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Background: The consecutive monoculture of Rehmannia glutinosa leads to a serious decrease in its production and quality. Previous studies have demonstrated that intercropping altered species diversity and rhizosphere microbial diversity. However, it remained unknown whether the impaired growth of monocultured plants could be restored by enhanced belowground interspecific interactions. Method: In the present research, a continuous cropping facilitator Achyranthes bidentata was intercropped with R. glutinosa under pot conditions, and three different types of root barrier treatments were set, including that complete belowground interaction (N), partial belowground interaction (S), and no belowground interspecies interaction (M), with the aims to investigate belowground interaction and the underlying mechanism of alleviated replanting disease of R. glutinosa by intercropping with A. bidentata. Results: The results showed that the land equivalent ratio (LER) of the two years was 1.17, and the system productivity index (SPI) increased by 16.92 % under S treatment, whereas no significant difference was found in N and M regimes. In the rhizosphere soil, intercropping systems had significantly increased the contents of sugars and malic acid in the soil of R. glutinosa, together with the content of organic matter and the invertase and urease activities. Meanwhile, intercropping increased the community diversity of fungi and bacteria, and the relative abundance of potential beneficial bacteria, such as Bacillus, Nitrospira, and Sphingomonas, despite the pathogenic Fusarium oxysporum was still the dominant genus in the rhizospheric soil of R. glutinosa under various treatments. The results of antagonism experiments and exogenous addition of specific bacteria showed that Bacillus spp. isolated from rhizosphere soil had a significant antagonistic effect on the pathogen of R. glutinosa. Conlusion: Taken together, our study indicated that the R. glutinosa//A. bidentata intercropping systems alleviate the consecutive monoculture problem of R. glutinosa by recruiting beneficial bacteria. The studies we have conducted have a positive effect on sustainable agricultural development.

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The rapid accumulation of lignin in the cell wall is one of important immune defense mechanism in response to adversity stress in plants. In this study, we found that the enlargement of the root tubers of Rehmannia glutinosa (R. glutinosa) is arrested under consecutive monoculture stress, and this process is accompanied by abnormal accumulation of lignin. Meanwhile, the function of key catalytic enzyme genes in lignin biosynthetic pathway under consecutive monoculture stress was systematically analyzed, of which roles of core genes were validated using reverse genetics. We elucidated that an abnormal deposition of lignin in R. glutinosa roots, induced by consecutive monoculture stress, and arrested the enlargement of root tubers. Additionally, by manipulating the key catalytic enzyme gene RgCCR6, we were able to alter lignin content of roots of R. glutinosa, thereby affecting tuber enlargement. We speculate that cell lignification is an important defense strategy in resistance against consecutive monoculture stress, but the overreacted defense hindered the normal enlargement of root tubers. The findings provide new insights for effectively improving yield reductions of root crops subjected to environmental stress.

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Atractylodes lancea is a type of typical traditional Chinese medicinal (TCM) herb that is economically important in China. The traditional planting method of A. lancea is to plant in situ continuously for many years, which often leads to impediments for its growth and development and soil-borne diseases. The root-associated microbiome is believed to play an important role in plant resistance and the quality of products from the plant. This study aims to reveal detailed changes in the populations of rhizosphere microorganisms, and providing theoretical guidance for the prevention and control of soil-borne diseases in A. lancea. A high-throughput sequencing approach was utilized to illustrate changes in the microbial community from different planting years. Results and conclusions: The results show that the diversity and composition of the root-associated microbiome was significantly impacted by the consecutive monoculture of A. lancea. At the level of the comparisons of the phyla, Bacteroidetes, Proteobacteria, Ascomycota, and Basidiomycota declined significantly. In contrast, the relative abundance of Actinobacteria, Acidobacteria, and Mortierellomycota distinctly increased. Comparisons at the genus level indicated that Sphingomonas, Flavobacterium, Pseudomonas, Pedobacter, and Tausonia decreased significantly, whereas Mortierella, Cylindrocarpon, Dactylonectria, and Mucor distinctly increased. In conclusion, this study helps to develop an understanding of the impediments involved in the consecutive monoculture of A. lancea.

