Long-term watermelon continuous cropping leads to drastic shifts in soil bacterial and fungal community composition across gravel mulch fields

Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil

As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.

Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing

Continuous cropping (CC) profoundly impacts soil ecosystems, including changes in soil factors and the structure and stability of microbial communities. These factors are interrelated and together affect soil health and plant growth. In this research, metagenomic sequencing was used to explore the effects of CC on physicochemical properties, enzyme activities, microbial community composition, and functional genes of the rhizosphere soil of patchouli. We found that this can lead to changes in various soil factors, including the continuous reduction of pH andNH 4 + -N and the unstable changes of many factors. In addition, S-PPO enzyme activity increased significantly with the cropping years, but S-NAG increased in the first 2 years and decreased in the third cropping year. Metagenomic sequencing results showed that CC significantly changed the diversity and composition of rhizosphere microbial communities. The relative abundance of Pseudomonas and Bacteroides decreased substantially from the phylum level. At the genus level, the number of microbial genera specific to the zero-year cropping (CK) and first (T1), second (T2), and third (T3) years decreased significantly, to 1798, 172, 42, and 44, respectively. The abundance of many functional genes changed, among which COG0823, a gene with the cellular process and signaling functions, significantly increased after CC. In addition,NH 4 + -N, S-CAT, S-LAP, and SOC were the main environmental factors affecting rhizosphere-dominant microbial communities at the phylum level, while pH, SOC, and AK were the key environmental factors affecting rhizosphere functional genes of Pogostemon cablin. In summary, this study showed the dynamic changes of soil factors and rhizosphere microorganisms during CC, providing a theoretical basis for understanding the formation mechanism and prevention of CC obstacles and contributing to the formulation of scientific soil management and fertilization strategies.

Effect of microbial fertilizers on soil microbial community structure in rotating and continuous cropping Glycyrrhiza uralensis

Introduction

Glycyrrhiza uralensis is a perennial medicinal plant. It's generally cultivated for three years, and should avoid long-term continuous cultivation. However, unreasonable crop rotation and extensive fertilization are common in G. uralensis cultivation, which leads to the imbalance of soil microflora structure, and the obstacle of continuous cropping are becoming increasingly serious. Some microbial fertilizers such as Bacillus amyloliquefaciens, Bacillus subtilis, and complex microbial agent have the advantage of regulating soil microbial community structure and improving the soil environment. Therefore, these three kinds of microbial fertilizers were applied to G. uralensis and their effects on soil microorganisms of G. uralensis were studied.

Methods

Combine microbial fertilizers with conventional fertilization for continuous cropping and rotating G. uralensis. High-throughput sequencing technology was used to determine soil microbial richness, diversity and distribution of community structure in rotating and continuous cropping G. uralensis.

Results and discussion

Continuous cropping reduced G. uralensis soil bacterial diversity by 7.56% and increased fungal richness by 17.01% compared with crop rotation. However, after the application of microbial fertilizers, the fungal richness and diversity of continuous cropping G. uralensis were significantly reduced by 4.76%~20.96%, and the soil bacterial diversity of continuous cropping and rotating G. uralensis was significantly increased by 7.22%~12.03% and 6.75%~11.69% compared with the respective controls, respectively. Continuous cropping and rotating G. uralensis soil dominant bacteria mainly include Proteobacteria, Actinobacteria and Gemmatimonadota, and the dominant fungi include Ascomycota, Basidiomycota and Zygomycota. The activity process of these microbial communities was mainly through carbohydrate metabolism and amino acid synthesis pathway in metabolism. The complex microbial agent significantly increased the relative abundance of soil dominant bacteria communities of continuous cropping and rotating G. uralensis by 3.11~11.54 percentage points, and significantly reduced the relative abundance of soil dominant fungal communities of continuous cropping G. uralensis by 1.57~8.93 percentage points, compared with the control. Of the three microbial fertilizers, the complex microbial agent had the most significant effects on optimizing the soil microbial community structure of continuous cropping and rotating G. uralensis. Conclusion: the application effect of different microbial fertilizers in continuous cropping G. uralensis was better than crop rotation, and the application effect of complex microbial agent was the best, which has more application value and development prospect in the cultivation management of G. uralensis.

