Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan

Abstract

Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.

Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management

“…Conventional farming, in contrast, slightly increased the abundance of xenobiotics biodegradation and metabolism, while organic farming was the lowest. This supported the idea that conventional farming, which relied on synthetic agrochemical usages (i.e., herbicides and NPK fertilizers), provided a toxic environment for the microbes, and xenobiotic-degrading genes were increased as a response (Liao et al, 2019). It also elevated the nitrogen metabolism of the phyllosphere microbes, including glutamine synthetase (K01915) and nitrite reductase (NADH) large subunit (K00362), which were identified as conventional-specific functions by LEfSe.…”

“…Co-occurrence network analysis was subsequently performed to compare the structure and complexity of phyllosphere microbial communities in response to farming practices. Network topology assessments showed that organic network had the highest number of edges, density, and connectivity, which might be linked to the strong resilience capabilities of the phyllosphere microbiota under this farm to disturbances or invasion of exogenous microbes ( Mendes et al, 2018 ; Banerjee et al, 2019 ; Liao et al, 2019 ). Moreover, greater complexity and connectivity in the organic network were followed by the number of hub species identified, while unsustainable farming was in contrast.…”

Distinct Root Microbial Communities in Nature Farming Rice Harbor Bacterial Strains With Plant Growth-Promoting Traits

“…Root microbiomes host a large variety of bacteria, many of which are associated with the host plant and enhance plant nutrition, stress tolerance or health. Previous studies have focused on soil microbial communities under organically or naturally managed farms (Li F. et al, 2017;Liao et al, 2018Liao et al, , 2019, but a limited number of studies have reported on plantassociated microbes. Elucidating whether farming practices, such as nature farming vs. conventional practices that employ chemical fertilizers, can influence root microbial communities is therefore of considerable interest.…”

“…Huang et al (2019) reported that long-term application of chemical fertilizers reduced the richness and diversity of soil microbes. On the other hand, organically managed fields had more positive effects on alpha-diversity parameters than conventionally managed fields (Hartmann et al, 2015;Gu et al, 2017;Liao et al, 2019). Xia et al (2015) reported that the diversity of the endophytic community associated with plants was higher under organic practices than under conventional practices.…”

“…The farming strategies in nature farming systems to improve plant and soil health include not relying on the application of agrochemicals such as fertilizer and pesticides, reducing soil tillage and plowing, using mulches with crop residue, crop rotation, intercropping and incorporating biofertilizer. These farming systems may enhance the abundance and diversity of plant and soil microbes, maintain soil physiochemical properties and improve the quality and safety of food production (Lenc et al, 2015;Gu et al, 2017;Liao et al, 2019).…”