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Radix pseudostellariae L. is one of the most common and highly-prized Chinese medicinal plants with various pharmacological effects, and mainly produced in acid soils in the Guizhou and Fujian provinces of southwestern and southeastern China, respectively (Wu et al. 2020). However, consecutive monoculture of R. pseudostellariae results in severe root rot and decline in biomass and quality of underground tubers. Root tubers of R. pseudostellariae are typically planted in December and harvested in next June. Root rot commonly starts developing in May. The disease incidence of root rot was ranging from 37 to 46% in root portions and basal stem of R. pseudostellariae under the consecutive monoculture fields in Shibing County, Guizhou Province, China (108°12'E, 27°03'N) (Li et al. 2017). Severe root rot was observed in Shibing County in May 2018. Infected plants displayed curly, withered, and yellow leaves, blight, retarded growth, root rot, and yield losses. Abundant whitish mycelia were observed on roots and surrounding soil. Two fungal isolates, designated GZ20190123 and GZ20190124, were obtained from symptomatic roots cultured on potato dextrose agar (PDA). The optimum temperature range for growth of the two isolates was 25 to 30°C. The optimum pH range for the growth of GZ20190123 was 5 to 5.5, whereas GZ20190124 grew better between pH 5 to 8.5. The mean mycelial growth rates of GZ20190123 and GZ20190124 at 30°C were 2.1 and 1.5 cm/day, respectively. Conidia of the two isolates were ovoid or obclavate and were produced in single or branched chains. The internal transcribed spacer (ITS) region was amplified with primers ITS1 and ITS4 (White et al. 1990). The sequences were deposited in GenBank as accession No. MN726736 for GZ20190123 and MN726738 for GZ20190124. Sequence comparison revealed 99% (GZ20190123) and 97% (GZ20190124) identity with previously reported isolate xsd08071 of Mucor racemosus Bull. (accession No. FJ582639.1) and isolate BM3 of Mucor fragilis Bainier (accession No. MK910058.1), respectively, which was confirmed by phylogenetic analysis. The two isolates were tested for pathogenicity on R. pseudostellariae. Six roots of R. pseudostellariae were surface-sterilized with 75% ethanol and stab inoculated with mycelia using a sterile toothpick for each isolate. Sterile distilled water was stab inoculated to twelve roots to serve as the control. Treated roots were incubated in a greenhouse with 16 h day length [light intensity 146.5 µmol/(m2·s)] and day/night temperature 26°C/18°C. The inoculated roots showed the expected symptoms on roots and sprouts 7 days after inoculation, whereas the control roots with sprouts did not show any symptom. The fungi were re-isolated from the diseased roots and confirmed as expected M. racemosus or M. fragilis based on the ITS sequences, which satisfied Koch's postulates. Thus, isolate GZ20190123 was identified as M. racemosus and GZ20190124 as M. fragilis. Previously, M. racemosus and M. fragilis have been reported as a pathogen on tomato (Kwon and Hong 2005) and grape (Ghuffar et al. 2018), respectively. To our knowledge, this is the first report of M. racemosus and M. fragilis causing root rot of R. pseudostellariae in southwestern China, where the disease could cause a significant loss to production of this important medicinal plant.

