Community structures of the rhizomicrobiomes of cultivated and wild soybeans in their continuous cropping

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus

Astragalus mongholicus is a medicinal plant that is known to decrease in quality in response to continuous cropping. However, the differences in the root-associated microbiome and root exudates in the rhizosphere soil that may lead to these decreases are barely under studies. We investigated the plant biomass production, root-associated microbiota, and root exudates of A. mongholicus grown in two different fields: virgin soil (Field I) and in a long-term continuous cropping field (Field II). Virgin soil is soil that has never been cultivated for A. mongholicus. Plant physiological measurements showed reduced fresh and dry weight of A. mongholicus under continuous cropping conditions (i.e. Field II). High-throughput sequencing of the fungal and bacterial communities revealed differences in fungal diversity between samples from the two fields, including enrichment of potentially pathogenic fungi in the roots of A. mongholicus grown in Field II. Metabolomic analysis yielded 20 compounds in A. mongholicus root exudates that differed in relative abundance between rhizosphere samples from the two fields. Four of these metabolites (2-aminophenol, quinic acid, tartaric acid, and maleamate) inhibited the growth of A. mongholicus, the soil-borne pathogen Fusarium oxysporum, or both. This comprehensive analysis enhances our understanding of the A. mongholicus microbiome, root exudates, and interactions between the two in response to continuous cropping. These results offer new information for future design of effective, economical approaches to achieving food security.

Galaxolide-contaminated soil and tolerance strategies in soybean plants using biofertilization and selenium nanoparticle supplementation

The current study aimed to address the response of soybean (Glycine max) plants to biofertilization and selenium supplementation treatments under galaxolide contamination of soil. In this regard, a pot experiment was carried out where the soybean plants were treated with the plant growth-promoting Actinobacteria (Actinobacterium sp.) as a biofertilizer (PGPB treatment) and/or selenium nanoparticles (Se treatment; 25 mg L-1) under two non-polluted and galaxolide-polluted soils (250 mg galaxolide per kg of soil) to assess the modifications in some plant physiological and biochemical traits. Although higher accumulation of oxidative biomarkers, including hydrogen peroxide (+180%), malondialdehyde (+163%), and protein oxidation (+125%), indicating oxidative stress in galaxolide-contaminated plants, an apparent decline in their contents was observed in response to biofertilization/supplementation treatments in contaminated soil, especially. It was mainly related to the higher detoxification of ROS in PGPB- and Se-treated plants under galaxolide-induced oxidative stress, in which the direct ROS-scavenging enzymes (+44 -179%), enzymatic (+34 - 293%) and non-enzymatic (+35 - 98%) components of the ascorbate-glutathione pathway, and antioxidant molecules (+38 - 370%) were more activated than in control plants. In addition, a higher accumulation of detoxification activity markers, including phytochelatins (+32%) and metallothioneins (+79%), were found in the combined treatments (PGPB+Se) under galaxolide contamination. Moreover, combined treatment with PGPB and Se ameliorated the levels of chlorophyll a content (+58%), stomatal conductance (+57%), the maximum efficiency of photosystem II (PSII) (+36%), and photorespiratory metabolism (including +99% in glycolate oxidase and +54% in hydroxypyruvate reductase activity) in leaves under galaxolide contamination, which resulted in higher photosynthesis capacity (+36%) and biomass production (+74%) in galaxolide-stressed plants as compared to control group. In conclusion, the application of beneficial Actinobacteria and selenium nanoparticles as biofertilization/supplementation is expected to be useful for improving plant toleration and adaptation against galaxolide contamination.

Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China

Introduction

The microbiome inhabiting plant leaves is critical for plant health and productivity. Wild soybean (Glycine soja), which originated in China, is the progenitor of cultivated soybean (Glycine max). So far, the community structure and assembly mechanism of phyllosphere microbial community on G. soja were poorly understood.

Methods

Here, we combined a national-scale survey with high-throughput sequencing and microsatellite data to evaluate the contribution of host genotype vs. climate in explaining the foliar microbiome of G. soja, and the core foliar microbiota of G. soja were identified.

