Rhizospheric soil and root endogenous fungal diversity and composition in response to continuous Panax notoginseng cropping practices

Assessing the biodiversity of rhizosphere and endophytic fungi in Knoxia valerianoides under continuous cropping conditions

BACKGROUND

Rhizosphere and endophytic fungi play important roles in plant health and crop productivity. However, their community dynamics during the continuous cropping of Knoxia valerianoides have rarely been reported. K. valerianoides is a perennial herb of the family Rubiaceae and has been used in herbal medicines for ages. Here, we used high-throughput sequencing technology Illumina MiSeq to study the structural and functional dynamics of the rhizosphere and endophytic fungi of K. valerianoides.

RESULTS

The findings indicate that continuous planting has led to an increase in the richness and diversity of rhizosphere fungi, while concomitantly resulting in a decrease in the richness and diversity of root fungi. The diversity of endophytic fungal communities in roots was lower than that of the rhizosphere fungi. Ascomycota and Basidiomycota were the dominant phyla detected during the continuous cropping of K. valerianoides. In addition, we found that root rot directly affected the structure and diversity of fungal communities in the rhizosphere and the roots of K. valerianoides. Consequently, both the rhizosphere and endophyte fungal communities of root rot-infected plants showed higher richness than the healthy plants. The relative abundance of Fusarium in two and three years old root rot-infected plants was significantly higher than the control, indicating that continuous planting negatively affected the health of K. valerianoides plants. Decision Curve Analysis showed that soil pH, organic matter (OM), available K, total K, soil sucrase (S_SC), soil catalase (S_CAT), and soil cellulase (S_CL) were significantly related (p < 0.05) to the fungal community dynamics.

CONCLUSIONS

The diversity of fungal species in the rhizosphere and root of K. valerianoides was reported for the first time. The fungal diversity of rhizosphere soil was higher than that of root endophytic fungi. The fungal diversity of root rot plants was higher than that of healthy plants. Soil pH, OM, available K, total K, S_CAT, S_SC, and S_CL were significantly related to the fungal diversity. The occurrence of root rot had an effect on the community structure and diversity of rhizosphere and root endophytic fungi.

Multi-year crop rotation and quicklime application promote stable peanut yield and high nutrient-use efficiency by regulating soil nutrient availability and bacterial/fungal community

Diversifying cultivation management, including different crop rotation patterns and soil amendment, are effective strategies for alleviating the obstacles of continuous cropping in peanut (Arachis hypogaea L.). However, the peanut yield enhancement effect and temporal changes in soil chemical properties and microbial activities in response to differential multi-year crop rotation patterns and soil amendment remain unclear. In the present study, a multi-year localization experiment with the consecutive application of five different cultivation managements (including rotation with different crops under the presence or absence of external quicklime as soil amendment) was conducted to investigate the dynamic changes in peanut nutrient uptake and yield status, soil chemical property, microbial community composition and function. Peanut continuous cropping led to a reduction in peanut yield, while green manure-peanut rotation and wheat-maize-peanut rotation increased peanut yield by 40.59 and 81.95%, respectively. A combination of quicklime application increased yield by a further 28.76 and 24.34%. Alterations in cultivation management also strongly affected the soil pH, nutrient content, and composition and function of the microbial community. The fungal community was more sensitive than the bacterial community to cultivation pattern shift. Variation in bacterial community was mainly attributed to soil organic carbon, pH and calcium content, while variation in fungal community was more closely related to soil phosphorus content. Wheat-maize-peanut rotation combined with quicklime application effectively modifies the soil acidification environment, improves the soil fertility, reshapes the composition of beneficial and harmful microbial communities, thereby improving soil health, promoting peanut development, and alleviating peanut continuous cropping obstacles. We concluded that wheat-maize-peanut rotation in combination with quicklime application was the effective practice to improve the soil fertility and change the composition of potentially beneficial and pathogenic microbial communities in the soil, which is strongly beneficial for building a healthy soil micro-ecology, promoting the growth and development of peanut, and reducing the harm caused by continuous cropping obstacles to peanut.

Leaf litter from Cynanchum auriculatum Royle ex Wight leads to root rot outbreaks by Fusarium solani, hindering continuous cropping

Cynanchum auriculatum Royle ex Wight (CA) is experiencing challenges with continuous cropping obstacle (CCO) due to soil-borne fungal pathogens. The leaf litter from CA is regularly incorporated into the soil after root harvesting, but the impact of this practice on pathogen outbreaks remains uncertain. In this study, a fungal strain D1, identified as Fusarium solani, was isolated and confirmed as a potential factor in CCO. Both leave extract (LE) and root extract (RE) were found to inhibit seed germination and the activities of plant defense-related enzymes. The combinations of extracts and D1 exacerbated these negative effects. Beyond promoting the proliferation of D1 in soil, the extracts also enhanced the hypha weight, spore number, and spore germination rate of D1. Compared to RE, LE exhibited a greater degree of promotion in the activities of pathogenesis-related enzymes in D1. Additionally, caffeic acid and ferulic acid were identified as potential active compounds. LE, particularly in combination with D1, induced a shift in the composition of fungal communities rather than bacterial communities. These findings indicate that the water extract of leaf litter stimulated the growth and proliferation of fungal strain D1, thereby augmenting its pathogenicity toward CA and ultimately contributing to the CCO process.

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.

Characterization of rhizospheric fungi and their in vitro antagonistic potential against myco-phytopathogens invading Macrotyloma uniflorum plants

Microorganisms have become more resistant to pesticides, which increases their ability to invade and infect crops resulting in decreased crop productivity. The rhizosphere plays a crucial role in protecting plants from harmful invaders. The purpose of the study was to investigate the antagonistic efficiency of indigenous rhizospheric fungal isolates against phytopathogens of M. uniflorum plants so that they could be further used as potent Biocontrol agents. Thirty rhizospheric fungal isolates were collected from the roots of the Macrotyloma uniflorum plant and initially described morphologically for the present study. Further, in vitro tests were conducted to evaluate the antifungal activity of these strains against four myco-phytopathogens namely Macrophamina phaseolina, Phomopsis sp. PhSFX-1, Nigrospora oryzae, and Boeremia exigua. These pathogens are known to infect the same crop plant, M. uniflorum, and cause declines in crop productivity. Fifteen fungal strains out of the thirty fungal isolates showed some partial antagonistic activity against the myco-phytopathogens. The potent fungal isolates were further identified using molecular techniques, specifically based on the internal transcribed spacer (ITS) region sequencing. Penicillium mallochii, Cladosporium pseudocladosporioides, Aspergillus chevalieri, Epicoccum nigrum, Metarhizium anisopliae, and Mucor irregularis were among the strains that were identified. These potent fungal strains showed effective antagonistic activity against harmful phytopathogens. Current findings suggest that these strains may be taken into consideration as synthetic fungicides which are frequently employed to manage plant diseases alternatives.

The Combination of Biochar and Bacillus subtilis Biological Agent Reduced the Relative Abundance of Pathogenic Bacteria in the Rhizosphere Soil of Panax notoginseng

In the continuous cropping of Panax notoginseng, the pathogenic fungi in the rhizosphere soil increased and infected the roots of Panax notoginseng, resulting in a decrease in yield. This is an urgent problem that needs to be solved in order to effectively overcome the obstacles associated with the continuous cropping of Panax notoginseng. Previous studies have shown that Bacillus subtilis inhibits pathogenic fungi in the rhizosphere of Panax notoginseng, but the inhibitory effect was not stable. Therefore, we hope to introduce biochar to help Bacillus subtilis colonize in soil. In the experiment, fields planted with Panax notoginseng for 5 years were renovated, and biochar was mixed in at the same time. The applied amount of biochar was set to four levels (B0, 10 kg·hm-2; B1, 80 kg·hm-2; B2, 110 kg·hm-2; B3, 140 kg·hm-2), and Bacillus subtilis biological agent was set to three levels (C1, 10 kg·hm-2; C2, 15 kg·hm-2; C3, 25 kg·hm-2). The full combination experiment and a blank control group (CK) were used. The experimental results show that the overall Ascomycota decreased by 0.86%~65.68% at the phylum level. Basidiomycota increased by -73.81%~138.47%, and Mortierellomycota increased by -51.27%~403.20%. At the genus level, Mortierella increased by -10.29%~855.44%, Fusarium decreased by 35.02%~86.79%, and Ilyonectria increased by -93.60%~680.62%. Fusarium mainly causes acute bacterial wilt root rot, while Ilyonectria mainly causes yellow rot. Under different treatments, the Shannon index increased by -6.77%~62.18%, the Chao1 index increased by -12.07%~95.77%, the Simpson index increased by -7.31%~14.98%, and the ACE index increased by -11.75%~96.12%. The good_coverage indices were all above 0.99. The results of a random forest analysis indicated that Ilyonectria, Pyrenochaeta, and Xenopolyscytalum were the top three most important species in the soil, with MeanDecreaseGini values of 2.70, 2.50, and 2.45, respectively. Fusarium, the primary pathogen of Panax notoginseng, ranked fifth, and its MeanDecreaseGini value was 2.28. The experimental results showed that the B2C2 treatment had the best inhibitory effect on Fusarium, and the relative abundance of Fusarium in Panax notoginseng rhizosphere soil decreased by 86.79% under B2C2 treatment; the B1C2 treatment had the best inhibitory effect on Ilyonectria, and the relative abundance of Ilyonectria in the Panax notoginseng rhizosphere soil decreased by 93.60% under B1C2 treatment. Therefore, if we want to improve the soil with acute Ralstonia solanacearum root rot, we should use the B2C2 treatment to improve the soil environment; if we want to improve the soil with yellow rot disease, we should use the B1C2 treatment to improve the soil environment.

