Hiseq Base Molecular Characterization of Soil Microbial Community, Diversity Structure, and Predictive Functional Profiling in Continuous Cucumber Planted Soil Affected by Diverse Cropping Systems in an Intensive Greenhouse Region of Northern China

Abstract

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.

Effects of Continuous Sugar Beet Cropping on Rhizospheric Microbial Communities

“…The dominant genus Pseudombrophila in T5 (14.3%) became one of the least abundant genera in T30 (1.5%). These observed differences in different groups further support previous reports demonstrating that the abundance and structure of fungal communities are highly influenced by continuous cropping [11][12][13][14].…”

“…Rhizosphere microflora has been shown to be a key component of agricultural ecosystems that not only plays a significant role in basic soil processes, but is also actively involved in enhancing soil fertility and crop productivity [9]. Previous studies on soybean, ginger, potato, cucumber, and cotton have found that the alpha diversity of bacteria and fungi was decreased due to continuous cropping year, and the soil microbial metabolic diversity and soil physicochemical properties were also significantly affected [10][11][12][13]. The relative abundance of pathogenic fungi in rhizospheric soil was revealed to be significantly higher in continuous cropping than in cropping rotation systems [14].…”

Garlic Substrate Induces Cucumber Growth Development and Decreases Fusarium Wilt through Regulation of Soil Microbial Community Structure and Diversity in Replanted Disturbed Soil

“…Soil sickness, soil-borne pathogens and the accumulation of autotoxins/phytotoxins have been associated with cucumber continuous cropping systems [ 9 , 11 , 12 ]. Previous studies revealed long-term negative soil–plant feedback, in which a 50% reduction of the total dry biomass occurred over seven years of consecutive monocropping of cucumber [ 8 , 9 , 13 , 14 ]. In addition, re-cropping PGVC soil has shown 31–42% lower soil organic matter (SOM) than in open field soils [ 10 , 15 ] and thus degraded soil becomes vulnerable to the incidence of Fusarium wilt [ 13 , 16 ], caused by the soil-borne fungus Fusarium oxysporum f. sp.…”

Transcriptome Analysis Reveals the Different Response to Toxic Stress in Rootstock Grafted and Non-Grafted Cucumber Seedlings

“…Consecutive monoculture problem (CMP) happens when one plant is cultivated in the same field year after year, which results in growth decline, crop yield reduction, quality degradation, and disease susceptibility. Previous studies have indicated that the causes of the CMP include soil physicochemical properties deterioration, microbial community structure imbalance, and autotoxicity of root exudates [1][2][3]. Cucumber (Cucumis sativus L.) suffers from a severe consecutive monoculture problem especially under greenhouse cultivation, and the main cause for this CMP in cucumber is the secretion of autotoxins.…”