Effects of Continuous Sugar Beet Cropping on Rhizospheric Microbial Communities

Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora

For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC-MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.

Response of soil microbial community diversity to continuous cucumber cropping in facilities along the Yellow River irrigation area

Cucumber is an important cash crop; however, continuous cropping obstacles readily occur within the intensive production processes of facility horticulture. This study aimed to determine the effects of continuous cropping on soil quality and the microbial community in the rhizosphere soil of cucumbers. Rhizosphere soil of cucumber planted continuously for 4, 8, and 12 years was investigated, and soil that was not continuously planted was used as the control. Soil physicochemical properties, enzyme activity, microbial diversity, and richness were determined. The results showed that with the increase in continuous cropping years (0, 4, 8, and 12 years), soil total salt content continuously increased, while the pH value significantly decreased. Compared with the control, soil organic matter, alkali-hydrolyzed nitrogen, available phosphorus, available potassium, and nitrate nitrogen contents increased significantly after 4 and 8 years of continuous cropping. Spearman correlation analysis showed that pH was negatively correlated with sucrase or sucrose and available phosphorus was positively correlated with alkaline phosphatase. Compared with the control, the diversity and abundance of bacterial and fungal communities in cucumber rhizosphere soil decreased after 4 and 12 years of continuous cropping. Continuous cropping led to a significant increase in the richness of the dominant phylum of cucumber rhizosphere soil. Principal coordinates analysis showed that, compared with the control, the soil microbial community structure was significantly separated after 4, 8, and 12 years of continuous cropping, and the microbial community structure was most similar after 4 and 8 years of continuous cropping. In addition, redundancy analysis showed that pH was the main driver of soil microbial dominance. In conclusion, continuous cropping of cucumber along the Yellow River irrigation area has led to the deterioration of soil nutrients and microbial communities in that region. This experiment provides a theoretical foundation for addressing the challenges associated with continuous cropping in cucumber cultivation.

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.

New insights into the occurrence of continuous cropping obstacles in pea (Pisum sativum L.) from soil bacterial communities, root metabolism and gene transcription

BACKGROUND

Continuous cropping is a significant obstacle to sustainable development in the pea (Pisum sativum L.) industry, but the underlying mechanisms of this remain unclear. In this study, we used 16 S rDNA sequencing, transcriptomics, and metabolomics to analyze the response mechanism of roots and soil bacteria to continuous cropping and the relationship between soil bacteria and root phenotypes of different pea genotypes (Ding wan 10 and Yun wan 8).

RESULTS

Continuous cropping inhibited pea growth, with a greater effect on Ding wan 10 than Yun wan 8. Metabolomics showed that the number of differentially accumulated metabolites (DAMs) in pea roots increased with the number of continuous cropping, and more metabolic pathways were involved. Transcriptomics revealed that the number of differentially expressed genes (DEGs) increased with the number of continuous cropping. Continuous cropping altered the expression of genes involved in plant-pathogen interaction, MAPK signal transduction, and lignin synthesis pathways in pea roots, with more DEGs in Ding wan 10 than in Yun wan 8. The up-regulated expression of genes in the ethylene signal transduction pathway was evident in Ding wan 10. Soil bacterial diversity did not change, but the relative abundance of bacteria significantly responded to continuous cropping. Integrative analysis showed that the bacteria with significant relative abundance in the soil were strongly associated with the antioxidant synthesis and linoleic acid metabolism pathway of pea roots under continuous cropping once. Under continuous cropping twice, the bacteria with significant relative abundance changes were strongly associated with cysteine and methionine metabolism, fatty acid metabolism, phenylpropanoid biosynthesis, terpenoid backbone biosynthesis, linoleic acid, and amino sugar and nucleotide sugar metabolism.

CONCLUSION

Ding wan 10 was more sensitive to continuous cropping than Yun wan 8. Continuous cropping times and pea genotypes determined the differences in root metabolic pathways. There were common metabolic pathways in the two pea genotypes in response to continuous cropping, and the DEGs and DAMs in these metabolic pathways were strongly associated with the bacteria with significant changes in relative abundance in the soil. This study provides new insights into obstacles to continuous cropping in peas.

