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The shortage of land resources restricts the sustainable development of agricultural production. Multiple cropping has been widely used in Southern China, but whether the continuous planting will cause a decline in soil quality and crop yield is unclear. To test whether multiple cropping could increase grain yield, we investigated the farmlands with different cultivation years (10–20 years, 20–40 years, and >40 years). Results showed that tobacco-rice multiple cropping rotation significantly increased soil pH, nitrogen nutrient content, and grain yield, and it increased the richness of the bacterial community. The farmland with 20–40 years of cultivation has the highest soil organic carbon (SOC), ammonium nitrogen, and grain yield, but there is no significant difference in the diversity and structure of the bacterial community in farmlands with different cultivation years. The molecular ecological network indicated that the stability of the bacterial community decreased across the cultivation years, which may result in a decline of farmland yields in multiple cropping system> 40 years. The Acidobacteria members as the keystone taxa (Zi ≥ 2.5 or Pi ≥ 0.62) appeared in the tobacco-rice multiple cropping rotation farmlands, and the highest abundance of Acidobacteria was found in the farmland with the highest SOC and ammonium nitrogen content, suggesting Acidobacteria Gp4, GP7, GP12, and GP17 are important taxa involved in the soil carbon and nitrogen cycle. Therefore, in this study, the multiple cropping systems for 20 years will not reduce the crop production potential, but they cannot last for more than 40 years. This study provides insights for ensuring soil quality and enhancing sustainable agricultural production capacity.

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.

Continuous cropping barriers lead to huge agriculture production losses, and fumigation and biological agents are developed to alleviate the barriers. However, there is a lack of literature on the differences between strong chemical fumigant treatment and moderate biological agent treatment. In this study, we investigated those differences and attempted to establish the links between soil properties, rhizosphere microbial community, and plant performance in both fumigation- and bioagent-treated fields. The results showed that the fumigation had a stronger effect on both soil functional microbes, i.e., ammonia oxidizers and soil-borne bacterial pathogens, and therefore, led to a significant change in soil properties, higher fertilizer efficiency, lower disease infections, and improved plant growth, compared with untreated control fields. Biological treatment caused less changes to soil properties, rhizosphere bacterial community, and plant physiology. Correlation and modeling analyses revealed that the bioagent effect was mainly direct, whereas fumigation resulted in indirect effects on alleviating cropping barriers. A possible explanation would be the reconstruction of the soil microbial community by the fumigation process, which would subsequently lead to changes in soil characteristics and plant performance, resulting in the effective alleviation of continuous cropping barriers.

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