Effects of different preceding crops on soil nutrients and foxtail millet productivity and quality

Crop rotation can affect crop productivity and soil characteristics; however, the impact of preceding crops on the yield and quality of foxtail millet and the relationship between these two factors have not been well characterised. To further investigate the effects of preceding crops on foxtail millet, this study cultivated maize, mung beans, soybeans, potatoes, and proso millet as the preceding crops and rotated them with Zhangzagu10 foxtail millet. A randomised complete block design was employed for the study, and soil and millet samples were collected after harvest. The performance of Zhangzagu10 foxtail millet grown with five different preceding crops was explored by measuring yield and quality indicators and comprehensively analysing various quality traits and their interrelationships. The physicochemical and nutritional characteristics of millet grains were significantly influenced by the preceding crop. The yield of Zhangzagu10 cultivated after mung bean was significantly higher (8277.47 kg/hm2) than that of millet cultivated after the other crops. Additionally, the colour characteristics (a*, b*, and △E values) were superior, with the rice exhibiting the strongest yellow colour. Foxtail millet preceded by soybean showed a significantly higher thousand-grain weight, indicating well-filled grains. Furthermore, this treatment had rich contents of carotenoids and polyphenols at 34.79 mg/kg and 76.27 mg/100 g, respectively, and significantly higher levels of minerals such as V, Cr, Fe, Co, Ni, Se, and Sn compared to the other treatments. Foxtail millet following mung bean and soybean demonstrated excellent grain quality, featuring high breakage values and gelatinisation, along with low cooking values and gelatinisation temperatures and moderately low setback values. Zhangzagu10 cultivated after potato exhibited a polyphenol content of 67.13 mg/100 g, showcasing strong antioxidant effects. In contrast, proso millet preceded by foxtail millet had relatively lower content levels across various substances, resulting in an overall subpar performance. In summary, selecting appropriate preceding crops can significantly enhance both the yield and quality of Zhangzagu millet. Moreover, soybeans, potatoes, and mung beans can be effectively incorporated into a sustainable crop rotation plan for millet. In the future, we aim to further explore the interaction mechanisms between preceding crops and millet to optimise rotation strategies and improve foxtail millet quality.

Towards Sustainable Productivity of Greenhouse Vegetable Soils: Limiting Factors and Mitigation Strategies

Greenhouse vegetable production has become increasingly important in meeting the increasing global food demand. Yet, it faces severe challenges in terms of how to maintain soil productivity from a long-term perspective. This review discusses the main soil productivity limiting factors for vegetables grown in greenhouses and identifies strategies that attempt to overcome these limitations. The main processes leading to soil degradation include physical (e.g., compaction), chemical (e.g., salinization, acidification, and nutrient imbalances), and biological factors (e.g., biodiversity reduction and pathogen buildup). These processes are often favored by intensive greenhouse cultivation. Mitigation strategies involve managing soil organic matter and mineral nutrients and adopting crop rotation. Future research should focus on precisely balancing soil nutrient supply with vegetable crop demands throughout their life cycle and using targeted organic amendments to manage specific soil properties. To ensure the successful adoption of recommended strategies, socioeconomic considerations are also necessary. Future empirical research is required to adapt socioeconomic frameworks, such as Science and Technology Backyard 2.0, from cereal production systems to greenhouse vegetable production systems. Addressing these issues will enable the productivity of greenhouse vegetable soils that meet growing vegetable demand to be sustained using limited soil resources.

Effects of Trichoderma harzianum on Growth and Rhizosphere Microbial Community of Continuous Cropping Lagenaria siceraria

This study analyzed the effects of Trichoderma harzianum on the growth of continuous cropping Lagenaria siceraria and the physical and chemical properties of rhizosphere soil and microbial community structure, using Illumina Miseq (PE300) high-throughput sequencing technology along with physiological and biochemical detection. The results indicated that after applying T. harzianum, the growth of L. siceraria was significantly promoted, with increases in plant height, fresh weight, and dry weight of 21.42%, 24.5%, and 4.5%, respectively. The pH of the rhizosphere soil decreased from 7.78 to 7.51, while the electrical conductivity, the available phosphorus, the available potassium, and the total nitrogen were markedly higher compared to the control group and increased by 13.95%, 22.54%, 21.37%, and 16.41%, respectively. The activities of catalase and sucrase in the rhizosphere increased by 18.33% and 61.47%, and the content of soil organic carbon (SOC) increased by 27.39%, which indicated that T. harzianum could enhance soil enzyme activity and promotes the transformation of organic matter. The relative abundance of beneficial bacteria such as Pseudomonas increased, while the relative abundance of harmful fungi such as Fusarium and Podosphaera decreased significantly.