Biochar-Dual Oxidant Composite Particles Alleviate the Oxidative Stress of Phenolic Acid on Tomato Seed Germination

Phenolic acid is a well-known allelochemical, but also a pollutant in soil and water impeding crop production. Biochar is a multifunctional material widely used to mitigate the phenolic acids allelopathic effect. However, phenolic acid absorbed by biochar can still be released. In order to improve the removal efficiency of phenolic acids by biochar, the biochar-dual oxidant (BDO) composite particles were synthesized in this study, and the underlying mechanism of the BDO particles in ameliorating p-coumaric acid (p-CA) oxidative damage to tomato seed germination was revealed. Upon p-CA treatment, the BDO composite particles application increased the radical length, radical surface area, and germination index by 95.0%, 52.8%, and 114.6%, respectively. Compared to using biochar or oxidants alone, the BDO particles addition resulted in a higher removal rate of p-CA and produced more O₂^•-, HO^•, SO₄^•- and ¹O₂ radicals via autocatalytic action, suggesting that BDO particles removed phenolic acid by both adsorption and free radical oxidation. The addition of BDO particles maintained the levels of the antioxidant enzyme activity close to the control, and reduced the malondialdehyde and H₂O₂ by 49.7% and 49.5%, compared to the p-CA treatment. Integrative metabolomic and transcriptomic analyses revealed that 14 key metabolites and 62 genes were involved in phenylalanine and linoleic acid metabolism, which increased dramatically under p-CA stress but down-regulated with the addition of BDO particles. This study proved that the use of BDO composite particles could alleviate the oxidative stress of phenolic acid on tomato seeds. The findings will provide unprecedented insights into the application and mechanism of such composite particles as continuous cropping soil conditioners.

The relationship between shifts in the rhizosphere microbial community and root rot disease in a continuous cropping American ginseng system

The root rot disease causes a great economic loss, and the disease severity usually increases as ginseng ages. However, it is still unclear whether the disease severity is related to changes in microorganisms during the entire growing stage of American ginseng. The present study examined the microbial community in the rhizosphere and the chemical properties of the soil in 1-4-year-old ginseng plants grown in different seasons at two different sites. Additionally, the study investigated ginseng plants' root rot disease index (DI). The results showed that the DI of ginseng increased 2.2 times in one sampling site and 4.7 times in another during the 4 years. With respect to the microbial community, the bacterial diversity increased with the seasons in the first, third, and fourth years but remained steady in the second year. The seasonal changing of relative abundances of bacteria and fungi showed the same trend in the first, third, and fourth years but not in the second year. Linear models revealed that the relative abundances of Blastococcus, Symbiobacterium, Goffeauzyma, Entoloma, Staphylotrichum, Gymnomyces, Hirsutella, Penicillium and Suillus spp. were negatively correlated with DI, while the relative abundance of Pandoraea, Rhizomicrobium, Hebeloma, Elaphomyces, Pseudeurotium, Fusarium, Geomyces, Polyscytalum, Remersonia, Rhizopus, Acremonium, Paraphaeosphaeria, Mortierella, and Metarhizium spp. were positively correlated with DI (P < 0.05). The Mantel test showed that soil chemical properties, including available nitrogen, phosphorus, potassium, calcium, magnesium, organic matter, and pH, were significantly correlated to microbial composition. The contents of available potassium and nitrogen were positively correlated with DI, while pH and organic matter were negatively correlated with DI. In summary, we can deduce that the second year is the key period for the shift of the American ginseng rhizosphere microbial community. Disease aggravation after the third year is related to the deterioration of the rhizosphere microecosystem.

Effects of continuous cropping Jiashi muskmelon on rhizosphere microbial community

Introduction

The continuous cropping of crops can result in the deterioration of the soil environment and cause a decline in plant health and yield, which complicates agricultural production. However, the effects of continuous melon cropping on rhizospheric microbial communities remain poorly understood.

Methods

In this study, high-throughput absolute quantification 16S rRNA gene amplicon sequencing was employed to analyze the bacterial community structure of greenhouse rhizosphere soil from Jiashi muskmelon replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively).

Results

The results showed that long- term continuous cropping caused significant changes in soil physicochemical properties. The bacterial absolute abundances increased, but the bacterial community richness and diversity were significantly lost (p < 0.05). The composition of bacterial community was more similar after 2 and 3 years of continuous cropping. The longer the continuous cropping years were, the greater the shift in the bacterial diversity and abundance. Analysis of potential functional components revealed that different bacterial groups were enriched in different continuous cropping years. The significant reduction of the taxa associated with nitrate reduction may be responsible for the loss of soil nitrogen in continuous cropping soil.

