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Zhongyi Zhang - One of the best experts on this subject based on the ideXlab platform.
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rhizosphere fungal community dynamics associated with rehmannia glutinosa replant disease in a consecutive Monoculture regime
Phytopathology, 2018Co-Authors: Linkun Wu, Jun Chen, Zhigang Xiao, Juanying Wang, Hongmiao Wu, Muhammad Umar Khan, Zhongyi ZhangAbstract:: Consecutive Monoculture of Rehmannia glutinosa in the same field leads to a severe decline in both quality and yield of tuberous roots, the most useful part in traditional Chinese medicine. Fungi are an important and diverse group of microorganisms in the soil ecosystem and play crucial roles in soil health. In this study, high-throughput pyrosequencing of internal transcribed spacer 2 ribosomal DNA amplicons was applied to gain insight into how consecutive Monoculture practice influence and stimulate R. glutinosa rhizosphere and bulk soil fungal communities. The results from nonmetric multidimensional scaling ordination and clustering analysis revealed distinctive differences between rhizosphere and bulk soil fungal communities. However, longer-term Monocultured bulk soils were more similar to the rhizosphere soils in comparison with the shorter-term Monocultured bulk soils. Moreover, consecutive Monoculture caused a gradual shift in the composition and structure of the soil fungal community. The cultivation of this plant led to the appearance of some exclusive operational taxonomic units in rhizosphere or bulk soils that were assigned to the genera Fusarium, Rhizoctonia, and so on. Furthermore, the sum of the relative abundance of species of Fusarium, Cylindrocarpon, and Gibberella (belonging to the family Nectriaceae); Rhizoctonia, Thanatephorus, and Ceratobasidium (belonging to the family Ceratobasidiaceae); and Lectera and Plectosporium (belonging to the family Plectosphaerellaceae) was significantly higher in consecutively Monocultured (CM) than in newly planted (NP) soil in both rhizosphere and bulk soils. In particular, Fusarium abundance was significantly higher in CM than in NP in the rhizosphere, and higher in rhizosphere soils than in bulk soils for each treatment. A pathogenicity test showed that both Fusarium strains isolated were pathogenic to R. glutinosa seedlings. In addition, the culture filtrate and mycotoxins produced by Fusarium oxysporum significantly repressed the growth of the antagonistic bacterium, Pseudomonas aeruginosa. In conclusion, consecutive Monoculture of R. glutinosa restructured the fungal communities in both rhizosphere and bulk soils but bulk effects developed more slowly over time in comparison with rhizosphere effects. Furthermore, microbial interactions might lead to a reduction in the abundance of beneficial microbes.
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Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture
MDPI AG, 2018Co-Authors: Jun Chen, Zhigang Xiao, Xiaocheng Zhu, Juanying Wang, Zhongyi Zhang, Wenxiong LinAbstract: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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Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture
MDPI AG, 2018Co-Authors: Juanying Wang, Jun Chen, Zhigang Xiao, Zhongyi Zhang, Xianjin Qin, Wenxiong LinAbstract:Consecutive Monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive Monoculture. The results showed R. glutinosa Monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year Monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year Monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive Monoculture
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effects of consecutive Monoculture of pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing
Scientific Reports, 2016Co-Authors: Jun Chen, Juanying Wang, Zhongyi Zhang, Muhammad Umar Khan, Sheng Lin, Wenxiong LinAbstract:Under consecutive Monoculture, the biomass and quality of Pseudostellaria heterophylla declines significantly. In this study, a three-year field experiment was conducted to identify typical growth inhibition effects caused by extended monoculturing of P. heterophylla. Deep pyrosequencing was used to examine changes in the structure and composition of soil fungal community along a three-year gradient of Monoculture. The results revealed a distinct separation between the newly planted plot and the two-year, three-year Monocultured plots. The Shannon and Simpson diversity indices were significantly higher in the two-year and three-year Monoculture soils than in the newly planted soil. Consecutive Monoculture of this plant led to a significant increase in relative abundance of Fusarium, Trichocladium and Myrothecium and Simplicillium, etc., but a significant decrease in the relative abundance of Penicillium. Quantitative PCR analysis confirmed a significant increase in Fusarium oxysporum, an agent known to cause wilt and rot disease of P. heterophylla. Furthermore, phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth of pathogenic F. oxysporum. Overall, this study demonstrated that consecutive Monoculture of P. heterophylla can alter the fungal community in the rhizosphere, including enrichment of host-specific pathogenic fungi at the expense of plant-beneficial fungi.
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correction corrigendum plant microbe rhizosphere interactions mediated by rehmannia glutinosa root exudates under consecutive Monoculture
Scientific Reports, 2016Co-Authors: Linkun Wu, Jun Chen, Juanying Wang, Hongmiao Wu, Weimin Huang, Yanqiu Yang, Zhongyi ZhangAbstract:Under consecutive Monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive Monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under Monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the Monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during Monoculture. Prolonged Monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended Monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended Monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
Bernhard Schmid - One of the best experts on this subject based on the ideXlab platform.
