Cover crops are key determinants of the ecological stability and sustainability of continuous cropping soils. However, their agro-ecological role in differentially reshaping the microbiome structure and functioning under a degraded agroecosystem remains poorly investigated. Therefore, structural and metabolic changes in soil bacterial community composition in response to diverse plant species were assessed. Winter catch leafy vegetables crops were introduced as cover plants in a cucumber-fallow period. The results indicate that cover crop diversification promoted beneficial changes in soil chemical and biological attributes, which increased crop yields in a cucumber double-cropping system. Illumina high-throughput sequencing of 16S rRNA genes indicated that the bacterial community composition and diversity changed through changes in the soil properties. Principal component analysis (PCA) coupled with non-metric multidimensional scaling (NMDS) analysis reveals that the cover planting shaped the soil microbiome more than the fallow planting (FC). Among different cropping systems, spinach–cucumber (SC) and non-heading Chinese cabbage–cucumber (NCCC) planting systems greatly induced higher soil nutrient function, biological activity, and bacterial diversity, thus resulting in higher cucumber yield. Quantitative analysis of linear discriminant analysis effect size (LEfSe) indicated that Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria were the potentially functional and active soil microbial taxa. Rhizospheres of NCCC, leaf lettuce–cucumber (LLC), coriander–cucumber (CC), and SC planting systems created hotspots for metabolic capabilities of abundant functional genes, compared to FC. In addition, the predictive metabolic characteristics (metabolism and detoxification) associated with host–plant symbiosis could be an important ecological signal that provides direct evidence of mediation of soil structure stability. Interestingly, the plant density of non–heading Chinese cabbage and spinach species was capable of reducing the adverse effect of arsenic (As) accumulation by increasing the function of the arsenate reductase pathway. Redundancy analysis (RDA) indicated that the relative abundance of the core microbiome can be directly and indirectly influenced by certain environmental determinants. These short-term findings stress the importance of studying cover cropping systems as an efficient biological tool to protect the ecological environment. Therefore, we can speculate that leafy crop diversification is socially acceptable, economically justifiable, and ecologically adaptable to meet the urgent demand for intensive cropping systems to promote positive feedback between crop–soil sustainable intensification.

Garlic substrate could influence plant growth through affecting soil microbiome structure. The relationship mechanism between changes in soil microbial communities, disease suppression and plant development, however, remains unclear, particularly in the degraded soil micro-ecological environment. In this study, garlic substrates as a soil amendment were incorporated with different ratios (1:100, 3:100 and 5:100 g/100 g of soil) in a replanted disturbed soil of long-term cucumber monoculture (annual double cropping system in a greenhouse). The results indicated that higher amount of C-amended garlic substrate significantly induced soil suppressiveness (35.9% greater than control (CK) against the foliar disease incidence rate. This inhibitory effect consequently improved the cucumber growth performance and fruit yield to 20% higher than the non-amended soil. Short-term garlic substrate addition modified the soil quality through an increase in soil organic matter (SOM), nutrient availability and enzymatic activities. Illumina MiSeq sequencing analysis revealed that soil bacterial and fungal communities in the garlic amendment were significantly different from the control. Species richness and diversity indices significantly increased under treated soil. The correlation-based heat map analysis suggested that soil OM, nutrient contents and biological activators were the primary drivers reshaping the microbial community structure. Furthermore, garlic substrate inhibited soil-borne pathogen taxa (Fusarium and Nematoda), and their reduced abundances, significantly affecting the crop yield. In addition, the host plant recruited certain plant-beneficial microbes due to substrate addition that could directly contribute to plant–pathogen inhibition and crop biomass production. For example, abundant Acidobacteria, Ascomycota and Glomeromycota taxa were significantly associated with cucumber yield promotion. Firmicutes, Actinobacteria, Bacteroidetes, Basidiomycota and Glomeromycota were the associated microbial taxa that possibly performed as antagonists of Fusarium wilt, with plant pathogen suppression potential in monocropped cucumber-planted soil.

