Diversity and function of soybean rhizosphere microbiome under nature farming

Abstract

Nature farming is a farming system that entails cultivating crops without using chemical fertilizers and pesticides. The present study investigated the bacterial and fungal communities in the rhizosphere of soybean grown in conventional and nature farming soils using wild-type and non-nodulating mutant soybean. The effect of soil fumigant was also analyzed to reveal its perturbation of microbial communities and subsequent effects on the growth of soybean. Overall, the wild-type soybean exhibited a better growth index compared to mutant soybean and especially in nature farming. Nodulation and arbuscular mycorrhiza (AM) fungi colonization were higher in plants under nature farming than in conventionally managed soil; however, fumigation drastically affected these symbioses with greater impacts on plants in nature farming soil. The rhizosphere microbiome diversity in nature farming was higher than that in conventional farming for both cultivars. However, the diversity was significantly decreased after fumigation treatment with a greater impact on nature farming. Principal coordinate analysis revealed that nature farming and conventional farming soil harbored distinct microbial communities and that soil fumigation significantly altered the communities in nature farming soils but not in conventional farming soils. Intriguingly, some beneficial microbial taxa related to plant growth and health, including Rhizobium, Streptomyces, and Burkholderia, were found as distinct microbes in the nature farming soil but were selectively bleached by fumigant treatment. Network analysis revealed a highly complex microbial network with high taxa connectivity observed under nature farming soil than in conventional soil; however, fumigation strongly broke it. Overall, the results highlighted that nature farming embraced higher microbial diversity and the abundance of beneficial soil microbes with a complex and interconnected network structure, and also demonstrated the underlying resilience of the microbial community to environmental perturbations, which is critical under nature farming where chemical fertilizers and pesticides are not applied.

The silicon regulates microbiome diversity and plant defenses during cold stress in Glycine max L.

“…The current results of low diversity variations among treatments suggest that the cold conditions reduced the overall diversity. In previous reports, the plant microbiomes are directly impacted by external climatic conditions and indirectly by plant responses such as plant morphology, antioxidant defense, and genetics ( Trivedi et al., 2022 ; Agyekum et al., 2023 ; Yang et al., 2023 ).…”

Stem rot affects the structure of rhizosphere microbiome in Berseem Clover (Trifolium alexandrinum)

“…Rhizosphere is a complex environment where microorganisms interact with plant roots and ultimately affect the plant health and productivity (Banerjee et al, 2018; Karuppiah et al, 2020). Microbial diversity in the rhizosphere is considered an important factor that influences plant health and helps to suppress various bacterial and fungal diseases (Miao et al, 2016; Agyekum et al 2023). At the flowering stage, maximum microbial diversity was observed as compared to the later stage of plant development.…”

“…Microbial diversity in the rhizosphere is considered an important factor that influences plant health and helps to suppress various bacterial and fungal diseases (Miao et al, 2016;Agyekum et al 2023). At the flowering stage, maximum microbial diversity was observed as compared to the (which was not certified by peer review) is the author/funder.…”

Soil Microorganisms in Agricultural Fields and Agronomic Regulation Pathways

“…However, conventional tillage practices have been observed to disrupt the original soil microbial community structure, leading to a decrease in soil fungal abundance and the proliferation of eutrophic microorganisms [44,45]. In contrast, natural tillage methods, devoid of chemical fertilizer and pesticides, promote symbiosis between leguminous crops and nitrogen-fixing microorganisms [18,46,47]. This enhances soil microbial diversity, fostering the emergence of probiotic flora that are absent in conventional tillage systems, including Rhizobium, Streptomyces, and Burkholderia.…”

“…Likewise, water management affects soil microbes by regulating soil effectiveness [6,7,17]. Farmland ecosystems, distinguished by human intervention, exhibit distinct microclimates shaped by crops and artificial soil interventions that profoundly influence the composition and function of soil microorganisms [18,19]. Hence, optimizing farmland management practices to improve the soil microbial structure and functional diversity is crucial.…”