Results

Our findings revealed that both the host genotype and environmental factors (i.e., geographic location and climatic conditions) were important factors regulating foliar community assembly of G. soja. Host genotypes explained 0.4% and 3.6% variations of the foliar bacterial and fungal community composition, respectively, while environmental factors explained 25.8% and 19.9% variations, respectively. We further identified a core microbiome thriving on the foliage of all G. soja populations, including bacterial (dominated by Methylobacterium-Methylorubrum, Pantoea, Quadrisphaera, Pseudomonas, and Sphingomonas) and fungal (dominated by Cladosporium, Alternaria, and Penicillium) taxa.

Conclusion

Our study revealed the significant role of host genetic distance as a driver of the foliar microbiome of the wild progenitor of soya, as well as the effects of climatic changes on foliar microbiomes. These findings would increase our knowledge of assembly mechanisms in the phyllosphere of wild soybeans and suggest the potential to manage the phyllosphere of soya plantations by plant breeding and selecting specific genotypes under climate change.

Differentially enriched fungal communities in root rot resistant and susceptible varieties of tobacco (Nicotiana tabacum L.) under continuous monoculture cropping

Root rot is a major disease of tobacco that causes crop losses of up to 15-20% of global tobacco production. The present study aimed to compare the fungal communities, and physicochemical properties of rhizosphere soil of root rot resistant (Yunyan 87; Y) and susceptible (Honghua Dajinyuan; H) tobacco varieties. Four treatments of each variety under continuous monocropping cultures included: control groups (HT0 and YT0); 2 years of continuous cropping (HT2 and YT2); 4 years of continuous cropping (HT4 and YT4); and 8 years of continuous cropping (YT8 and HT8). The soil physicochemical properties including available nitrogen (AN), available phosphorus (AP), available potassium (AK), and organic matter (OM) were increased (p < 0.05) from HT0 to HT8, whereas the resistant variety (Y) showed an inconsistent trend from YT0 to YT8. The pH was decreased (p < 0.05) from HT0 to HT8 and YT0 to YT8. Further, the disease incidence rate and disease index of the H variety also increased (p < 0.05) from HT0 to HT8. Alpha diversity analysis revealed that susceptible variety had higher fungal diversity from HT0 to HT8, while resistant variety exhibited lower diversity from YT0 to YT8. Ascomycota and Mortierellomycota were the dominant phyla in H and Y. Ascomycota abundance was increased (p < 0.05), whereas Mortierellomycota was decreased (p < 0.05) for continuous cropping years in H and Y. Penicillium, Fusarium, and Chrysosporium were the top three abundant genera in both varieties. The relative abundance of Penicillium spp. was increased (p < 0.05) in Y, whereas decreased (p < 0.05) in H variety. Specifically, Chrysosporium spp. was increased (p < 0.05) whereas Fusarium spp. was decreased (p < 0.05) in YT2. Redundancy analysis (RDA) revealed that fungal communities in H and Y rhizospheres were influenced by pH and carbon content, respectively. The top three highly enriched (p < 0.05) pathways in both varieties were fatty acid elongation, fatty acid β-oxidation I, and glyoxylate cycle. Our study concluded that resistant variety exhibited lower fungal diversity and functionally enriched metabolic pathways than susceptible variety that might be the result of molecular breeding practices, however, the relative abundance of Penicillium spp. were increased in resistant variety under long-term monoculture cropping.

Chitin amendments eliminate the negative impacts of continuous cropping obstacles on soil properties and microbial assemblage

Continuous cropping of soybean leads to soil environment deterioration and soil-borne disease exacerbation, which in turn limits the sustainability of agricultural production. Chitin amendments are considered promising methods for alleviating soybean continuous cropping obstacles; however, the underlying mechanisms of soil sickness reduction remain unclear. In this study, soil amendments with pure and crude chitin at different addition dosages were employed to treat diseased soil induced by continuous cropping of soybean for five years. Chitin amendments, especially crude chitin, remarkably increased soil pH, available phosphorus (AP), potassium (AK) and nitrate nitrogen ( NO 3 - -N) contents, and improved soybean plant growth and soil microbial activities (FDA). Additionally, chitin application significantly enriched the relative abundances of the potential biocontrol bacteria Sphingomonas, Streptomyces, and Bacillus and the fungi Mortierella, Purpureocillium, and Metarhizium while depleted those of the potential plant pathogens Fusarium, Cylindrocarpon and Paraphoma. Moreover, chitin amendments induced looser pathogenic subnetwork structures and less pathogenic cooperation with other connected microbial taxa in the rhizosphere soils. The structural equation model (SEM) revealed that pure and crude chitin amendments promoted soybean plant growth by indirectly regulating soil pH-mediated soil microbial activities and potentially beneficial microbes, respectively. Therefore, the reduction strategies for continuous cropping obstacles by adding pure and crude chitin were distinct; pure chitin amendments showed general disease suppression, while crude chitin exhibited specific disease suppression. Overall, chitin amendments could suppress potential plant pathogens and improve soil health, thereby promoting soybean growth, which provides new prospects for cultivation practices to control soybean continuous cropping obstacles.