Discussion

In summary, continuous cropping had a significant impact on the bacterial community structure of Jiashi muskmelon rhizospheric soil, and these results will provide a reference for soil management and scientific fertilization of melon and other crops under a continuous cropping regime.

Understanding the sugar beet holobiont for sustainable agriculture

The importance of crop-associated microbiomes for the health and field performance of plants has been demonstrated in the last decades. Sugar beet is the most important source of sucrose in temperate climates, and-as a root crop-yield heavily depends on genetics as well as on the soil and rhizosphere microbiomes. Bacteria, fungi, and archaea are found in all organs and life stages of the plant, and research on sugar beet microbiomes contributed to our understanding of the plant microbiome in general, especially of microbiome-based control strategies against phytopathogens. Attempts to make sugar beet cultivation more sustainable are increasing, raising the interest in biocontrol of plant pathogens and pests, biofertilization and -stimulation as well as microbiome-assisted breeding. This review first summarizes already achieved results on sugar beet-associated microbiomes and their unique traits, correlating to their physical, chemical, and biological peculiarities. Temporal and spatial microbiome dynamics during sugar beet ontogenesis are discussed, emphasizing the rhizosphere formation and highlighting knowledge gaps. Secondly, potential or already tested biocontrol agents and application strategies are discussed, providing an overview of how microbiome-based sugar beet farming could be performed in the future. Thus, this review is intended as a reference and baseline for further sugar beet-microbiome research, aiming to promote investigations in rhizosphere modulation-based biocontrol options.

Crop microbiome: their role and advances in molecular and omic techniques for the sustenance of agriculture

This review is an effort to provide in-depth knowledge of microbe's interaction and its role in crop microbiome using combination of advanced molecular and OMICS technology to translate this information for the sustenance of agriculture. Increasing population, climate change and exhaustive agricultural practices either influenced nutrient inputs of soil or generating biological and physico-chemical deterioration of the soils and affecting the agricultural productivity and agro-ecosystems. Alarming concerns toward food security and crop production claim for renewed attention in microbe-based farming practices. Microbes are omnipresent (soil, water, and air) and their close association with plants would help to accomplish sustainable agriculture goals. In the last few decades, the search for beneficial microbes in crop production, soil fertilization, disease management, and plant growth promotion is the thirst for eco-friendly agriculture. The crop microbiome opens new paths to utilize beneficial microbes and manage pathogenic microbes through integrated advanced biotechnology. The crop microbiome helps plants acquire nutrients, growth, resilience against phytopathogens, and tolerance to abiotic stresses, such as heat, drought, and salinity. Despite the emergent functionality of the crop microbiome as a complicated constituent of the plant fitness, our understanding of how the functionality of microbiome influenced by numerous factors including genotype of host, climatic conditions, mobilization of minerals, soil composition, nutrient availability, interaction between nexus of microbes, and interactions with other external microbiomes is partially understood. However, the structure, composition, dynamics, and functional contribution of such cultured and uncultured crop microbiome are least explored. The advanced biotechnological approaches are efficient tools for acquiring the information required to investigate the microbiome and extract data to develop high yield producing and resistant variety crops. This knowledge fills the fundamental gap between the theoretical concepts and the operational use of these advanced tools in crop microbiome studies. Here, we review (1) structure and composition of crop microbiome, (2) microbiome-mediated role associated with crops fitness, (3) Molecular and -omics techniques for exploration of crop microbiome, and (4) current approaches and future prospectives of crop microbiome and its exploitation for sustainable agriculture. Recent -omic approaches are influential tool for mapping, monitoring, modeling, and management of crops microbiome. Identification of crop microbiome, using system biology and rhizho-engineering, can help to develop future bioformulations for disease management, reclamation of stressed agro-ecosystems, and improved productivity of crops. Nano-system approaches combined with triggering molecules of crop microbiome can help in designing of nano-biofertilizers and nano-biopesticides. This combination has numerous merits over the traditional bioinoculants. They stimulate various defense mechanisms in plants facing stress conditions; provide bioavailability of nutrients in the soil, helps mitigate stress conditions; and enhance chances of crops establishment.