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Replanting disease caused by negative plant-soil feedback in continuous monoculture of Radix pseudostellariae is a critical factor restricting the development of this common and popular Chinese medicine, although wild R. pseudostellariae plants were shown to grow well without occurrence of disease in the same site for multiple years. Therefore, we aimed to identify the changes in microbial community composition in the rhizosphere soil of wild R. pseudostellariae thus providing a potential method for controlling soil-borne diseases. We analyzed differences in soil physicochemical properties, changes in soil microbial community structure, and root exudates of wild R. pseudostellariae under different biotopes. And then, simple sequence repeats amplification was used to isolate and collect significantly different formae speciales of Fusarium oxysporum. Finally, we analyzed the pathogenicity testing and influence of root exudates on the growth of F. oxysporum. We found that the different biotopes of R. pseudostellariae had significant effects on the soil microbial diversity. The soil fungal and bacterial abundances were significantly higher and the abundance of F. oxysporum was significantly lower under the rhizosphere environment of wild R. pseudostellariae than under consecutive monoculture. The relative abundances of most genera were Penicillium, Aspergillus, Fusarium, Nitrobacter, Nitrospira, Streptomyces, Actinoplanes, and Pseudomonas. Venn diagram and LEfSe analyses indicated numerously specific microbiome across all the samples, and the numbers of specific fungi were higher than the shared ones in the four biotopes. Eight types of phenolic acids were identified across all the rhizosphere soils. Mixed phenolic acids and most of the examined single phenolic acids had negative effects on the growth of isolated pathogenic F. oxysporum strains and promoted the growth of non-pathogenic strains. Similarly, correlation analysis suggested that most of the identified phenolic acids were positively associated with beneficial Pseudomonas, Nitrobacter, Nitrospira, Streptomyces, and Bacillus. This study suggested that wild R. pseudostellariae was able to resist or tolerate disease by increasing soil microbial diversity, and reducing the accumulation of soil-borne pathogens.

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Polygonatum odoratum is a historically traditional Chinese medicine plant. However, the consecutive monoculture problem (CMP) widespread in other Chinese medicine limiting their cultivation on a large scale. In this study, the physiological data showed the adverse effect of CMP on the growth of P. odoratum under the consecutive cropping (CC) compared with the first cropping (FC). Then the high-throughput sequencing of miRNA and mRNA libraries of leaves and roots from FC and CC P. odoratum plants identified 671 differentially expressed genes (DEGs) and 184 differentially expressed miRNAs and revealed that the DEGs and target genes of the miRNAs were mainly involved in starch and sucrose metabolism, phenylpropanoid and brassinosteroid biosynthesis. The KEGG analysis revealed that the DEGs between CC and FC roots were enriched in the plant-pathogen interaction pathway. This study provided the expression regulation of genes related to CMP of P. odoratum but also suggested that CMP may result in the serious damage of pathogens to roots and cause the slow growth in the consecutive cropping plants.

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Biochar amendment has been extensively used to improve plant performance and suppress disease in monoculture systems; however, few studies have focused on the underlying control mechanisms of replanting disease. In this study, we assessed the effects of biochar application on Radix pseudostellariae plant growth, rhizosphere soil microbial communities, and the physiological properties of microorganisms in a consecutive monoculture system. We found that biochar addition had little impact on the physiological parameters of tissue cultures of R. pseudostellaria but did significantly mediate microbial abundance in the rhizosphere soil of different consecutive monoculture years, leading to decreases in the abundance of pathogenic Fusarium oxysporum, Talaromyces helicus, and Kosakonia sacchari. Furthermore, biochar amendment had negative effects on the growth of beneficial bacteria, such as Burkholderia ambifaria, Pseudomonas chlororaphis, and Bacillus pumilus. Metabolomic analysis indicated that biochar significantly influenced the metabolic processes of F. oxysporum while inhibiting the mycelial growth and abating the virulence on plants. In summary, this study details the potential mechanisms responsible for the biochar-stimulated changes in the abundances and metabolism of rhizosphere bacteria and fungi, decreases in the contents of pathogens, and therefore improvements in the environmental conditions for plants growth. Further research is needed to evaluate the effects of biochar in long-term field trials.