Continuous cropping system altered soil microbial communities and nutrient cycles

Understanding the response of microbial communities and their potential functions is essential for sustainability of agroecosystems under long-term continuous cropping. However, limited research has focused on investigating the interaction between soil physicochemical factors and microbial community dynamics in agroecosystems under long-term continuous cropping. This study probed into the physicochemical properties, metabolites, and microbial diversity of tobacco rhizosphere soils cropped continuously for 0, 5, and 20 years. The relative abundance of bacterial genera associated with nutrient cycling (e.g., Sphingomonas) increased while potential plant pathogenic fungi and beneficial microorganisms showed synergistic increases with the duration of continuous cropping. Variations in soil pH, alkeline nitrogen (AN) content, and soil organic carbon (SOC) content drove the shifts in soil microbial composition. Metabolites such as palmitic acid, 3-hydroxypropionic acid, stearic acid, and hippuric acid may play a key role in soil acidification. Those results enhance our ability to predict shifts in soil microbial community structure associated with anthropogenic continuous cropping, which can have long-term implications for crop production.

Improvement in gravel-mulched land soil nutrient and bacterial community diversity with Lonicera japonica

Gravel-mulched land in China suffers from poor natural resources and fragile ecological environment, posing a challenge to effective restoration of ecological function. Lonicera japonica, a traditional Chinese herb used for treating human diseases, is a highly adaptable and resilient plant species, can effectively improve the soil properties, and may have important implications for the ecology and economy of gravel-mulched land. A study was conducted in a gravel-mulched field to measure the impact of planting the L. japonica (including control (CK), 1-year, 2-year, and 4-year cultivation of plants) on (i) dynamic changes in soil nutrient and enzyme activity properties, and (ii) soil rhizosphere microbial community structure characteristics. We found that the concentration of soil organic carbon, available nitrogen, available phosphorus and available potassium in L. japonica soil after cultivation for 1-4 years increased by 11-409%. The urease, phosphatase and catalase activities were increased by 11-560%, with the highest nutrient concentration and enzyme activity in 4-year plants. The pH value gradually decreased after cultivation. The improved soil environments increased soil bacterial community diversity. Planting L. japonica significantly increased the bacterial ACE, Chao1 index, Simpson index, and Shannon-Wiener index. The Firmicutes, Proteobacteria and Bacteroidetes were observed in dominant phyla. The relative abundance of eight genera, including Streptococcus, Veillonella and Rothia, was significantly reduced by more than 1%. Taken together, these soil indicators suggest that planting L. japonica in the short term would be a cost-effective strategy to combat soil degradation in a gravel-mulched ecosystem.

Metagenomics-based exploration of key soil microorganisms contributing to continuously planted Casuarina equisetifolia growth inhibition and their interactions with soil nutrient transformation

Casuarina equisetifolia (C. equisetifolia) is an economically important forest tree species, often cultivated in continuous monoculture as a coastal protection forest. Continuous planting has gradually affected growth and severely restricted the sustainable development of the C. equisetifolia industry. In this study, we analyzed the effects of continuous planting on C. equisetifolia growth and explored the rhizosphere soil microecological mechanism from a metagenomic perspective. The results showed that continuous planting resulted in dwarfing, shorter root length, and reduced C. equisetifolia seedling root system. Metagenomics analysis showed that 10 key characteristic microorganisms, mainly Actinoallomurus, Actinomadura, and Mycobacterium, were responsible for continuously planted C. equisetifolia trees. Quantitative analysis showed that the number of microorganisms in these three genera decreased significantly with the increase of continuous planting. Gene function analysis showed that continuous planting led to the weakening of the environmental information processing-signal transduction ability of soil characteristic microorganisms, and the decrease of C. equisetifolia trees against stress. Reduced capacity for metabolism, genetic information processing-replication and repair resulted in reduced microbial propagation and reduced microbial quantity in the rhizosphere soil of C. equisetifolia trees. Secondly, amino acid metabolism, carbohydrate metabolism, glycan biosynthesis and metabolism, lipid metabolism, metabolism of cofactors and vitamins were all significantly reduced, resulting in a decrease in the ability of the soil to synthesize and metabolize carbon and nitrogen. These reduced capacities further led to reduced soil microbial quantity, microbial carbon and nitrogen, microbial respiration intensity, reduced soil enzyme nutrient cycling and resistance-related enzyme activities, a significant reduction in available nutrient content of rhizosphere soils, a reduction in the ion exchange capacity, and an impediment to C. equisetifolia growth. This study provides an important basis for the management of continuously planted C. equisetifolia plantations.