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation

The effects of cropping practices on the rhizosphere soil physical properties and microbial communities of Bupleurum chinense have not been studied in detail. The chemical properties and the microbiome of rhizosphere soil of B. chinense were assessed in the field trial with three cropping practices (continuous monocropping, Bupleurum-corn intercropping and Bupleurum-corn rotation). The results showed cropping practices changed the chemical properties of the rhizosphere soil and composition, structure and diversity of the rhizosphere microbial communities. Continuous monocropping of B. chinense not only decreased soil pH and the contents of NO₃⁻-N and available K, but also decreased the alpha diversity of bacteria and beneficial microorganisms. However, Bupleurum-corn rotation improved soil chemical properties and reduced the abundance of harmful microorganisms. Soil chemical properties, especially the contents of NH₄⁺-N, soil organic matter (SOM) and available K, were the key factors affecting the structure and composition of microbial communities in the rhizosphere soil. These findings could provide a new basis for overcoming problems associated with continuous cropping and promote development of B. chinense planting industry by improving soil microbial communities.

Determining why continuous cropping reduces the production of the morel Morchella sextelata

Artificial cultivation of Morchella sextelata and other morels is expanding in China, but continuous cropping reduces Morchella for unknown reasons. Here, we investigated soil that had been used or not used for M. sextelata cultivation for 0, 1, and 2 years. We found that the continuous cropping of M. sextelata substantially reduced the pH and the nutrient content of the hyphosphere soil and increased sclerotia formation by M. sextelata. Changes in the structure of bacterial and fungal communities were associated with levels of available nitrogen (N) and phosphorus in the soil. With continuous cropping, the richness and diversity of fungal and bacterial communities increased, but the abundance of Bacillus and Lactobacillus decreased and the abundance of pathogenic fungi increased. FAPROTAX analysis indicated that N cycle functions were enriched more with than without continuous cultivation, and that enrichment of N cycle and sulfate respiration functions was higher in the second than in the first year of cultivation. FunGuild analysis indicated that the functions related to pathotrophs and wood saprotrophs were enriched by M. sextelata cultivation. Overall, the results suggest that continuous cropping may reduce M. sextelata production by acidifying the soil and increasing the abundance of pathogenic fungi. Additional research is needed to determine whether increases in the abundance of pathogenic fungi and changes in soil chemistry result in the declines in production that occur with continuous M. sextelata cultivation.

The response of sugar beet rhizosphere micro-ecological environment to continuous cropping

Continuous cropping can lead to increased soil-borne diseases of sugar beet (Beta vulgaris L.), resulting in a reduction in its yield quality. However, our understanding of the influence of continuous cropping on sugar beet-associated microbial community is limited and their interactions remain unclear. Here, we described and analyzed microbial diversity (N = 30) from three sugar beet belowground compartments (bulk soil, rhizosphere soil, and beetroot) using 16S rRNA and ITS sequencing. The continuous cropping showed lower bacterial alpha diversity in three belowground compartments and higher fungal alpha diversity in roots compared to the non-continuous cropping. There were significant differences in fungal community composition between the two groups. Compared with non-continuous cropping, continuous cropping increased the relative abundance of potentially pathogenic fungi such as Tausonia, Gilbellulopsis, and Fusarium, but decreased the relative abundance of Olpidium. The fungal flora in the three compartments displayed different keystone taxa. Fungi were more closely related to environmental factors than bacteria. Overall, changes in microbial diversity and composition under continuous cropping were more pronounced in the fungal communities, and the results of the study could guide development strategies to mitigate continuous crop adversity.

Seedborne Cercospora beticola Can Initiate Cercospora Leaf Spot from Sugar Beet (Beta vulgaris) Fruit Tissue

Cercospora leaf spot (CLS) is a globally important disease of sugar beet (Beta vulgaris) caused by the fungus Cercospora beticola. Long-distance movement of C. beticola has been indirectly evidenced in recent population genetic studies, suggesting potential dispersal via seed. Commercial sugar beet "seed" consists of the reproductive fruit (true seed surrounded by maternal pericarp tissue) coated in artificial pellet material. In this study, we confirmed the presence of viable C. beticola in sugar beet fruit for 10 of 37 tested seed lots. All isolates harbored the G143A mutation associated with quinone outside inhibitor resistance, and 32 of 38 isolates had reduced demethylation inhibitor sensitivity (EC₅₀ > 1 µg/ml). Planting of commercial sugar beet seed demonstrated the ability of seedborne inoculum to initiate CLS in sugar beet. C. beticola DNA was detected in DNA isolated from xylem sap, suggesting the vascular system is used to systemically colonize the host. We established nuclear ribosomal internal transcribed spacer region amplicon sequencing using the MinION platform to detect fungi in sugar beet fruit. Fungal sequences from 19 different genera were identified from 11 different sugar beet seed lots, but Fusarium, Alternaria, and Cercospora were consistently the three most dominant taxa, comprising an average of 93% relative read abundance over 11 seed lots. We also present evidence that C. beticola resides in the pericarp of sugar beet fruit rather than the true seed. The presence of seedborne inoculum should be considered when implementing integrated disease management strategies for CLS of sugar beet in the future.