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Continuous cropping of soybean often causes significant declines in yields of soybean because of the outbreaks of soil-borne fungal diseases. It has been reported that wild crops often harbour a unique microbiome to benefit the host plants. Thus, it is necessary to find the different community structures of the rhizomicrobiomes associated with cultivated and wild soybeans in their continuous cropping. In this study, we simulated monocropping of cultivated and wild soybeans under greenhouse conditions to investigate the rhizomicrobiomes of both soybeans. Results indicated that the bacterial community structure still maintained a changing trend after four continuous planting seasons, while fungal community structure showed a stable trend as indicated by the high similarity in the fungal community structure between the third and fourth planting rotations in both soybeans. In addition, by comparing the continuous cropping of the two soybeans, we found different fungal groups in their rhizospheres between the wild and cultivated soybeans following each passage. Spizellomycetaceae was more highly enriched in the rhizosphere following cultivation of the cultivated soybean, while Chaetomiaceae and Orbiliaceae were more highly enriched in the rhizosphere of wild soybean. Taken together, results of this study suggested that although there was the same trend of stabilized fungal development in the rhizospheres of both soybeans, wild soybean rhizosphere had different fungal groups compared with that of cultivated soybean following their continuous cropping. The findings of this study may provide useful information for the farmers with regard to planting soybean, especially when they consider growing soybean in monoculture.

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Rehmannia glutinosa, a perennial herbaceous species, belongs to the family Scrophularia-ceae. As a staple medicinal material, its tuberous roots are highly valued in traditional Chinese medicine. However, R. glutinosa suffers from serious consecutive monoculture problems in production, which leads to a decline in both productivity and quality. Phyllosphere bacteria, the most abundant component of phyllosphere microorganisms, play crucial roles in plant growth and health. Characterization of phyllosphere bacteria could provide new insights into the mechanisms of consecutive monoculture problems and their control measures. Meanwhile, the varied taxa could be served as an important indicator of consecutive monoculture problems. The barcoded pyrosequencing of 16S rDNA genes combined with a culture-dependent approach was applied to characterize the shifts of bacterial community structure and diversity in the phyllosphere under consecutive monoculture of R. glutinosa. The results showed that consecutive monoculture clearly affected bacterial community structure in the phyllosphere. The phyllosphere bacterial communities of the two-year monocultured (TY) and the diseased plants (DP) were more similar, and different from the one-year monocultured (OY). The evenness, Shannon and Simpson diversity indices were significantly lower in TY and DP than in OY. Species annotation showed that bacterial community in R. glutinosa phyllosphere mainly consisted of Proteobacteria (91.2%), Firmicutes (5.1%) and Actinobacteria (3.7%). There was no significant difference in the number of detected bacterial taxa. However, Proteobacteria was significantly increased while Firmicutes and Actinobacteria were significantly decreased under consecutive monoculture. At the genus level, the relative abundances of genera Exiguobacterium, Bacillus and Arthrobacter, potentially beneficial microorganisms, were significantly higher in OY than that in TY and DP, but it was opposite for the genus Pseudomonas. The results from the culture-dependent approach and pathogenicity test showed that Pseudomonas plecoglossicida D9, widely isolated from the diseased leaves, was highly pathogenic to leaves. In conclusion, R. glutinosa monoculture resulted in distinct phyllosphere bacterial community variation with the accumulation of pathogen loads at the expense of beneficial microorganisms, which could contribute to the occurrence of leaf disease symptoms,and aggravate R. glutinosa replant disease in a monoculture regime.