Biocontrol Potential of Trichoderma Ghanense and Trichoderma Citrinoviride toward Pythium aphanidermatum

Pythium-induced damping-off of cucumber is a major constraint to cucumber production in different parts of the world. Although chemical fungicides are used for managing this disease, they have many drawbacks to the environment. The ability of the antagonistic fungi isolated from the rhizosphere and endosphere of Dactyloctenium robecchii and Moraea sisyrinchium in the control of soilborne pathogen Pythium aphanidermatum was inspected. Native Trichoderma isolates, Trichoderma ghanense and Trichoderma citrinoviride, were isolated from plant stem and soil samples collected from Al-Seeb, Oman. Using a dual culture technique, the antagonistic activity of the fungal isolates against P. aphanidermatum was examined in vitro. Among Trichoderma isolates, T. ghanense was more efficient in restraining the mycelial growth of P. aphanidermatum, causing an inhibition percentage of 44.6%. Further, T. citrinoviride induced significantly lower cessation of P. aphanidermatum mycelial growth (31.3%). Microscopic and electrolyte leakage inspection of the pathogen mycelia depicted extreme morphological malformations in their mycelium, which can be attributed to the antifungal metabolites of antagonists. Greenhouse studies demonstrated the effectivity of T. ghanense in controlling Pythium damping-off of cucumber plants, where the number of surviving plants was over 90% when the biocontrol agents were used compared to 0 in the control plants. Furthermore, treatment of the plants with the antagonists promoted growth characteristics of plants compared to uninoculated plants. This included improvements in shoot and root lengths, leaf length and width, and dry weight. These findings suggest that T. ghanense and T. citrinoviride can be developed as alternatives to synthetic chemical fungicides to manage soilborne pathogens of cucumber. This research is also the first to clarify the biocontrol ability of T. citrinoviride and T. ghanense against cucumber damping-off caused by P. aphanidermatum.

Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease

Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.

Short-term continuous monocropping reduces peanut yield mainly via altering soil enzyme activity and fungal community

Continuous monocropping can lead to soil sickness and increase of soil-borne disease, which finally reduces crop yield. Microorganisms benefit plants by increasing nutrient availability, participating in auxin synthesis, and defending against pathogens. However, little is known about the influence of short-term successive peanuts cropping on soil properties, enzyme activities, its yield, plant-associated microbes, and their potential correlations in peanut production. Here, we examined the community structure, composition, network structure and function of microbes in the rhizosphere and bulk soils under different monocropping years. Moreover, we assessed the impact of changes in the soil micro-environment and associated soil microbes on peanut yield. Our results showed that increase of monocropping year significantly decreased most soil properties, enzyme activities and peanut yield (p < 0.05). Principal co-ordinates analysis (PCoA) and analysis of similarities (ANOSIM) indicated that monocropping year significantly influenced the fungal community structure in the rhizosphere and bulk soils (p < 0.01), while had no effect on the bacterial community. With the increase of continuous monocropping year, peanut selectively decreased (e.g., Candidatus_Entotheonella, Bacillus and Bryobacter) or increased (e.g., Nitrospira, Nocardioides, Ensifer, Gaiella, and Novosphingobium) the abundance of some beneficial bacterial genera in the rhizosphere. Continuous monocropping significantly increased the abundance of plant pathogens (e.g., Plectosphaerella, Colletotrichum, Lectera, Gibberella, Metarhizium, and Microdochium) in the rhizosphere and negatively affected the balance of fungal community. Besides, these species were correlated negatively with L-leucine aminopeptidase (LAP) activity. Network co-occurrence analysis showed that continuous monocropping simplified the interaction network of bacteria and fungi. Random forest and partial least squares path modeling (PLS-PM) analysis further showed that fungal community, pathogen abundance, soil pH, and LAP activity negatively affected peanut yield. In conclusion, short-term continuous monocropping decreased LAP activity and increased potential fungal pathogens abundance, leading to reduction of peanut yield.

Multiomics Reveals Mechanisms of Alternaria oxytropis Inhibiting Pathogenic Fungi in Oxytropis ochrocephala

Endophytic fungi can benefit the host plant and increase the plant resistance. Now, there is no in-depth study of how Alternaria oxytropis (A. oxytropis) is enhancing the ability of inhibiting pathogenic fungi in Oxytropis ochrocephala (O. ochrocephala). In this study, the fungal community and metabolites associated with endophyte-infected (EI) and endophyte-free (EF) O. ochrocephala were compared by multiomics. The fungal community indicated that there was more A. oxytropis, less phylum Ascomycota, and less genera Leptosphaeria, Colletotrichum, and Comoclathris in the EI group. As metabolic biomarkers, the levels of swainsonine and apigenin-7-O-glucoside-4-O-rutinoside were significantly increased in the EI group. Through in vitro validation experiments, swainsonine and apigenin-7-O-glucoside-4-O-rutinoside can dramatically suppress the growth of pathogenic fungi Leptosphaeria sclerotioides and Colletotrichum americae-borealis by increasing the level of oxidative stress. This work suggested that O. ochrocephala containing A. oxytropis could increase the resistance to fungal diseases by markedly enhancing the content of metabolites inhibiting pathogenic fungi.

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.

Allelopathy and allelobiosis: efficient and economical alternatives in agroecosystems

Chemical interactions in plants often involve plant allelopathy and allelobiosis. Allelopathy is an ecological phenomenon leading to interference among organisms, while allelobiosis is the transmission of information among organisms. Crop failures and low yields caused by inappropriate management can be related to both allelopathy and allelobiosis. Therefore, research on these two phenomena and the role of chemical substances in both processes will help us to understand and upgrade agroecosystems. In this review, substances involved in allelopathy and allelobiosis in plants are summarized. The influence of environmental factors on the generation and spread of these substances is discussed, and relationships between allelopathy and allelobiosis in interspecific, intraspecific, plant-micro-organism, plant-insect, and mechanisms, are summarized. Furthermore, recent results on allelopathy and allelobiosis in agroecosystem are summarized and will provide a reference for the future application of allelopathy and allelobiosis in agroecosystem.

Rhizoglomus variabile and Nanoglomus plukenetiae, Native to Peru, Promote Coffee Growth in Western Amazonia

Coffee (Coffea arabica) is among the world's most economically important crops. Coffee was shown to be highly dependent on arbuscular mycorrhizal fungi (AMF) in traditionally managed coffee plantations in the tropics. The objective of this study was to assess AMF species richness in coffee plantations of four provinces in Perú, to isolate AMF isolates native to these provinces, and to test the effects of selected indigenous AMF strains on coffee growth. AMF species were identified by morphological tools on the genus level, and if possible further to the species level. Two native species, Rhizoglomus variabile and Nanoglomus plukenetiae, recently described from the Peruvian mountain ranges, were successfully cultured in the greenhouse on host plants. In two independent experiments, both species were assessed for their ability to colonize coffee seedlings and improve coffee growth over 135 days. A total of 35 AMF morphospecies were identified from 12 plantations. The two inoculated species effectively colonized coffee roots, which resulted in 3.0-8.6 times higher shoot, root and total biomass, when compared to the non-mycorrhizal controls. R. variabile was superior to N. plukenetiae in all measured parameters, increasing shoot, root, and total biomass dry weight by 4.7, 8.6 and 5.5 times, respectively. The dual inoculation of both species, however, did not further improve plant growth, when compared to single-species inoculations. The colonization of coffee by either R. variabile or N. plukenetiae strongly enhances coffee plant growth. R. variabile, in particular, offers enormous potential for improving coffee establishment and productivity. Assessment of further AMF species, including species from other AMF families should be considered for optimization of coffee growth promotion, both alone and in combination with R. variabile.