Harnessing nitrate over ammonium to sustain soil health during monocropping

Introduction

In achieving food security and sustainable agricultural development, improving and maintaining soil health is considered as a key driving factor. The improvement based on different forms of nitrogen fertilization has aroused great public interest in improving and restoring monocropping obstacles for specific soil problems.

Methods

For this, a short-term cucumber cropping field experiment was conducted in the subtropical region of China under four fertilization treatments: ammonium (AN), nitrate (NN), ammonium with dicyandiamide (AN+DCD), nitrate with dicyandiamide (NN+DCD). In this study, we measured the effects of nitrogen forms addition on plant productivity and soil health in a monocropping system over seven seasons.

Results

To systematically evaluate soil health, a wide range of soil environmental factors were measured and incorporated into the soil health index (SHI) by entropy method. Compared with ammonium treatment (SHI_AN = 0.059, SHI_AN+DCD = 0.081), the positive effect of nitrate was mainly reflected in improving soil health (SHI_NN = 0.097, SHI_NN+DCD = 0.094), which was positively correlated with the increase in plant productivity of cucumber after seven seasons of monocropping. The most critical factor affecting SHI is soil ammonium nitrogen content, which was negatively correlated with plant productivity.

Discussion

Nitrate promotes soil health and plant productivity by optimizing soil environmental factors. The study thus emphasized the necessity of nitrate input for the sustenance of soil-crop ecosystems, with the consequent possibility of application of the results in planning monoculture obstacle prevention and management measures.

Temporal and Habitat Dynamics of Soil Fungal Diversity in Gravel-Sand Mulching Watermelon Fields in the Semi-Arid Loess Plateau of China

Mulching is an important agricultural management tool for increasing watermelon productivity and land-use efficiency because it helps improve water use efficiency and reduce soil erosion. However, there is relatively little available information regarding the effects of long-term continuous monoculture farming on soil fungal communities and related fungal pathogens in arid and semiarid regions. In this study, we characterized the fungal communities of four treatment groups, including gravel-sand-mulched farmland, gravel-sand-mulched grassland, fallow gravel-sand-mulched grassland, and native grassland, using amplicon sequencing. Our results revealed that the soil fungal communities differed significantly between mulched farmland and mulched grassland as well as the fallow mulched grassland. Gravel-sand mulch significantly impaired the diversity and composition of soil fungal communities. Soil fungal communities were more sensitive to gravel-sand mulch in grassland than in other habitats. Long-term continuous monoculture (more than 10 years) led to decreased abundance of Fusarium species, which contains include agronomically important plant pathogens. In the gravel-mulched cropland, some Penicillium and Mortierella fungi were significantly enriched with increasing mulch duration, suggesting potential beneficial properties of those fungi that could be applied to disease control. We also found that long-term gravel mulching in continuous monoculture farming could potentially form disease-suppressive soils and alter soil microbial biodiversity and fertility. Our study provides insights into the exploration of novel agricultural management strategies along with continuous monoculture practice to control watermelon wilt disease by maintaining a more sustainable and healthier soil environment. IMPORTANCE Gravel-sand mulching is a traditional agricultural practice in arid and semiarid regions, providing a surface barrier for soil and water conservation. However, application of such practice in monocropping systems may lead to outbreaks of several devastating plant diseases, such as watermelon Fusarium wilt. Our results with amplicon sequencing suggest that soil fungal communities differ significantly between mulched farmland and mulched grassland and are more sensitive to gravel-sand mulch in grassland. Under continuous monoculture regimens, long-term gravel mulch is not necessarily detrimental and may result in decreased Fusarium abundance. However, some known beneficial soil fungi may be enriched in the gravel-mulch cropland as mulch duration increases. A possible explanation for the reduction in Fusarium abundance may be the formation of disease-suppressive soils. This study provides insight into the need to explore alternative strategies using beneficial microbes for sustainable watermelon wilt control in continuous monocropping system.

Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum

Introduction

Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

Methods

In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

Results

The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

Discussion

This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.