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The consecutive monoculture obstacle is a major problem in the field of Rehmannia glutinosa( R. glutinosa),has severely declined the yield and quality of R. glutinosa. Here,using hi TAIL-PCR and RACE techniques,we have cloned the full-length transcript( 1 573 bp) of Unigene 29334＿All screened by DGE as a consecutive monoculture obstacle response gene of R. glutinosa. Based on ORF Finder prediction,all ORFs detected in the full-length transcript were less than 300 nt,which suggested that the above transcript was confirmed to be a long non-coding RNA( LncRNA). With alignment in R. glutinosa transcriptome,this LncRNA was partially homologous to alanine glyoxylate transaminase 2 gene( Rg AGT2),which was named LncRNA-RgATG2. To further explore the function of LncRNA-RgAGT2,we have examined expression patterns of LncRNA-RgAGT2 and Rg AGT2 at five critical development stages( seedling,elongation,pre-expanding,mid-expanding,late-expanding) in the first and second year replanting of R. glutinosa,respectively. The results indicated that LncRNA-RgAGT2,as a potential regulator,is possible to play a vital role in Rg AGT2 expression regulation. Meanwhile,LncRNA-RgAGT2 has presented significant variation in all development stages of R. glutinosa,which could be used as a " diagnostic label" to assess consecutive monoculture obstacle. This study,for the first time,showed that LncRNA was responsible for the response and regulation of consecutive monoculture obstacle,which would be a powerful supplement to reveal the molecular mechanisms of consecutive monoculture obstacle of R. glutinosa.

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Soil bacteria play key roles in determining soil health and plant growth. In this study, four sweet potato fields that had been consecutively monocultured for 1, 2, 3, and 4 years were used to investigate the effect of monoculture on soil physicochemical properties and soil bacterial communities. The results revealed that continuous cropping led to a significant decline in soil pH, soil organic carbon, and soil bacterial abundance. Miseq pyrosequencing analysis of 16S rRNA genes revealed that Proteobacteria and Bacteroidetes were the main phyla in the sweet potato monoculture soils, comprising up to 66.24% of the total sequences. The relative abundances of beneficial bacteria, including Actinobacteria, Gemmatimonadetes, Firmicutes, Xanthomonadaceae, Rhodospirillaceae, and Syntrophobacteraceae, as well as their subgroups at the genus and operational taxonomic unit (OTU) levels, decreased considerably as the number of continuous cropping years increased. In contrast, the number of potentially pathogenic bacteria, such as Acidobacteria, Sphingomonadaceae, and Pedobacter accumulated with increasing years. The results also showed the alterations to the bacterial community in the sweet potato monoculture soils were mainly driven by soil pH and soil organic matter. Overall, the decline in soil quality after successive sweet potato monoculture can be attributed to the imbalance in soil properties and soil microbes, including the decrease in soil pH and soil organic carbon, and the enrichment of pathogenic bacteria at the expense of plant-beneficial bacteria.

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The consecutive monoculture obstacle is a major problem in the field of Rehmannia glutinosa( R. glutinosa),has severely declined the yield and quality of R. glutinosa. Here,using hi TAIL-PCR and RACE techniques,we have cloned the full-length transcript( 1 573 bp) of Unigene 29334＿All screened by DGE as a consecutive monoculture obstacle response gene of R. glutinosa. Based on ORF Finder prediction,all ORFs detected in the full-length transcript were less than 300 nt,which suggested that the above transcript was confirmed to be a long non-coding RNA( LncRNA). With alignment in R. glutinosa transcriptome,this LncRNA was partially homologous to alanine glyoxylate transaminase 2 gene( Rg AGT2),which was named LncRNA-RgATG2. To further explore the function of LncRNA-RgAGT2,we have examined expression patterns of LncRNA-RgAGT2 and Rg AGT2 at five critical development stages( seedling,elongation,pre-expanding,mid-expanding,late-expanding) in the first and second year replanting of R. glutinosa,respectively. The results indicated that LncRNA-RgAGT2,as a potential regulator,is possible to play a vital role in Rg AGT2 expression regulation. Meanwhile,LncRNA-RgAGT2 has presented significant variation in all development stages of R. glutinosa,which could be used as a " diagnostic label" to assess consecutive monoculture obstacle. This study,for the first time,showed that LncRNA was responsible for the response and regulation of consecutive monoculture obstacle,which would be a powerful supplement to reveal the molecular mechanisms of consecutive monoculture obstacle of R. glutinosa.