Plant growth and stress-regulating metabolite response to biochar utilization boost crop traits and soil health

Introduction

The utilization of biochar (BC) as a soil amendment in agriculture has gained significant traction among many farmers and researchers, primarily due to its eco-friendly role in boosting crop output. However, the performance of specific metabolites (e.g., zeatin, melatonin, sucrose, and phenyllactic acid) in the various tissues of sugarcane plant (leaf, stem, and root) and rhizosphere soil-deemed plant growth and stress regulators in a long-term BC-amended field remains poorly understood. Additionally, literature on the shift in soil attributes and crop growth triggered by the strong response of these bioactive compounds to longterm BC utilization remains undocumented.

Methods

Metabolome integrated with highthroughput sequencing analyses were conducted to identify and quantify the performance of plant growth and stress-regulating metabolites in a long-term BC-amended field. Additionally, we investigated how the response of these compounds to BC-treated soil influences crop traits and soil biochemical properties.

Results

We also identified and quantified the performance of pathogenic bacteria and unraveled the association between these compounds and potential plant growth-promoting bacteria. The BC-supplemented soil significantly boosted the crop traits, including brix, sucrose content, and chlorophyll, as well as soil nutrients, such as soil total nitrogen (TN), ammonium (NH4 +-N), and nitrate (NO3 --N). We also noticed that metabolite-deemed plant growth and stress regulators, including melatonin and phenyllactic acid, were enriched considerably in the stem and root tissues of the BC-amended soil. Zeatin in the leaf, stem, and root tissues exhibited the same trend, followed by sucrose in the leaf tissue of the BC-treated soil, implying that the strong response of these compounds to BC utilization contributed to the promotion of crop traits and soil quality. Pathogenic bacteria belonging to Proteobacteria and Acidobacteria were suppressed under the BC-supplemented soil, especially in the root tissue and rhizosphere soil, whereas plant growth-regulating bacteria, mainly Bradyrhizobium, responded strongly and positively to several metabolites.

Discussion

Our finding provides valuable information for agronomists, farmers, and environmentalists to make informed decisions about crop production, land use, and soil management practices. Proper soil assessment and understanding of the interaction between the attributes of soil, BC, and metabolites are essential for promoting sustainable agriculture practices and land conservation.

Panax notoginseng-microbiota interactions: From plant cultivation to medicinal application

BACKGROUND

Microbiomes and their host plants are closely linked with each other; for example, the microbiome affects plant growth, fitness, nutrient uptake, stress tolerance and pathogen resistance, whereas the host plant supports the photosynthetically carbon-rich nutrition of the microbiome. The importance of the microbiome in plant‒soil ecosystems is unquestioned and has expanded to influence the medicinal application of some herbal plants via the gut microbiota.

PURPOSE

Herbal plant-microbiome interactions may provide novel knowledge to enhance the robustness of herbal plant crop performance and medicinal applications, which requires a systematic review and preceding discussion.

STUDY DESIGN AND METHODS

The interactions between Panax notoginseng and microorganisms (from soil to host) were reviewed from the literature. The terms "Panax notoginseng" and "microbiota" were used in combination with the keywords "microbiota/microbes", "bacteria/bacterium" or "fungi/fungus" or "endophyte", as well as our targeted bioactive phytochemicals, including saponins and ginsenosides.

RESULT

Our study focuses on the famous medicinal herb Panax notoginseng F. H. Chen and proposes that the microbiota is a crucial participant not only in the cultivation of this herbal plant but also in its medicinal application. We also summarize and discuss how these plant‒microbe co-associations shape the assembly of plant-related microbiomes and produce bioactive phytochemicals, as well as influence beneficial herbal traits, such as herbal plant health and pharmacology. In addition, we also highlight future directions.

CONCLUSION

The rhizosphere and endophytic microbiome of Panax notoginseng are indirectly or directly involved in plant health, biomass production, and the synthesis/biotransformation of plant secondary metabolites. Harnessing the microbiome to improve the quality of traditional Chinese medicine and improve the value of medicinal plants for human health is highly promising.

Sustained organic amendments utilization enhances ratoon crop growth and soil quality by enriching beneficial metabolites and suppressing pathogenic bacteria

Introduction

Organic soil amendments such as filter mud (FM) and biochar (BC) can potentially influence the abundance and composition of metabolites. However, our current understanding of the stimulatory effects of FM and BC's long-term impact on stress-regulating metabolites, such as abscisic acid (ABA), jasmonic acid (JA), melatonin, and phenyllactic acid (PLA), and these substrates regulatory effects on disease-causing bacteria in sugarcane ratooning field, which is susceptible to nutrients depletion, diseases, etc., remain poorly understood. Additionally, little is known about how the long-term interaction of these substrates and compounds influences sugarcane ratooning soil enzyme activities, nutrient cycling, and crop growth performance.

Methods

To answer these questions, we adopted metabolomics tools combined with high-throughput sequencing to explore the stimulatory effects of the long-term addition of FM and BC on metabolites (e.g., PLA and abscisic aldehyde) and quantify these substrates' regulatory effects on disease-causing bacteria, soil enzyme activities, nutrient cycling, and crop growth performance.

Results

The result revealed that ratoon crop weight, stem diameter, sugar content, as well as soil physico-chemical properties, including soil nitrate (NH3 +-N), organic matter (OM), total nitrogen (TN), total carbon (TC), and β-glucosidase, marked a significant increase under the BC and FM-amended soils. Whereas soil available potassium (AK), NO3 -N, cellulase activity, and phosphatase peaked under the BC-amended soil, primarily due to the enduring effects of these substrates and metabolites. Furthermore, BC and FM-amended soils enriched specific stress-regulating metabolites, including JA, melatonin, abscisic aldehyde, etc. The sustained effects of both BC and FM-amended soils suppressed disease-causing bacteria, eventually promoting ratooning soil growth conditions. A number of key bioactive compounds had distinct associations with several beneficial bacteria and soil physico-chemical properties.

Discussion

This study proves that long-term BC and FM application is one of the eco-friendly strategies to promote ratoon crop growth and soil quality through the enrichment of stress-regulating metabolites and the suppression of disease-causing bacteria.

Rhizosphere Microbiome and Phenolic Acid Exudation of the Healthy and Diseased American Ginseng Were Modulated by the Cropping History

The infection of soil-borne diseases has the potential to modify root exudation and the rhizosphere microbiome. However, the extent to which these modifications occur in various monocropping histories remains inadequately explored. This study sampled healthy and diseased American ginseng (Panax quinquefolius L.) plants under 1-4 years of monocropping and analyzed the phenolic acids composition by HPLC, microbiome structure by high-throughput sequencing technique, and the abundance of pathogens by quantitative PCR. First, the fungal pathogens of Fusarium solani and Ilyonectria destructans in the rhizosphere soil were more abundant in the diseased plants than the healthy plants. The healthy American ginseng plants exudated more phenolic acid, especially p-coumaric acid, compared to the diseased plants after 1-2 years of monocropping, while this difference gradually diminished with the increase in monocropping years. The pathogen abundance was influenced by the exudation of phenolic acids, e.g., total phenolic acids (r = -0.455), p-coumaric acid (r = -0.465), and salicylic acid (r = -0.417), and the further in vitro test confirmed that increased concentration of p-coumaric acid inhibited the mycelial growth of the isolated pathogens for root rot. The healthy plants had a higher diversity of rhizosphere bacterial and fungal microbiome than the diseased plants only after a long period of monocropping. Our study has revealed that the cropping history of American ginseng has altered the effect of pathogens infection on rhizosphere microbiota and root exudation.

A Systematic Review on the Continuous Cropping Obstacles and Control Strategies in Medicinal Plants

Continuous cropping (CC) is a common practice in agriculture, and usually causes serious economic losses due to soil degeneration, decreased crop yield and quality, and increased disease incidence, especially in medicinal plants. Continuous cropping obstacles (CCOs) are mainly due to changes in soil microbial communities, nutrient availability, and allelopathic effects. Recently, progressive studies have illustrated the molecular mechanisms of CCOs, and valid strategies to overcome them. Transcriptomic and metabolomics analyses revealed that identified DEGs (differently expressed genes) and metabolites involved in the response to CCOs are involved in various biological processes, including photosynthesis, carbon metabolism, secondary metabolite biosynthesis, and bioactive compounds. Soil improvement is an effective strategy to overcome this problem. Soil amendments can improve the microbial community by increasing the abundance of beneficial microorganisms, soil fertility, and nutrient availability. In this review, we sum up the recent status of the research on CCOs in medicinal plants, the combination of transcriptomic and metabolomics studies, and related control strategies, including uses of soil amendments, crop rotation, and intercropping. Finally, we propose future research trends for understanding CCOs, and strategies to overcome these obstacles and promote sustainable agriculture practices in medicinal plants.

