial plant microbe interaction. Wagner et al (2016) reported significant plant genotype effects and G × E interaction of wild perennial mustard (Boechera stricta) on the microbiome community of leaves as well as effect of the plant age.…”