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The production and quality of Rehmannia glutinosa can be dramatically reduced by replant disease under consecutive monoculture. The root-associated microbiome, also known as the second genome of the plant, was investigated to understand its impact on plant health. Culture-dependent and culture-independent pyrosequencing analysis was applied to assess the shifts in soil bacterial communities in the rhizosphere and rhizoplane under consecutive monoculture. The results show that the root-associated microbiome (including rhizosphere and rhizoplane microbiomes) was significantly impacted by rhizocompartments and consecutive monoculture. Consecutive monoculture of R. glutinosa led to a significant decline in the relative abundance of the phyla Firmicutes and Actinobacteria in the rhizosphere and rhizoplane. Furthermore, the families Flavobacteriaceae, Sphingomonadaceae, and Xanthomonadaceae enriched while Pseudomonadaceae, Bacillaceae, and Micrococcaceae decreased under consecutive monoculture. At the genus level, Pseudomonas, Bacillus, and Arthrobacter were prevalent in the newly planted soil, which decreased in consecutive monocultured soils. Besides, culture-dependent analysis confirmed the widespread presence of Pseudomonas spp. and Bacillus spp. in newly planted soil and their strong antagonistic activities against fungal pathogens. In conclusion, R. glutinosa monoculture resulted in distinct root-associated microbiome variation with a reduction in the abundance of beneficial microbes, which might contribute to the declined soil suppressiveness to fungal pathogens in the monoculture regime.

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KEY MESSAGE: The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis. The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called "replanting benefit" is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants.

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Although consecutive monoculture problems have been studied for many years, no effective treatments are currently available. The complexity of systems triggered the formation of consecutive monoculture problems was one major cause. This paper elaborated the physiological and ecological mechanisms of consecutive monoculture problem formation based on the interaction relationship among multiple factors presented in the rhizosphere soil of consecutive monoculture plants. At same time, in this paper the multiple interactions among cultivated medicinal plants, autotoxic allelochemicals and rhizosphere microbial were proposed to be most important causes that derived the formation of consecutive monoculture problem. The paper also highlighted the advantage of 'omics' technologies integrating plant functional genomics and metabolomics as well as microbial macro-omics in understanding the multiple factor interaction under a particular ecological environment. Additionally, taking R. glutinosa as an example, the paper reviewed the molecular mechanism for the formation of R. glutinosa consecutive monoculture problem from the perspective of the accumulation of allelopathic autotoxins, the rhizosphere microecology catastrophe and theresponding of consecutive monoculture plants. Simultaneously, the roles of mutilple 'omics' technologies in comprehending these formation mechanism were described in detail. This paper provides finally a new insight to solve systematically the mechanism of consecutive monoculture problem formation on molecular level.

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This paper clarified in detail the definition, characteristics of allelopathy and its association with consecutive monoculture problem.Most of studies have indicated that it is critical to parse the formation mechanisms of consecutive monoculture problem that identification of allelochemicals and verification of its function. Here, we proposed a new approach to separate and identify the allelochemical group precisely and effectively, in which the "knock-out/in" methods of targeting ingredients in the model of medicinal effect identification and quality control were applied. This method will contribute to deep understanding plant allelopathy, and provide theoretical basis and technical support for alleviating consecutive monoculture problems simultaneously.