Impacts of continuous and rotational cropping practices on soil chemical properties and microbial communities during peanut cultivation

Long-term monocultures have severely inhibited the cultivation of Chinese peanut (Arachis hypogaea L.). In this study, the effects of continuous cropping on soil chemical properties and microbial communities were investigated in peanut fields that had been in crop rotation for 10 years and in monoculture for 10 years. The results found that long-term monoculture increased the activities of available potassium, available phosphorus, available nitrogen, soil organic matter, urease, acid phosphatase and catalase; while decreasing the activity of catalase. The diversity and abundance of soil bacteria and fungi is higher under continuous peanut cultivation. At the genus level, the relative abundance of potentially beneficial microflora genera was higher in the rhizosphere soil of rotational cropping than in continuous cropping, while the opposite was true for the relative abundance of potentially pathogenic fungal genera. Principal coordinates and cluster analysis indicated that continuous cropping altered the structure of the microbial community. The results of the functional predictions showed significant differences in the functioning of the rhizosphere microbial community between continuous and rotational cropping. In conclusion, long-term continuous cropping changed the chemical properties of the soil, altered the structure and function of the soil bacterial and fungal communities in peanut rhizosphere, which to some extent reduced the relative abundance of potentially beneficial microbial genera and increased the relative abundance of potentially pathogenic fungal genera, thus increasing the potential risk of soil-borne diseases and reducing the yield and quality of peanut. Therefore, in the actual production process, attention should be paid not only to the application of chemical fertilizers, but also to crop rotation and the application of microbial fertilizers.

Diversity and structure of the rhizosphere microbial communities of wild and cultivated ginseng

BACKGROUND

The resources of wild ginseng have been reducing sharply, and it is mainly dependent on artificial cultivation in China, Korea and Japan. Based on cultivation modes, cultivated ginseng include understory wild ginseng (the seeds or seedlings of cultivated ginseng were planted under the theropencedrymion without human intervention) and farmland cultivated ginseng (grown in farmland with human intervention). Cultivated ginseng, can only be planted on the same plot of land consecutively for several years owing to soilborne diseases, which is mainly because of the variation in the soil microbial community. In contrast, wild ginseng can grow for hundreds of years. However, the knowledge of rhizosphere microbe communities of the wild ginseng is limited.

RESULT

In the present study, the microbial communities in rhizosphere soils of the three types of ginseng were analyzed by high-throughput sequencing of 16 S rRNA for bacteria and internal transcribed spacer (ITS) region for fungi. In total, 4,381 bacterial operational taxonomic units (OTUs) and 2,679 fungal OTUs were identified in rhizosphere soils of the three types of ginseng. Among them, the shared bacterial OTUs was more than fungal OTUs by the three types of ginseng, revealing fungal communities were to be more affected than bacterial communities. In addition, the composition of rhizosphere microbial communities and bacterial diversity were similar between understory wild ginseng and wild ginseng. However, higher bacterial diversity and lower fungal diversity were found in rhizosphere soils of wild ginseng compared with farmland cultivated ginseng. Furthermore, the relative abundance of Chloroflexi, Fusarium and Alternaria were higher in farmland cultivated ginseng compared to wild ginseng and understory wild ginseng.

CONCLUSIONS

Our results showed that composition and diversity of rhizosphere microbial communities were significantly different in three types of ginseng. This study extended the knowledge pedigree of the microbial diversity populating rhizospheres, and provided insights into resolving the limiting bottleneck on the sustainable development of P. ginseng crops, and even the other crops of Panax.