Changes in Bulk and Rhizosphere Soil Microbial Diversity Communities of Native Quinoa Due to the Monocropping in the Peruvian Central Andes

Quinoa (Chenopodium quinoa) is a highly nutritious crop that is resistant to adverse conditions. Due to the considerable increase in its commercial production in Andean soils, the plant is suffering the negative effects of monocropping, which reduces its yield. We used for the first time a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the bulk and rhizosphere in soils of native C. quinoa affected by monocropping in the central Andes of Peru. The results showed that the bacterial and fungal community structure among the treatments was significantly changed by the monocropping and the types of soil (rhizosphere and bulk). Also, in soils subjected to monocropping, there was an increase in Actinobacteria and a decrease in Proteobacteria, and the reduction in the presence of Ascomycota and the increase in Basidiomycota. By alpha-diversity indices, lower values of bacteria and fungi were observed in the monoculture option compared to the soil not affected by monocropping, and sometimes significant differences were found between both. We detected differentially abundant phytopathogenic fungi and bacteria with growth-stimulating effects on plants. Also, we denoted a decrease in the abundance of the functional predictions in bacteria in the monocropped soils. This research will serve as a starting point to explore the importance and effects of microorganisms in degraded soils and their impact on the growth and quality of quinoa crops.

Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng

Introduction

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported.

Methods

We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment.

Results

The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng's survival rate and stimulated plant growth, ensuring P. notoginseng's healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins' niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria.

Conclusion

In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.

Dynamics of rhizosphere bacterial communities and soil physiochemical properties in response to consecutive ratooning of sugarcane

Ratooning in sugarcane often leads to soil problems such as degradation, acidification, and soil-borne diseases that negatively impact agriculture output and sustainability. Understanding the alteration in bacterial communities, activities, and their diversity connected to the plant and soil under consecutive ratooning still needs to be clarified. To address this gap, multidisciplinary approaches such as Illumina sequencing and measurement of soil nutrients and enzymes were used in this study to analyze soil samples in a field with three consecutive ratooning sugarcane crops. The results revealed a decline in crop yield and significant changes (P < 0.05) in soil nutrients and bacterial diversity. Ratooning resulted in an acidic environment that potentially affected soil nutrients and enzyme activity responsible for the cycling of carbon, nitrogen, and phosphorous. Non-metric dimensional scaling (NMDS) confirmed the effect of ratooning on soil attributes. Moreover, a positive correlation between soil physiochemical properties and soil enzymes was observed. Alpha diversity indices indicated greater bacterial diversity in ratooning sugarcane. Bacterial diversity varied throughout the ratooning crop, and significant (P < 0.05) changes in the relative abundance of specific phyla were observed. For example, the relative abundance of Proteobacteria was decreased, and Acidobacteria was increased. Furthermore, the relative abundance of bacterial phyla was strongly correlated with soil attributes (enzymes and nutrients). Additionally, ratooning results in the depletion or enrichment of important agriculture microbial genera such as Sphingomonas, Burkholderia, and Acidothermus (P < 0.05), respectively. In conclusion, ratooning led to soil acidification, decreased fertility, and altered microbial structure and activity. Thus, restraining soil acidity by means of liming or biofertilizers to maintain soil nutrients, enzymatic activities, and microbial structure could benefit plants and soil to help create a long-term eco-friendly sugarcane cropping system.

Effect of Trichoderma viride on rhizosphere microbial communities and biocontrol of soybean root rot

Biological seed dressing is a cost-effective means to protect plant roots from pathogens. Trichoderma is generally considered as one of the most common biological seed dressings. However, there is still a dearth of information on the effects of Trichoderma on microbial community of rhizosphere soil. High-throughput sequencing was used to analyze the effects of Trichoderma viride and a chemical fungicide on microbial community of soybean rhizosphere soil. The results showed that both T. viride and chemical fungicide could significantly reduce the disease index of soybean (15.11% for Trichoderma and 17.33% for Chemical), while no significant difference was observed between them. Both T. viride and chemical fungicide could affect the structure of rhizosphere microbial community, they increased the β-diversity of microbial community and significantly reduce the relative abundance of Saprotroph-Symbiotroph. Chemical fungicide could reduce the complexity and stability of co-occurrence network. However, T. viride is beneficial for maintaining network stability and increasing network complexity. There were 31 bacterial genera and 21 fungal genera significantly correlated with the disease index. Furthermore, several potential plant pathogenic microorganisms were also positively correlated with disease index, such as Fusarium, Aspergillus, Conocybe, Naganishia, and Monocillium. From this work, T. viride may be used as a substitute for chemical fungicide to control soybean root rot and be more friendly to soil microecology.

Comparative Analysis of Rhizosphere and Endophytic Microbial Communities Between Root Rot and Healthy Root of Psammosilene tunicoides

The wild resources of Psammosilene tunicoides have decreased sharply because of the long-term mining and excavation, which has led to the increased demand for its artificial cultivation. However, root rot represents a significant obstacle leading to a poor quality and product of P. tunicoides. Previous reports have not focused on root rot in P. tunicoides. Therefore, this study explores the rhizospheric and root endophytic microbial community structure and composition of healthy and root rot P. tunicoides to understand the mechanism underlying root rot. The properties of the rhizosphere soil were assessed using physiochemical methods, and the bacterial and fungal populations were studied through amplicon sequencing of the 16S rRNA genes and ITS regions in the root and soil. Compared to healthy samples, the pH, hydrolysis N, available P, and available K were significantly decreased in the diseased samples while the organic matter and total organic carbon were significantly increased in the diseased samples. Redundancy analysis (RDA) showed that soil environmental factors are related to changes in the root and rhizosphere soil microbial community of P. tunicoides indicating that the physiochemical properties of soil affect plant health. Alpha diversity analysis showed that the microbial communities of healthy and diseased samples were similar. Some bacterial and fungal genera were significantly increased or decreased (P < 0.05) in diseased P. tunicoides, and certain microbial factors that antagonized root rot were further explored. This study provides an abundant microbial resource for future studies and contributes to improving soil quality and P. tunicoides agricultural production.

Application of UPLC-Orbitrap-HRMS targeted metabolomics in screening of allelochemicals and model plants of ginseng

Continuous cropping of ginseng leads to serious declines in yield and quality because of self-toxicity of allelochemicals and other factors in soil. However, because of the long growth cycle and low survival rate of ginseng, rapid screening of autotoxic activity is difficult. Therefore, it is important to analyze the allelochemicals and identify a model plant with autotoxic responses similar to those of ginseng. In this study, UPLC-Orbitrap-HRMS targeted metabolomics and verification of autotoxic activity were used to analyze a problem soil from continuously cropped ginseng. Allelochemical markers were screened by OPLS-DA. Seeds and seedlings of maize, Chinese cabbage, cucumber, green beans, wheat, sunflower, and oats were selected to identify potential model plants. Model plants with autotoxic responses similar to those of ginseng were evaluated by comparing morphological, physiological, and biochemical characteristics. The n-butanol extract of the continuously cropped problem soil had the most significant autotoxic activity. Twenty-three ginsenosides and the contributions to autotoxic effects were screened and evaluated. Of potential model plants, seeds and seedlings of cucumber showed similar growth inhibition to that of ginseng under the action of allelochemicals. Thus, metabolomics can be used to screen allelochemicals in soil and predict the autotoxic effects, and the cucumber plant model can be used to rapidly screen allelopathic activity of ginseng. The study will provide reference for methodology in allelopathy research on ginseng.

TMT-Based Proteomic Analysis of Continuous Cropping Response in Codonopsis tangshen Oliv

The growth and development of Codonopsis tangshen, an important herb used in Chinese traditional medicine, have been seriously affected by continuous cropping obstacles. Therefore, understanding the molecular responses of C. tangshen to continuous cropping is imperative to improve its resistance to continuous cropping obstacles. Here, physiological and biochemical results showed that the levels of chlorophyll and malonaldehyde (MDA) were higher in the continuous cropping (LZ) group compared with those of the non-continuous cropping (FLZ) group, while superoxide dismutase (SOD) content was lower in the LZ group than in the FLZ group. Tandem mass tag (TMT)-based proteomic analysis was performed to investigate the response mechanism to continuous cropping obstacles in C. tangshen. A total of 70 differentially expressed proteins (DEPs) were significantly involved in relevant pathways, including photosynthesis, oxidative phosphorylation, ribosome activity, and secondary metabolites. The results suggest that these DEPs in C. tangshen might play a critical role in response to continuous cropping. These findings could provide scientific basis for improving C. tangshen’s resistance to continuous cropping obstacles.