Monotonous cucumber double-cropping systems under plastic greenhouse vegetable cultivation (PGVC) previously intensified by long-term anthropogenic activities and manipulative treatments leads to a crop productivity reduction and soil biota disturbances. In this study, the role of the indigenous arbuscular mycorrhizal strain (AM: Glomus versiforme L.) and organic substrate (GS: Garlic stalk) application were assessed for plant microbe interaction and crop productivity feedback in a greenhouse (2016–2018) under a cultivated Anthrosol characterized as a replanted degraded soil. We found that repetitively adding AM inocula with organic substrates (GS) improved the cucumber growth and physiology. The useful trait of AM symbiosis with C-amended organic substrates preferentially manifested as increased root colonization, hyphal density proliferation, AM sporulation, root activity, and suppressed Fusarium incidence. The post AM development further prevailed the synergistic interaction, and the co-inoculation effect resulted in an increase in fruit nutrition uptake, seasonal cucumber yield and fruit quality attributes. Illumina MiSeq analysis of the 18S rRNA gene amplicons revealed that the dominant AM genera that are particularly enriched with the Glomus taxon may be important ecological drivers associated with plant productivity and fruit quality characteristics. These results suggest that the AM-organic substrate association might be a pragmatic option for use as an economic and efficient biological resource and as a newly-sustainable plant microbe mediator to enhance the regional ecosystem services and plant productivity of the anthropogenic PGVC of this region.

Garlic is considered to have a strong positive effect on the growth and yield of receptors under soil cultivation conditions. However, how this positive promotion is produced by changing the growth environment of the receptors or directly acting on the receptors is still not very clear. The direct influence of co-culturing with different quantities of garlic plants (the control 5, 10, 15, 20) on the growth and biochemical processes of cucumber plants was studied using a hydroponic co-culture system. Different numbers of garlic bulbs inhibited the growth of cucumber plants and increased the production and induction of reactive oxygen species, which accompanied the enhancement of lipid peroxidation and oxidative damage to cucumber. This allelopathic exposure further reduced the chlorophyll contents and photosynthesis rate, and consequently impaired the photosynthetic performance of photosystem II (PSII). Garlic root exudates increased the leaves’ carbohydrates accumulation, such as soluble sugar contents and sucrose levels by regulating the activities of metabolismic enzymes; however, no such accumulation was observed in the roots. Our results suggested that garlic root exudates can mediate negative plant–plant interactions and its phytotoxic influence on cucumber plants may have occurred through the application of oxidative stress, which consequently imbalanced the source-to-sink photo-assimilate flow.

A decreased soil biological environment in terms of an unstable microbial population and diversity index is primarily caused by intensive continuous cropping systems. In this study, a crop rotation system was established to evaluate the soil fungal diversity using a pyrosequencing-based analysis during three successive growing seasons (2013, 2014, and 2015) under a field pot investigation. We found that overall green garlic/cucumber rotational effects increased cucumber productivity under these growing practices. Analysis of fungal communities in rhizosphere soils by high-throughput pyrosequencing showed that the estimated treatment effects were more obvious during the three-year trials, and OTU richness was much higher than the control in cucumber-planted soils. The relative frequencies of fungal diversity showed variable responses before and after rotation practices, and mainly α-diversity of fungi increased in garlic planted soil and again decreased after cucumber planted soil in each year. The phylogenetic classification illustrated that the fungal communities were dominated by the taxa Ascomycota, Basidiomycota, Chytridiomycota, Glomeromycota, and Zygomycota across all samples. Particularly, the relative abundance of the taxon Ascomycota was largely and predominantly enriched with the increasing number of garlic bulbs during the three years. Moreover, the majority of abundant taxa positively correlated with available P and K contents, while being highly negatively correlated with soil pH, EC, and SOC. These results indicate that garlic-cucumber-based crop rotations induce fungal richness and diversity and promote the sustainability of agricultural ecosystems, thus enhancing crop growth and production.