Impact of pesticide/fertilizer mixtures on the rhizosphere microbial community of field-grown sugarcane

The rhizosphere microbial community is important for plant health and is shaped by numerous environmental factors. This study aimed to unravel the effects of a pesticide/fertilizer mixture on the soil rhizosphere microbiome of field-grown sugarcane. A field trial on sugarcane was conducted in Zhanjian City, Guangdong Province, China, and soil samples from the rhizosphere were collected after clothianidin pesticide and/or organic fertilizer treatments. The effects of pesticide and/or organic fertilizer treatments on the composition, diversity, and predictive function of the rhizosphere microbial communities were examined using 16S rRNA gene and ITS1 amplicon sequencing. Compared with the controls (no pesticide or fertilizer used), the microbial community that resulted from treatment with the pesticide/fertilizer mixture (SPF) had a higher relative bacterial diversity and fungal richness, and contributed more beneficial functions to sugarcane, including xenobiotics biodegradation and metabolism of amino acids. The bacterial and fungal compositions at various taxonomic levels were not significantly different in SPF and SP (pesticide only) treatments compared to treatments without the pesticide, suggesting that the clothianidin addition did not cause a detrimental impact on the soil microbiome. Moreover, five bacterial genera, including Dyella, Sphingomonas, Catenulispora, Mucilaginibacter, and Tumebacillus, were significantly more abundant in the SPF and SP treatments, which could be associated with the pesticide addition. With the addition of organic fertilizers in SPF, the abundances of some soil-beneficial bacteria Bacillus, Paenibacillus, and Brevibacillus were highly increased. Our study provides insights into the interactions between the rhizosphere soil microbiome and pesticide-fertilizer integration, which may help improve the application of pesticide-fertilizer to sugarcane fields.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02770-3.

Effects of continuous cropping of sweet potatoes on the bacterial community structure in rhizospheric soil

BACKGROUND

Continuous cropping obstacles from sweet potatoes are widespread, which seriously reduce the yield and quality, causing certain economic losses. Bacteria of rhizospheric soil are the richest and are associated with obstacles to continuous cropping. However, few studies have examined how continuous sweet potato cropping affects the rhizospheric soil bacterial community structure.

RESULTS

In the study, the Illumina MiSeq method was used to explore the variations in rhizospheric soil bacterial community structure of different sweet potato varieties after continuous cropping, as well as the correlation between soil characteristics and the bacterial community. The results showed that (1) the dominant bacterial phyla in rhizospheric soils from both Xushu 18 and Yizi 138 were Proteobacteria, Acidobacteria, and Actinobacteria. The most dominant genus was Subgroup 6_norank. The relative abundance of rhizospheric soil bacteria varied significantly between the two sweet potato varieties. (2) The richness and diversity indexes of bacteria were higher in Xushu 18 rhizospheric soil than in Yizi 138 soil after continuous cropping. Moreover, beneficial Lysobacter and Bacillus were more prevalent in Xushu 18, while Yizi 138 contained more harmful Gemmatimonadetes. (3) Soil pH decreased after continuous cropping, and redundancy analysis indicated that soil pH was significantly correlated with the bacterial community. Spearman's rank correlation coefficient analysis demonstrated that pH was positively associated with Planctomycetes and Acidobacteria, but negatively associated with Actinobacteria and Firmicutes.

CONCLUSIONS

After continuous cropping, the bacterial community structure and physicochemical properties of sweet potato rhizospheric soil were changed, and the changes from different sweet potato varieties were different. The contents of Lysobacter and Bacillus were higher in the sweet potato variety resistant to continuous cropping. It provides a basis for developing new microbial fertilizers for sweet potatoes to alleviate the continuous cropping obstacle.

Integration of Transcriptomics and Metabolomics Reveals the Responses of Sugar Beet to Continuous Cropping Obstacle

Sugar beet is vulnerable to years of continuous cropping, and allelopathy is one of the important factors leading to continuous cropping disorder. To explore the physiological and molecular mechanisms behind continuous cropping obstacles on sugar beet, this study combined transcriptomics and metabolomics to analyze the effects of different years of continuous cropping on metabolite changes, differential gene expression, and root exudate regulation in sugar beet. We collected sugar beet's root samples from 1-, 3-, and 5-year continuous cropping systems for metabolome and transcriptome analyses. Our data revealed that T3 and T5 had 50 and 33 metabolites significantly different from T1, respectively. The autotoxic substance salicylaldehyde was found to continuously accumulate in root exudates with increasing years of continuous cropping. Sucrose was highly reduced in T3 (4.05-fold decrease) and T5 (2.01-fold decrease) compared to T1. Respectively, 2,660 and 3,515 differentially expressed genes (DEGs) were significantly regulated in T3 and T5 compared to T1. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that metabolic pathways and biosynthesis of secondary metabolites were perturbed in T3 and T5 vs. T1. Integrated metabolomics analyses identified 73 DEGs involved in enriched metabolic pathways, all of which were the oxidation-reduction process pathways. In conclusion, this study provides evidence that continuous cropping obstacles can change the metabolome and transcriptome of sugar beet, affecting its growth and quality.