Changing Rhizosphere Microbial Community and Metabolites with Developmental Stages of Coleus barbatus

Coleus barbatus is a medicinal herb belonging to Lamiaceae. It is the only living organism known to produce forskolin, which is a labdane diterpene and is reported to activate adenylate cyclase. Microbes associated with plants play an important role in maintaining plant health. Recently, the targeted application of beneficial plant-associated microbes and their combinations in abiotic and biotic stress tolerance has gained momentum. In this work, we carried out the rhizosphere metagenome sequencing of C. barbatus at different developmental stages to understand how rhizosphere microflora are affected by and affect the metabolite content in plants. We found that the Kaistobacter genus was abundantly present in the rhizosphere of C. barbatus and its accumulation pattern appears to correlate with the quantities of forskolin in the roots at different developmental stages. Members of the Phoma genus, known for several pathogenic species, were in lower numbers in the C. barbatus rhizosphere in comparison with C. blumei. To our knowledge, this is the first metagenomic study of the rhizospheric microbiome of C. barbatus, which may help to explore and exploit the culturable and non-culturable microbial diversity present in the rhizosphere.

Integrated Analysis of microRNA and RNA-Seq Reveals Phenolic Acid Secretion Metabolism in Continuous Cropping of Polygonatum odoratum

Polygonatum odoratum (Mill.) Druce is an essential Chinese herb, but continuous cropping (CC) often results in a serious root rot disease, reducing the yield and quality. Phenolic acids, released through plant root exudation, are typical autotoxic substances that easily cause root rot in CC. To better understand the phenolic acid biosynthesis of P. odoratum roots in response to CC, this study performed a combined microRNA (miRNA)-seq and RNA-seq analysis. The phenolic acid contents of the first cropping (FC) soil and CC soil were determined by HPLC analysis. The results showed that CC soils contained significantly higher levels of p-coumaric acid, phenylacetate, and caffeic acid than FC soil, except for cinnamic acid and sinapic acid. Transcriptome identification and miRNA sequencing revealed 15,788 differentially expressed genes (DEGs) and 142 differentially expressed miRNAs (DEMs) in roots from FC and CC plants. Among them, 28 DEGs and eight DEMs were involved in phenolic acid biosynthesis. Meanwhile, comparative transcriptome and microRNA-seq analysis demonstrated that eight miRNAs corresponding to five target DEGs related to phenolic acid synthesis were screened. Among them, ath-miR172a, ath-miR172c, novel_130, sbi-miR172f, and tcc-miR172d contributed to phenylalanine synthesis. Osa-miR528-5p and mtr-miR2673a were key miRNAs that regulate syringyl lignin biosynthesis. Nta-miR156f was closely related to the shikimate pathway. These results indicated that the key DEGs and DEMs involved in phenolic acid anabolism might play vital roles in phenolic acid secretion from roots of P. odoratum under the CC system. As a result of the study, we may have a better understanding of phenolic acid biosynthesis during CC of roots of P. odoratum.

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.

Green remediation of cadmium-contaminated soil by cellulose nanocrystals

Cellulose nanocrystals (CNC) were used as a novel, green eluent to remediate Cd-contaminated soil in this study. The influence of washing conditions on the removal of Cd, including CNC concentration, pH value, liquid/solid (L/S) ratio, contact time and temperature were investigated. The effect of CNC remediation of Cd-contaminated soil on soil health and the possible remediation mechanism were also explored. The results showed that CNC concentration, pH value and contact time had a significant effect on the removal efficiency of Cd. CNC rapidly removed heavy metals in soil within 30 min. When the pH value of the eluent was 9.0, the removal efficiency of Cd could reach 86.3 %. The eluent mainly removed exchangeable and reducible fractions of Cd, which could effectively reduce the bioavailability of heavy metals. CNC washing had no negative effects on seed growth, species abundance and Shannon index. C-O, -COO^- groups on CNC played an important role in the reaction between CNC and soil Cd, and other oxygen-containing functional groups on CNC could also assist in adsorption, ion exchange and chemical complexation processes. Therefore, cellulose nanocrystals had the potential to remediate heavy metal-contaminated soils in a green and efficient manner.

Passion fruit plants alter the soil microbial community with continuous cropping and improve plant disease resistance by recruiting beneficial microorganisms

Passion fruit (Passiflora edulis) is widely grown in tropical and subtropical regions, showing high economic and ornamental value. Microorganisms are indicators for the stability and health of the soil ecosystem, which can affect the yield and quality of passion fruit under continuous cropping. High-throughput sequencing and interactive analysis were used to analyse the variation of microbial communities in the noncultivated soil (NCS), cultivated soil (CS), and the rhizosphere soil of purple passion fruit (Passiflora edulis f. edulis ×Passiflora edulis f. flavicarpa, RP) and yellow passion fruit (Passiflora edulis f. flavicarpa, RY). An average of 98,001 high-quality fungal internal transcribed spacer (ITS) sequences, mainly from Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota and Glomeromycota, as well as an average of 71,299 high-quality bacterial 16S rRNA sequences, mainly from Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi, were obtained per sample. It was found that the continuous cropping of passion fruit increased the richness but reduced the diversity of soil fungi, while it dramatically increased the richness and diversity of soil bacteria. In addition, during the continuous cropping, grafting different scions in the same rootstock contributed to the aggregation of differential rhizosphere microbial communities. Among fungal genera, Trichoderma showed higher abundance in RY than in RP and CS, while the opposite was observed in the pathogen Fusarium. Moreover, the co-occurrence network and potential function analyses also showed that the appearance of Trichoderma was related to Fusarium and its contribution to plant metabolism was significantly greater in RY than in RP and CS. In conclusion, the rhizosphere of yellow passion fruit may be beneficial for the enrichment of disease-resistant microbes, such as Trichoderma, which may be an important factor inducing stronger resistance to stem rot. It will help to form a potential strategy for overcoming the pathogen-mediated obstacles in passion fruit and improve its yield and quality.

Land use differentially affects fungal communities and network complexity in northeast China

Background

The soil fungal community is one of the most important drivers of the soil nutrient cycling that sustains plant growth. However, little research has been done on the effects of different land uses on soil fungal communities in northeast China.

Methods

In this study, we conducted a field experiment to investigate the effects of continuous cropping of grass, maize, and alfalfa on their respective fungal communities and co-occurrence networks.

Results

We showed that the physicochemical properties of the soil, such as nitrate (NO3-N), available phosphorus, and soil pH, were the most important driving factors affecting the structure of the soil fungal community in different cropping systems. In addition, compared to the cultivation of grass and maize, the continuous cropping of alfalfa increased the abundance of several beneficial as well as pathogenic species, such as Mortierella and Gaiellales. In addition, the networks differed among plant species and according to the number of years of continuous cultivation.

Conclusion

This suggests that the continuous cropping of alfalfa results in greater cooperation among fungi, which may be beneficial to the soil as well as to the development of the alfalfa.

Effect of Different Types of Continuous Cropping on Microbial Communities and Physicochemical Properties of Black Soils

The barriers caused by continuous tillage have had a negative impact on the crop and soil environment. Black soils are economically important as a valuable natural resource in Northeast China, but limited soil resources have led to continuous planting of major food crops and medicinal plants. At present, the extent to which two different types of plants—grains and medicinal plants that are successively grown on the same soil—have an impact on soil quality and microbiology is not known. In this study, we investigated the effects of different types of long-term continuous cropping on soil and soil microbial communities by determining the physicochemical properties, the soil community composition and function of grain crops and medicinal-plant soils with more than five years of continuous cropping, as well as fallow soils. The results showed that long-term continuous cropping reduced the pH of different types of soils, but there was no significant difference in the content of AK. The relative abundance of beneficial dominant phyla, such as Actinomycetes, Acidobacteria, and Green Campylobacter decreased and the relative abundance of pathogenic genera such as Alternaria and Didymellaceae, increased after the long-term continuous cropping of DM (grain crops) and DG (medicinal plants). Specifically, continuous cropping increased the relative abundance of fungi with pathogenic potential, such as Sordariomycetes, Dothideomycetes, Saccharomycetes, and Mucoromycetes in grain soils and Agaricostilbomycetes in herb soils. Among the soil physicochemical properties, NH4+-N and pH were the most important factors contributing to changes in the composition of bacterial and fungal communities, respectively. Continuous cropping of different types of plants altered the diversity of the microbial communities, with the most significant effect from the continuous cropping of food crops. Our findings provide a scientific and theoretical basis for future agricultural research to improve soil microbial activity, mitigate continuous-cropping barriers, and increase productivity.