Metabolomics and Microbiomics Reveal Impacts of Rhizosphere Metabolites on Alfalfa Continuous Cropping

Alfalfa long-term continuous cropping (CC) can pose a serious threat to alfalfa production. However, the mechanism of alfalfa CC obstacle is unclear as of today. Our preliminary study showed that the main factors of CC obstacle were not the lack of nutrients or water in alfalfa rhizosphere soils. Further, we evaluated physic-chemical property, microbial population structure, and metabolite differences of alfalfa rhizosphere soils with CC for 1, 7, and 14 years based on analysis of metabolomics and microbiomics. Four phenolic acid metabolites, including p-coumaric acid, ferulic acid, vanillic acid, and p-hydroxybenzoic acid, were found to have significant differences among different CC years, which may be the key factors of CC obstacle. Among them, p-coumaric acid and ferulic acid could significantly decrease the germination rate of alfalfa seeds by 21.11 and 16.67% at the concentration of 100 μg/mL and the height (root length) of alfalfa seedlings by 21% (32.9%) and 13.72% (16.45%). Moreover, these metabolites could effectively promote the growth of some pathogenic fungi, causing alfalfa root rot. Among them, p-coumaric acid obviously and significantly aggravated the occurrence of alfalfa root rot. With the increase of CC years, soil microbial community changed from fungi to bacteria; fungi decreased by 10.83%, fungi increased by 8.08%, and beneficial microorganisms decreased with the increase of CC years. Field analysis and experimental verification showed that the above results were consistent with that of CC obstacle in the field. Among the key metabolites, the autotoxicity of p-coumaric acid was the strongest. This study fully proved that the continuous accumulation of autotoxic substances in alfalfa rhizosphere was the key factor causing alfalfa CC obstacles.

Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication

Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.

Wild rice harbors more root endophytic fungi than cultivated rice in the F1 offspring after crossbreeding

BACKGROUND

Rice, which serves as a staple food for more than half of the world's population, is grown worldwide. The hybridization of wild and cultivated rice has enabled the incorporation of resistance to varying environmental conditions. Endophytic microbiota are known to be transferred with their host plants. Although some studies have reported on the endophytic microbiota of wild and cultivated rice, the inheritance from wild and cultivated rice accessions in next generations, in terms of endophytic microbiota, has not been examined.

RESULTS

In the present study, the endophytic microbial community structures of Asian and African wild and cultivated rice species were compared with those of their F1 offspring. High-throughput sequencing data of bacterial 16S rDNA and fungal internal transcribed spacer regions were used to classify the endophytic microbiota of collected samples of rice. Results indicated that when either African or Asian wild rice species were crossed with cultivated rice accessions, the first generation harbored a greater number of root endophytic fungi than the cultivated parent used to make the crosses. Network analysis of the bacterial and fungal operational taxonomic units revealed that Asian and African wild rice species clustered together and exhibited a greater number of significant correlations between fungal taxa than cultivated rice. The core bacterial genus Acidovorax and the core fungal order Pleosporales, and genera Myrothecium and Bullera connected African and Asian wild rice accessions together, and both the wild rice accessions with their F1 offspring. On the other hand, the core bacterial genus Bradyrhizobium and the core fungal genera Dendroclathra linked the African and Asian cultivated rice accessions together.

CONCLUSIONS

This study has theoretical significance for understanding the effect of breeding on the inheritance of endophytic microbiota of rice and identifying beneficial endophytic bacteria and fungi among wild and cultivated rice species, and their F1 offspring.

Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community

The continuous cropping of plants can result in the disruption of the soil microbial community and caused significant declines in yields. However, there are few reports on the effects of continuous cropping of sugarcane on the microbial community structure and functional pathway. In the current study, we analyzed the structural and functional changes of microbial community structure in the rhizospheric soil of sugarcane in different continuous cropping years using Illumina Miseq high-throughput sequencing and metagenomics analysis. We collected rhizosphere soils from fields of no continuous cropping history (NCC), 10 years of continuous cropping (CC10), and 30 years of continuous cropping (CC30) periods in the Fujian province. The results demonstrated that continuous sugarcane cropping resulted in significant changes in the physicochemical properties of soil and the composition of soil bacterial and fungal communities. With the continuous cropping, the crop yield dramatically declined from NCC to CC30. Besides, the redundancy analysis (RDA) of the dominant bacterial and fungal phyla and soil physicochemical properties revealed that the structures of the bacterial and fungal communities were mainly driven by pH and TS. Analysis of potential functional pathways during the continuous cropping suggests that different KEGG pathways were enriched in different continuous cropping periods. The significant reduction of bacteria associated with rhizospheric soil nitrogen and sulfur cycling functions and enrichment of pathogenic bacteria may be responsible for the reduction of effective nitrogen and total sulfur content in rhizospheric soil of continuous sugarcane as well as the reduction of sugarcane yield and sugar content. Additionally, genes related to nitrogen and sulfur cycling were identified in our study, and the decreased abundance of nitrogen translocation genes and AprAB and DsrAB in the dissimilatory sulfate reduction pathway could be the cause of declined biomass. The findings of this study may provide a theoretical basis for uncovering the mechanism of obstacles in continuous sugarcane cropping and provide better guidance for sustainable development of the sugarcane.

Soil Bacterial Community in the Multiple Cropping System Increased Grain Yield Within 40 Cultivation Years

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.

Synergistic effects of organic fertilizer and corn straw on microorganisms of pepper continuous cropping soil in China

Because of the large population, large demand, limited arable land and many environmental factors, continuous cropping have become a very common phenomenon in China. However, long-term continuous cropping has caused a series of serious soil-borne diseases, and the yield and quality of crops to drop, which seriously restricted the sustainable development of agricultural industry. Therefore, in order to improve the yield of pepper and reduce the occurrence of soil-borne diseases, it is essential to understand the effect of continuous cropping of pepper on soil microbial community composition and abundance. In this study, high throughput sequencing was used to study the effects of seven treatments of organic fertilizers and corn straw on soil microbial community and function of pepper continuous cropping. The results showed that the yield of all treatments was significantly higher than that of the control. The soil microbial diversity and community composition showed that Proteobacteria and Ascomycota were the most abundant phylum in all treatments. In conclusion, there were significant differences among the seven treatments and the treatment of fowl dung with corn straw was the best fertilizer combination to improve the yield and output value of pepper. Besides, the addition of fowl dung and corn straw not only can improve the community and functions of microorganisms, but also enhance the ability of disease resistance, and ultimately decrease the soil-borne diseases. The results will help to provide scientific basis for rational application of organic fertilizer and corn straw, and overcoming continuous cropping obstacles.

The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi

Legumes are unique among plants as they can obtain nitrogen through symbiosis with nitrogen-fixing rhizobia that form root nodules in the host plants. Therefore they are valuable crops for sustainable agriculture. Increasing nitrogen fixation efficiency is not only important for achieving better plant growth and yield, but it is also crucial for reducing the use of nitrogen fertilizer. Arbuscular mycorrhizal fungi (AMF) are another group of important beneficial microorganisms that form symbiotic relationships with legumes. AMF can promote host plant growth by providing mineral nutrients and improving the soil ecosystem. The trilateral legume-rhizobia-AMF symbiotic relationships also enhance plant development and tolerance against biotic and abiotic stresses. It is known that domestication and agricultural activities have led to the reduced genetic diversity of cultivated germplasms and higher sensitivity to nutrient deficiencies in crop plants, but how domestication has impacted the capability of legumes to establish beneficial associations with rhizospheric microbes (including rhizobia and fungi) is not well-studied. In this review, we will discuss the impacts of domestication and agricultural practices on the interactions between legumes and soil microbes, focusing on the effects on AMF and rhizobial symbioses and hence nutrient acquisition by host legumes. In addition, we will summarize the genes involved in legume-microbe interactions and studies that have contributed to a better understanding of legume symbiotic associations using metabolic modeling.

Research Advances of Beneficial Microbiota Associated with Crop Plants

Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.