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BACKGROUND: Pseudostellaria heterophylla (P. heterophylla), a herbaceous perennial, belongs to Caryophyllaceae family and is one of the Chinese herbal medicine with high pharmacodynamic value. It can be used to treat the spleen deficiency, anorexia, weakness after illness and spontaneous perspiration symptoms. Our previous study found that consecutive monoculture of Pseudostellaria heterophylla could lead to the deterioration of the rhizosphere microenvironment. The specialized forms of pathogenic fungus Fusarium oxysporum f.Sp. heterophylla (F. oxysporum) in rhizosphere soils of P. heterophylla plays an important role in the consecutive monoculture of P. heterophylla. RESULTS: In this study, F. oxysporum was used to infect the tissue culture plantlets of P. heterophylla to study the responding process at three different infection stages by using RNA-sequencing. We obtained 127,725 transcripts and 47,655 distinct unigenes by de novo assembly and obtained annotated information in details for 25,882 unigenes. The Kyoto Encyclopedia of Genes and Genomes pathway analysis and the real-time quantitative PCR results suggest that the calcium signal system and WRKY transcription factor in the plant-pathogen interaction pathway may play an important role in the response process, and all of the WRKY transcription factor genes were divided into three different types. Moreover, we also found that the stimulation of F. oxysporum may result in the accumulation of some phenolics in the plantlets and the programmed cell death of the plantlets. CONCLUSIONS: This study has partly revealed the possible molecular mechanism of the population explosion of F. oxysporum in rhizosphere soils and signal response process, which can be helpful in unraveling the role of F. oxysporum in consecutive monoculture problems of P. heterophylla.

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KEY MESSAGE: We deeply investigated the mechanism underlying metabolic regulation in response to consecutive monoculture (replanting disease) and different abiotic stresses that unfolded the response mechanism to consecutive monoculture problem through RNA-seq analysis. The consecutive monoculture problem (CMP) resulted of complex environmental stresses mediated by multiple factors. Previous studies have noted that multiple stress factors in consecutive monoculture soils or plants severely limited the interpretation of the critical molecular mechanism, and made a predict that the specifically responding factor was autotoxic allelochemicals. To identify the specifically responding genes, we compared transcriptome changes in roots of Rehamannia glutinosa Libosch using consecutive monoculture, salt, drought, and ferulic acid as stress factors. Comparing with normal growth, 2502, 2672, 2485, and 1956 genes were differentially expressed in R. glutinosa under consecutive monoculture practice, salt, drought, and ferulic acid stress, respectively. In addition, 510 genes were specifically expressed under consecutive monoculture, which were not present under the other stress conditions. Integrating the biological and enrichment analyses of the differentially expressed genes, the result demonstrated that the plants could alter enzyme genes expression to reconstruct the complicated metabolic pathways, which used to tolerate the CMP and abiotic stresses. Furthermore, most of the affected pathway genes were closely related to secondary metabolic processes, and the influence of consecutive monoculture practice on the transcriptome genes expression profile was very similar to the profile under salt stress and then to the profile under drought stress. The outlined schematic diagram unfolded the putative signal regulation mechanism in response to the CMP. Genes that differentially up- or down-regulated under consecutive monoculture practice may play important roles in the CMP or replanting disease in R. glutinosa.

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Although consecutive monoculture problems have been studied for many years, no effective treatments are currently available. The complexity of systems triggered the formation of consecutive monoculture problems was one major cause. This paper elaborated the physiological and ecological mechanisms of consecutive monoculture problem formation based on the interaction relationship among multiple factors presented in the rhizosphere soil of consecutive monoculture plants. At same time, in this paper the multiple interactions among cultivated medicinal plants, autotoxic allelochemicals and rhizosphere microbial were proposed to be most important causes that derived the formation of consecutive monoculture problem. The paper also highlighted the advantage of 'omics' technologies integrating plant functional genomics and metabolomics as well as microbial macro-omics in understanding the multiple factor interaction under a particular ecological environment. Additionally, taking R. glutinosa as an example, the paper reviewed the molecular mechanism for the formation of R. glutinosa consecutive monoculture problem from the perspective of the accumulation of allelopathic autotoxins, the rhizosphere microecology catastrophe and theresponding of consecutive monoculture plants. Simultaneously, the roles of mutilple 'omics' technologies in comprehending these formation mechanism were described in detail. This paper provides finally a new insight to solve systematically the mechanism of consecutive monoculture problem formation on molecular level.