Maize-soybean relay strip intercropping reshapes the rhizosphere bacterial community and recruits beneficial bacteria to suppress Fusarium root rot of soybean

Rhizosphere microbes play a vital role in plant health and defense against soil-borne diseases. Previous studies showed that maize-soybean relay strip intercropping altered the diversity and composition of pathogenic Fusarium species and biocontrol fungal communities in the soybean rhizosphere, and significantly suppressed soybean root rot. However, whether the rhizosphere bacterial community participates in the regulation of this intercropping on soybean root rot is not clear. In this study, the rhizosphere soil of soybean healthy plants was collected in the continuous cropping of maize-soybean relay strip intercropping and soybean monoculture in the fields, and the integrated methods of microbial profiling, dual culture assays in vitro, and pot experiments were employed to systematically investigate the diversity, composition, and function of rhizosphere bacteria related to soybean root rot in two cropping patterns. We found that intercropping reshaped the rhizosphere bacterial community and increased microbial community diversity, and meanwhile, it also recruited much richer and more diverse species of Pseudomonas sp., Bacillus sp., Streptomyces sp., and Microbacterium sp. in soybean rhizosphere when compared with monoculture. From the intercropping, nine species of rhizosphere bacteria displayed good antagonism against the pathogen Fusarium oxysporum B3S1 of soybean root rot, and among them, IRHB3 (Pseudomonas chlororaphis), IRHB6 (Streptomyces), and IRHB9 (Bacillus) were the dominant bacteria and extraordinarily rich. In contrast, MRHB108 (Streptomyces virginiae) and MRHB205 (Bacillus subtilis) were the only antagonistic bacteria from monoculture, which were relatively poor in abundance. Interestingly, introducing IRHB3 into the cultured substrates not only significantly promoted the growth and development of soybean roots but also improved the survival rate of seedlings that suffered from F. oxysporum infection. Thus, this study proves that maize-soybean relay strip intercropping could help the host resist soil-borne Fusarium root rot by reshaping the rhizosphere bacterial community and driving more beneficial microorganisms to accumulate in the soybean rhizosphere.

The Structure and Function of Microbial Community in Rhizospheric Soil of American Ginseng (Panax quinquefolius L.) Changed with Planting Years

The changes of microbial communities of rhizospheric soil in different ages are speculated to cause soil-borne diseases and replanting problem in American ginseng (Panax quinquefolius L.) cultivation. This study analyzed the physicochemical properties and microbial communities of rhizospheric soil during the planting of American ginseng in the Wendeng area of Weihai, China. The water content and organic matter content of American ginseng rhizospheric soil decreased year by year. A decline in the diversity of bacteria and fungi was observed in the rhizospheric soils planting American ginseng compared with the traditional crop wheat in the control group. During the later planting stage, the abundances of Proteobacteria, Actinobacteria, and Basidiomycota were lower, whereas that of Acidobacteria, Firmicutes, and Mucoromycota were higher. Through the correlation analysis between environmental factors and microbial community, it was found that the content of soil phosphorus was significantly positively correlated with the root rot pathogen Fusarium. The results of functional prediction showed that the decrease of secondary metabolite synthesis of rhizospheric soil bacteria and the increase of plant pathogenic fungi may be the important reasons for the increase of diseases in the later stage of American ginseng planting. This study revealed the evolution of rhizosphere microbial community and function in the process of American ginseng planting, which is valuable for planting management.

Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil

Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.

The Rhizosphere Microbiome of Ginseng

The rhizosphere of ginseng contains a wide range of microorganisms that can have beneficial or harmful effects on the plant. Root exudates of ginseng, particularly ginsenosides and phenolic acids, appear to select for particular microbial populations through their stimulatory and inhibitory activities, which may account for the similarities between the rhizosphere microbiomes of different cultivated species of Panax. Many practices of cultivation attempt to mimic the natural conditions of ginseng as an understory plant in hilly forested areas. However, these practices are often disruptive to soil, and thus the soil microbiome differs between wild and cultivated ginseng. Changes in the microbiome during cultivation can be harmful as they have been associated with negative changes of the soil physiochemistry as well as the promotion of plant diseases. However, isolation of a number of beneficial microbes from the ginseng rhizosphere indicates that many have the potential to improve ginseng production. The application of high-throughput sequencing to study the rhizosphere microbiome of ginseng grown under a variety of conditions continues to greatly expand our knowledge of the diversity and abundance of those organisms as well as their impacts of cultivation. While there is much more to be learnt, many aspects of the ginseng rhizosphere microbiome have already been revealed.

Effects of Bacillus subtilis T6-1 on the Rhizosphere Microbial Community Structure of Continuous Cropping Poplar

Simple Summary

Long-term continuous cropping of poplar has led to a decline in soil fertility, the timber yield of poplar has decreased, and diseases and pests have increased. We aimed to develop a biological agent that regulates the structure of the microbial community of the poplar rhizosphere and alleviates the effects of continuous poplar cropping. The research showed that T6-1 could improve the structure of the microbial community of the poplar rhizosphere and promote the growth of poplars. Thus, it could be used as a biological control agent against continuous cropping obstacles for poplar trees.

Abstract

The continuous cropping obstacles in poplar cultivation cause declines in wood yield and serious soil-borne diseases, mainly because of structural alterations in the microbial community and the aggregation of pathogenic fungi. Bacillus subtilis T6-1, isolated from poplar rhizospheric soil, has strong antagonistic effects on poplar pathogens. We aimed to investigate the effects of B. subtilis T6-1 on the structure of the microbial community in the poplar rhizosphere. Poplar seedlings were replanted in three successive generations of soil. The diameter at breast height, plant height, and the number of culturable bacteria of the poplars inoculated with T6-1 exceeded those in the non-inoculated control group. qPCR analysis revealed that the total abundance of T6-1 bacteria in the treated poplars was remarkably higher in contrast to that in the control group. Illumina MiSeq sequencing was employed to track the alterations in diversity and structure of the total microbial community in the poplar rhizosphere inoculated with B. subtilis T6-1. Fungal diversity and abundance in the T6-1 rhizosphere were remarkably lower in contrast with those in the control rhizosphere. The proportion of Bacillus sp. in the total bacterial community in the T6-1 and control groups was 3.04% and 2.38%, respectively, while those of the Rhizoctonia sp. was 2.02% and 5.82%, respectively. In conclusion, B. subtilis T6-1 has the potential to serve as a microbial agent, enhancing the structure of the rhizosphere microbial community as well as promoting tree growth in poplar cultivation.

Integrated Analysis of Physiological, mRNA Sequencing, and miRNA Sequencing Data Reveals a Specific Mechanism for the Response to Continuous Cropping Obstacles in Pogostemon cablin Roots

Pogostemon cablin (patchouli) is a commercially important medicinal and industrial crop grown worldwide for its medicinal and aromatic properties. Patchoulol and pogostone, derived from the essential oil of patchouli, are considered valuable components in the cosmetic and pharmaceutical industries. Due to its high application value in the clinic and industry, the demand for patchouli is constantly growing. Unfortunately, patchouli cultivation has suffered due to severe continuous cropping obstacles, resulting in a significant decline in yield and quality. Moreover, the physiological and transcriptional changes in patchouli in response to continuous cropping obstacles remain unclear. This has greatly restricted the development of the patchouli industry. To explore the mechanism underlying the rapid response of patchouli roots to continuous cropping stress, integrated analysis of the transcriptome and miRNA profiles of patchouli roots under continuous and noncontinuous cropping conditions in different growth periods was conducted using RNA sequencing (RNA-seq) and miRNA-seq and complemented with physiological data. The physiological and biochemical results showed that continuous cropping significantly inhibited root growth, decreased root activity, and increased the activity of antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) and the levels of osmoregulators (malondialdehyde, soluble protein, soluble sugar, and proline). Subsequently, we found 4,238, 3,494, and 7,290 upregulated and 4,176, 3,202, and 8,599 downregulated differentially expressed genes (DEGs) in the three growth periods of continuously cropped patchouli, many of which were associated with primary carbon and nitrogen metabolism, defense responses, secondary metabolite biosynthesis, and transcription factors. Based on miRNA-seq, 927 known miRNAs and 130 novel miRNAs were identified, among which 67 differentially expressed miRNAs (DEMIs) belonging to 24 miRNA families were induced or repressed by continuous cropping. By combining transcriptome and miRNA profiling, we obtained 47 miRNA-target gene pairs, consisting of 18 DEMIs and 43 DEGs, that likely play important roles in the continuous cropping response of patchouli. The information provided in this study will contribute to clarifying the intricate mechanism underlying the patchouli response to continuous cropping obstacles. In addition, the candidate miRNAs and genes can provide a new strategy for breeding continuous cropping-tolerant patchouli.

Difference of Bacterial Community Structure in the Meadow, Maize, and Continuous Cropped Alfalfa in Northeast China

Maize and alfalfa (Medicago sativa L.) have been used extensively in the animal husbandry to compensate for the lack of livestock and fodder yields in the chilly northeast of China. Little is known, however, about the impact on soil characteristics of consecutive plantings in various crops and alfalfa. In this research, the soil characteristics, bacterial community diversity, and structure of the meadow, maize, and alfalfa continuous cropping fields (i.e., 6, 10, 14, 20, and 30 years) were measured. The results showed that maize cropping and continuous cropping of alfalfa increased the soil bacterial alpha diversity compared with meadow cropping, and alpha diversity of alfalfa increased with the continuous planting years. Soil pH, total phosphorus (TP), available P, total potassium (TK), and nitrate nitrogen (NO₃^–) content were soil variables significantly impacting the structure of soil bacterial communities in different plant types and different alfalfa continuous cropping systems. In addition, the relative abundance of some beneficial microbial species, such as Arthrobacter and Gaiellales, in the cropping maize and continuous cropping of alfalfa was much higher than that in the meadow field. Moreover, the networks differ among different plant types, and also differ among different continuous cropping years of alfalfa, and topologies of the networks suggested that continuous planting of alfalfa promotes cooperation between bacteria, which facilitates the long growth of alfalfa and is beneficial to the soil.