Microbial Inoculation for Productivity Improvements and Potential Biological Control in Sugar Beet Crops

Used mainly for sucrose production, sugar beet is one of the most important crops in Castilla y León (Spain). Several studies have demonstrated the benefits of microorganisms in different crop management programs, among which Plant Growth Promoting Rhizobacteria (PGPR). This research aims to assess the beneficial effects of two PGPRs strains (Pseudomonas fluorescens Pf0-1 and Pseudomonas chlororaphis CECT 462) on sugar beet (Beta vulgaris) production. Three treatments: a PGPRs co-inoculation assay of untreated seeds without any chemical treatment (TB), a conventional treatment with commercial seeds and fungicide application (TT); and a control with seeds without protective coating, bacterial inoculation and chemical treatment (ST). The efficacy of PGPRs inoculation on sugar beet production was determined measuring periodically the photosynthetic status of plants, and the final yield and quality of tubers. Aerial and root plant biomass, maximum beet perimeter, polarization, and sugar values of the sugar beet plants inoculated with PGPRs showed higher values and significant differences to sugar beet subjected to other treatments. We could see that PGPRs inoculation (TB treatment) produced significant differences in the quantum yield of PSII (ΦPSII). TB showed the highest value for ΦPSII and the NPQ (non-photochemical quenching), the lowest value, even though the PSII (maximum quantum yield of photosystem II) was very similar in all treatments. The two assayed PGPR strains triggered a significant increase in sugar beet production yield and quality. PGPRs inoculation techniques could be used in different crops and they could be applied as biofertilizers, improving the agricultural production.

Understanding the Impact of Cultivar, Seed Origin, and Substrate on Bacterial Diversity of the Sugar Beet Rhizosphere and Suppression of Soil-Borne Pathogens

The rhizosphere microbiome is crucial for plant health, especially for preventing roots from being infected by soil-borne pathogens. Microbiota-mediated pathogen response in the soil-root interface may hold the key for microbiome-based control strategies of phytopathogens. We studied the pathosystem sugar beet-late sugar beet root rot caused by Rhizoctonia solani in an integrative design of combining in vitro and in vivo (greenhouse and field) trials. We used five different cultivars originating from two propagation sites (France, Italy) with different degrees of susceptibility towards R. solani (two susceptible, one moderately tolerant and two cultivars with partial resistance). Analyzing bacterial communities in seeds and roots grown under different conditions by 16S rRNA amplicon sequencing, we found site-, cultivar-, and microhabitat-specific amplicon sequences variants (ASV) as well as a seed core microbiome shared between all sugar beet cultivars (121 ASVs representing 80%-91% relative abundance). In general, cultivar-specific differences in the bacterial communities were more pronounced in seeds than in roots. Seeds of Rhizoctonia-tolerant cultivars contain a higher relative abundance of the genera Paenibacillus, Kosakonia, and Enterobacter, while Gaiellales, Rhizobiales, and Kosakonia were enhanced in responsive rhizospheres. These results indicate a correlation between bacterial seed endophytes and Rhizoctonia-tolerant cultivars. Root communities are mainly substrate-derived but also comprise taxa exclusively derived from seeds. Interestingly, the signature of Pseudomonas poae Re*1-1-14, a well-studied sugar-beet specific biocontrol agent, was frequently found and in higher relative abundances in Rhizoctonia-tolerant than in susceptible cultivars. For microbiome management, we introduced microbial inoculants (consortia) and microbiome transplants (vermicompost) in greenhouse and field trials; both can modulate the rhizosphere and mediate tolerance towards late sugar beet root rot. Both, seeds and soil, provide specific beneficial bacteria for rhizosphere assembly and microbiota-mediated pathogen tolerance. This can be translated into microbiome management strategies for plant and ecosystem health.