Interactions Between Phenolic Acids and Microorganisms in Rhizospheric Soil From Continuous Cropping of Panax notoginseng

Large-scale intensive cultivation has made continuous cropping soil sickness more serious for Panax notoginseng in Yunnan. Autotoxic substances can promote the occurrence of continuous cropping soil sickness. Phenolic acids exert a strong autotoxic effect on P. notoginseng. Based on UPLC-MS/MS, the levels of six phenolic acids with the strongest autotoxicity of P. notoginseng rhizospheric soil were tested. Based on Illumina MiSeq high-throughput sequencing technology, the variation in the microbial diversity in the rhizospheric soil was used as an index to explore the interactions between phenolic acids and the soil microorganisms of the P. notoginseng rhizosphere. (1) Continuous P. notoginseng cropping significantly changed the microbial community structure. Continuous cropping increased bacterial Chao1 index and Shannon index and decreased fungal Shannon index. After P. notoginseng disease, bacterial Shannon index reduced and fungal Chao1 index decreased. (2) Phenolic acid significantly changed the bacterial community structure. VA significantly reduced the bacterial Shannon index. Exogenous p-HA, FA, SA, and VA significantly increased the fungal Chao1 index and p-HA showed the most significant effect. Para-HA affected bacterial specificity, and VA affected fungal specificity. (3) VA was positively correlated with most fungi and bacteria. Para-HA was positively correlated with Lelliottia and Flavobacterium. Para-HA was also positively correlated with plant pathogens (Fusarium and Ilyonectria). Para-HA and VA were able to promote the growth of primary pathogenic bacteria. Thus, p-HA and VA are the main phenolic acid-autotoxin substances in P. notoginseng under continuous cropping. (4) A correlation analysis of soil environmental factors associated with fungal and bacterial communities showed that AK, TN, OM, and HN were most strongly correlated with soil microorganisms. (5) The microorganisms in the rhizosphere of 3-year-old soil planted with P. notoginseng exhibited obvious effects on the degradation of the four phenolic acids. The effect of soil microorganisms on phenolic acids was first-order kinetic degradation with a high degradation rate and a half-life of less than 4.5 h. The results showed that phenolic acids could promote the growth of pathogenic bacteria. And the interaction between rhizospheric soil microorganisms and phenolic acids was the main cause of the disturbance of P. notoginseng rhizosphere microflora.

Morel Production Associated with Soil Nitrogen-Fixing and Nitrifying Microorganisms

True morels (Morchella, Pezizales) cultivated in soil are subject to complex influences from soil microbial communities. To explore the characteristics of soil microbial communities on morel cultivation, and evaluate whether these microbes are related to morel production, we collected 23 soil samples from four counties in Sichuan and Yunnan Provinces, China. Based on ITS and 16S rDNA amplicon sequencing, the alpha diversity analysis indicated that the biodiversity of morel cultivation soil showed a downward trend compared with the bare soil. The results also showed that there were no significant differences in soil microbial communities between OC (bare soil) and OO (after one-year suspension of sowing). This means that, after about one year of stopping sowing, the component and structure of soil that once cultivated morel would be restored. In co-occurrence networks, some noteworthy bacterial microbes involved in nitrogen fixation and nitrification have been identified in soils with high morel yields, such as Arthrobacter, Bradyhizobium, Devosia, Pseudarthrobacter, Pseudolabrys, and Nitrospira. In contrast, in soils with low or no morel yield, some pathogenic fungi accounted for a high proportion, including Gibberella, Microidium, Penicillium, Sarocladium, Streptomyces, and Trichoderma. This study provided valuable information for the isolation and culturing of some beneficial microbes for morel cultivation in further study and, potentially, to harness the power of the microbiome to improve morel production and health.

Evolutions and Managements of Soil Microbial Community Structure Drove by Continuous Cropping

Continuous cropping obstacles have increasingly become an important phenomenon affecting crop yield and quality. Its harm includes the deterioration of soil basic physical and chemical properties, changes of soil microbial community structure, accumulation of autotoxins, weakness of plant growth, and aggravation of diseases and pests. In this review, the evolutionary trend of soil microbial structure driven by continuous cropping was generalized, while drivers of these changes summed up as destruction of soil microbial living environment and competition within the community. We introduced a microorganism proliferation and working model with three basics and a vector, and four corresponding effective measures to reshape the structure were comprehensively expounded. According to the model, we also put forward three optimization strategies of the existing measures. In which, synthetic microbiology provides a new solution for improving soil community structure. Meanwhile, to ensure the survival and reproduction of soil microorganisms, it is necessary to consider their living space and carbon sources in soil fully. This review provided a comprehensive perspective for understanding the evolutionary trend of the soil microbial community under continuous cropping conditions and a summary of reshaping measures and their optimization direction.

Sugarcane–Peanut Intercropping System Enhances Bacteria Abundance, Diversity, and Sugarcane Parameters in Rhizospheric and Bulk Soils

Sugarcane–legume intercropping systems can effectively control pests and diseases as well as improve the fertility and health of farmland soil. However, little is known about the response of bacterial abundance, diversity, and community composition in the rhizosphere and non-rhizosphere soils under the sugarcane–peanut farming system. A field experiment was conducted with two treatments: sugarcane monoculture and sugarcane–peanut intercropping to examine the response of sugarcane parameters and edaphic factors. We also deciphered bacterial abundance, diversity, and community composition in the root endosphere, rhizosphere, and bulk soil by leveraging Illumina sequencing to conduct the molecular characterization of the 16S rRNA gene and nitrogenase (nifH) gene. We observed that sugarcane–peanut intercropping exhibited the advantages of tremendously increasing cane stalk height, stalk weight, and millable stalk number/20 m, and edaphic factors, namely, pH (1.13 and 1.93), and available phosphorus exhibited a fourfold and sixfold increase (4.66 and 6.56), particularly in the rhizosphere and bulk soils, respectively. Our result also showed that the sugarcane–peanut intercropping system significantly increased the bacterial richness of the 16S rRNA gene sequencing data by 13.80 and 9.28% in the bulk soil and rhizosphere soil relative to those in the monocropping sugarcane system, respectively. At the same time, sugarcane intercropping with peanuts significantly increased the Shannon diversity of nitrogen-fixing bacteria in the sugarcane rhizosphere soil. Moreover, most edaphic factors exhibited a positive regularity effect on bacterial community composition under the intercropping system. A linear discriminant analysis with effect size analysis of the 16S rRNA sequencing data revealed that bacteria in the root endosphere of the intercropped cane proliferated profoundly, primarily occupied by Devosia, Rhizobiales, Myxococcales, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Bradyrhizobium, and Sphingomonas. In conclusion, our findings demonstrated that sugarcane–peanut intercropping can enhance edaphic factors, sugarcane parameters, and bacterial abundance and diversity without causing adverse impacts on crop production and soil.

The Endosphere Microbiome of Ginseng

The endosphere of ginseng contains a variety of fungal, bacterial, archaeal and viral endophytes. Bacterial endophytes are primarily members of the Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes, and fungal endophytes are primarily members of the Ascomycota, Zygomycota and Basidiomycota. Although archaea and viruses have been detected in symptomless ginseng plants, little is known about them. Many but not all studies have shown roots having the highest abundance and diversity of bacterial and fungal endophytes, with some endophytes showing specificity to above or belowground tissues. Abundance often increases with root age, although diversity can decrease, possibly related to increases in potential latent fungal pathogen infections. The descriptions of many endophytes that can metabolize ginsenosides indicate an adaptation of the microbes to the unique combination of secondary metabolites found in ginseng tissues. Most research on the benefits provided by bacterial and fungal endophytes has concentrated on improved plant nutrition, growth promotion and increased disease resistance, but little on their ability to increase abiotic stress resistance. Some other areas where more research is needed is field trials with endophyte-treated plants grown in various environments, genomic/metagenomic analysis of endophytes, and the effects of endophytes on induced disease resistance and abiotic stress tolerance.

Different Fertilizers Applied Alter Fungal Community Structure in Rhizospheric Soil of Cassava (Manihot esculenta Crantz) and Increase Crop Yield

Soil microbes play an important role in the ecosystem and have a relationship with plant growth, development, and production. There are only a few reports on the effects of planting patterns of cassava on the microbial community structure in the rhizospheric soil. Here, we investigated the effects of different fertilization on the microbial community structure in the cassava rhizospheric soil. SC205 cultivar was used in this study as the experimental material. Compound fertilizer (CF) and reduced fertilizer (RF) were applied to the soil prior to planting. Soil samples were collected before harvest, and fungi were analyzed using IonS5^TMXL sequencing platform. Results showed that CF and RF treatments significantly increased cassava yield. Amplicon sequencing result indicated that the fungi richness in rhizospheric soil of cassava was increased after CF was applied, and the diversity was decreased. However, the fungal diversity and richness were decreased in rhizospheric soil after RF was applied. The most dominant fungal phylum was Ascomycota, which increased after fertilization. In addition, the abundance of beneficial fungi such as Chaetomium increased after fertilization, while that of pathogenic fungi such as Fusarium solani was decreased. The composition of the fungal community in rhizospheric soil with CF and RF applied was similar, but the richness and diversity of fungi were different. Canonical correspondence analysis (CCA) indicates there was a positive correlation between soil nutrition and fungal community structure. Overall, our results indicate that fertilization alters the fungal community structure of cassava rhizospheric soil, such that the abundance of potentially beneficial fungi increased, while that of potentially pathogenic fungi decreased, thereby significantly promoting plant growth and yield of cassava. Thus, during actual production, attention should be paid to maintain the stability of cassava rhizospheric soil micro-ecology.

Continuous Sugarcane Planting Negatively Impacts Soil Microbial Community Structure, Soil Fertility, and Sugarcane Agronomic Parameters

Continuous planting has a negative impact on sugarcane plant growth and reduces global sugarcane crop production, including in China. The response of soil bacteria, fungal, and arbuscular mycorrhizae (AM) fungal communities to continuous sugarcane cultivation has not been thoroughly documented. Using MiSeq sequencing technology, we analyzed soil samples from sugarcane fields with 1, 10, and 30 years of continuous cropping to see how monoculture time affected sugarcane yield, its rhizosphere soil characteristics and microbiota. The results showed that continuous sugarcane planting reduced sugarcane quality and yield. Continuous sugarcane planting for 30 years resulted in soil acidification, as well as C/N, alkali hydrolyzable nitrogen, organic matter, and total sulfur content significantly lower than in newly planted fields. Continuous sugarcane planting affected soil bacterial, fungal, and AM fungal communities, according to PCoA and ANOSIM analysis. Redundancy analysis (RDA) results showed that bacterial, fungal, and AM fungal community composition were strongly associated with soil properties and attributes, e.g., soil AN, OM, and TS were critical environmental factors in transforming the bacterial community. The LEfSe analysis revealed bacterial families (e.g., Gaiellaceae, Pseudomonadaceae, Micromonosporaceae, Nitrosomonadaceae, and Methyloligellaceae) were more prevalent in the newly planted field than in continuously cultivated fields (10 and 30 years), whereas Sphingomonadaceae, Coleofasciculaceae, and Oxyphotobacteria were depleted. Concerning fungal families, the newly planted field was more dominated than the continuously planted field (30 years) with Mrakiaceae and Ceratocystidaceae, whereas Piskurozymaceae, Trimorphomycetaceae, Lachnocladiaceae, and Stigmatodisc were significantly enriched in the continuously planted fields (10 and 30 years). Regarding AMF families, Diversisporaceae was considerably depleted in continuously planted fields (10 and 30 years) compared to the newly planted field. These changes in microbial composition may ultimately lead to a decrease in sugarcane yield and quality in the monoculture system, which provides a theoretical basis for the obstruction mechanism of the continuous sugarcane planting system. However, continuous planting obstacles remain uncertain and further need to be coupled with root exudates, soil metabolomics, proteomics, nematodes, and other exploratory methods.

Soil potentials to resist continuous cropping obstacle: Three field cases

Continuous cropping has become the most common system in intensive, modern agricultural production; however, obstacles often appear in continuous cropping patterns after a few years of use. There have been several studies about the impacts of continuous cropping on soil microbial, but few about differences between soil experiencing continuous cropping obstacles and those where such obstacles had been resisted. Here, after ten or twenty years of continuous tobacco cropping, we collected soil samples investigating discrepancies in soil property and bacterial community between soils experiencing continuous cropping obstacles and soils where the obstacles were resisted providing insight into preventing and controlling continuous cropping obstacles. Results showed that soil organic matter (SOM), available phosphorus (AP), total nitrogen (TN), nitrate-N (NO₃^--N), and bacterial diversity of samples where continuous cropping obstacles had been resisted were significantly higher than those where continuous cropping obstacles were present. Besides, SOM, AP, TN, and Ammonium-N (NH₄⁺-N) considerably affected the bacterial community. Among all variables, NH₄⁺-N explained the largest proportion of bacterial community variation. Molecular ecological networks were used to putatively identify keystone taxa, including Acidobacteria Gp1, Acidobacteria Gp2, Acidobacteria Gp16, and WPS-1_genera_incertae_sedis. Their relative abundance significantly changed between the two conditions. Overall, our results indicate that decreases in soil nutrient content and bacterial diversity, and significant changes in some keystone taxa abundances may be important factors leading to increased soil-borne diseases and reduced tobacco production potential or quality. Thus, during agricultural production, we could regulate the stability of the soil-crop-microbial ecological system via crop rotation, intercropping, or the use of specialized bio-fertilizers and soil conditioners to mitigate continuous cropping obstacles.

Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms

Sugarcane monoculture (SM) often leads to soil problems, like soil acidification, degradation, and soil-borne diseases, which ultimately pose a negative impact on agricultural productivity and sustainability. Understanding the change in microbial communities' composition, activities, and functional microbial taxa associated with the plant and soil under SM is unclear. Using multidisciplinary approaches such as Illumina sequencing, measurements of soil properties, and enzyme activities, we analyzed soil samples from three sugarcane fields with different monoculture histories (1-, 2-, and 4-year cultivation times, respectively). We observed that SM induced soil acidity and had adverse effects on soil fertility, i.e., soil organic matter (OM), total nitrogen (TN), total carbon (TC), and available potassium (AK), as well as enzyme activities indicative for carbon, phosphorus, and nitrogen cycles. Non-metric multidimensional scaling (NMDS) analysis showed that SM time greatly affected soil attribute patterns. We observed strong correlation among soil enzymes activities and soil physiochemical properties (soil pH, OM, and TC). Alpha diversity analysis showed a varying response of the microbes to SM time. Bacterial diversity increased with increasing oligotrophs (e.g., Acidobacteria and Chloroflexi), while fungal diversity decreased with reducing copiotrophs (e.g., Ascomycota). β-Diversity analysis showed that SM time had a great influence on soil microbial structure and soil properties, which led to the changes in major components of microbial structure (soil pH, OM, TC, bacteria and soil pH; TC, fungi). Additionally, SM time significantly stimulated (four bacterial and ten fungal) and depleted (12 bacterial and three fungal) agriculturally and ecologically important microbial genera that were strongly and considerably correlated with soil characteristics (soil pH, OM, TC, and AK). In conclusion, SM induces soil acidity, reduces soil fertility, shifts microbial structure, and reduces its activity. Furthermore, most beneficial bacterial genera decreased significantly due to SM, while beneficial fungal genera showed a reverse trend. Therefore, mitigating soil acidity, improving soil fertility, and soil enzymatic activities, including improved microbial structure with beneficial service to plants and soil, can be an effective measure to develop a sustainable sugarcane cropping system.

A Comparative Analysis on the Structure and Function of the Panax notoginseng Rhizosphere Microbiome

Panax notoginseng, an important Chinese medicinal herb, can be mainly cultivated in two planting patterns, cropland planting (DT) and understory planting (LX). We speculate that the rhizosphere microbiome may vary in DT and LX and may play an important role in promoting the growth and health of P. notoginseng. In the present study, culture-independent Illumina HiSeq was employed to investigate the rhizosphere bacteria and fungi under DT and LX planting patterns. Predominant phyla include Proteobacteria, Acidobacteria, Actinobacteria, Gemmatimonadetes, and Ascomycota in the two planting patterns. DT has higher alpha diversity index than LX. The predominant LX-core genera include Bradyrhizobium, Streptomyces, and Actinomadura, and the predominant DT-core genera include Sphingomonas, Variovorax, and Novosphingobium. Total relative abundance of the disease-suppression phylum (Proteobacteria, Firmicutes, and Actinobacteria) and the potential plant growth-promoting rhizobacteria (PGPR) were both significantly higher in LX than in DT. We also identified over-presented microbial functional traits mediating plant-microbe and microbe-microbe interactions, nutrition acquisition, and plant growth promotion in P. notoginseng rhizosphere. Our findings provide a valuable reference for studying beneficial microbes and pathogens of P. notoginseng planted in DT and LX.