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nematode communities plant nutrient economy and life cycle characteristics jointly determine plant Monoculture performance over 12 years
Oikos, 2020Co-Authors: Ernst Detlef Schulze, Bernhard Schmid, Peter Dietrich, Anna Roeder, Simone Cesarz, Nico Eisenhauer, Anne Ebeling, Cameron WaggAbstract:Knowledge from agriculture and ecological field studies suggests that plant Monocultures lose productivity over time, but the drivers underlying the long‐term performance of Monocultures of grassland species are not completely understood. We examined the performance of 60 grassland species growing in Monoculture for 12 years in a biodiversity experiment (Jena Experiment) and studied three groups of biotic drivers potentially affecting plant performance in Monocultures over time: 1) soil biota (nematode communities, arbuscular mycorrhizal fungi), 2) leaf traits related to leaf economics spectrum, and 3) plant life‐cycle characteristics related to buffered population growth (viable seeds in topsoil, seedling density, seed survival). Monocultures of 15 out of 60 species increased productivity, while Monocultures of the remaining 45 species showed slight to strong losses of productivity over time, resulting in zero biomass in 15 species. All three biotic drivers were related to the varying long‐term performance of Monocultures. Their combined influence on Monoculture performance could be interpreted as a tradeoff between ‘fast’ versus ‘slow’ life strategies. ‘Fast’ species showed rapid resource use and little buffering of population growth through a viable seed bank, which led to high biomass production in young Monocultures but a consecutive loss of biomass production over time. ‘Slow’ species were characterized by positive nematode effects (high abundance of predatory nematodes), conservative use of resources, and a viable seed bank with high recruitment success resulting in gradually increasing productivity over time. In summary, our study highlights the importance of studying long‐term field Monocultures to investigate the complex role of different biotic drivers responsible for productivity changes over time. These insights provide an essential baseline for estimating biodiversity effects on productivity as well as to understand and predict long‐term performance of plant populations.
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selection in response to community diversity alters plant performance and functional traits
Perspectives in Plant Ecology Evolution and Systematics, 2018Co-Authors: Sofia J Van Moorsel, Debra Zuppingerdingley, Marc W Schmid, Terhi Hahl, Bernhard SchmidAbstract:Abstract In grassland biodiversity experiments the positive biodiversity–ecosystem functioning relationship generally increases over time. However, we know little about the underlying short-term evolutionary processes. Using five plant species selected for twelve years in a biodiversity experiment in mixture or Monoculture and plants without such a selection history, we assessed whether differential selection altered productivity, biodiversity effects, and functional trait differences within newly assembled Monocultures and 2-species mixtures. Plants without a past community selection history in the biodiversity experiment produced the lowest assemblage biomass and showed the weakest biodiversity effects. In newly assembled mixtures, plants with a selection history in mixtures produced more biomass than plants with a Monoculture selection history. Biodiversity effects were generally positive and differed significantly between selection histories. However, contrary to our expectations, biodiversity effects were not stronger for mixture-type plants. Biodiversity effects were influenced by both trait differences between plants and community-weighted means, but these relationships were mostly independent of selection history. Our findings suggest that twelve years of selection history in Monocultures or species mixtures differentiated plants of each species into Monoculture- and mixture-types. Such rapid evolution of different community-types within grassland species and its effect on ecosystem services and functioning are likely to be important for species conservation practice.
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selection in response to community diversity alters plant performance and functional traits
bioRxiv, 2017Co-Authors: Sofia J Van Moorsel, Debra Zuppingerdingley, Marc W Schmid, Terhi Hahl, Bernhard SchmidAbstract:In grassland biodiversity experiments the positive biodiversity−ecosystem functioning relationship generally increases over time. However, we know little about the underlying short-term evolutionary processes. Using five plant species selected for twelve years in a biodiversity experiment in mixture or Monoculture and plants without such a selection history, we assessed whether differential selection altered productivity, biodiversity effects, and functional trait differences within newly assembled Monocultures and 2-species mixtures. Plants without past community selection history produced the lowest assemblage biomass and showed the weakest biodiversity effects. In newly assembled mixtures, plants with a selection history in mixtures produced more biomass than plants with a Monoculture selection history. Biodiversity effects were generally positive and differed significantly between selection histories. However, contrary to our expectations, biodiversity effects were not stronger for mixture-type plants. Biodiversity effects were influenced by both trait differences between plants and community-weighted means, but these relationships were mostly independent of selection history. Our findings suggest that twelve years of selection history in Monocultures or species mixtures differentiated plants of each species into Monoculture-and mixture-types. Such rapid evolution of different community-types within grassland species and its effect on ecosystem services and functioning are likely to be important for species conservation practice.
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selection in response to community diversity alters plant performance in newly assembled test communities
bioRxiv, 2017Co-Authors: Sofia J Van Moorsel, Debra Zuppingerdingley, Marc W Schmid, Terhi Hahl, Bernhard SchmidAbstract:In grassland biodiversity experiments the positive biodiversity–ecosystem functioning relationship generally increases over time. However, there is still a large gap in our understanding of the underlying short-term evolutionary processes. Research has shown that differential selection in Monoculture vs. mixed-species communities can lead to rapid evolution. We assessed whether selection history altered productivity, biodiversity effects and species complementarity within newly assembled Monocultures and 2-species mixtures using five plant species selected for twelve years in such a biodiversity experiment in mixture or Monoculture and plants without such a selection history. Plants without past community selection history produced the lowest community biomass and showed the weakest biodiversity effects. Furthermore, we found that twelve years of selection history in Monocultures or species mixtures differentiated plants into Monoculture- and mixture-types within species. In newly assembled mixtures, plants with a selection history in mixtures performed better than plants with a Monoculture selection history. Biodiversity effects were generally positive but, contrary to expectation, not stronger for mixture types. In addition, biodiversity effects were both influenced by trait differences among plants and community-weighted means, but these relationships were largely independent of selection history. Our findings indicate possible mechanisms underlying the rapid evolution of adapted subtypes within a species in grasslands. Uncovering these mechanisms contributes to our understanding of the biodiversity–ecosystem functioning relationship, which has the potential to influence species conservation practice.
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Complementarity among four highly productive grassland species depends on resource availability
Oecologia, 2016Co-Authors: Christopher Roscher, Olaf Kolle, Bernhard Schmid, Ernst Detlef SchulzeAbstract:Positive species richness–productivity rela- tionships are common in biodiversity experiments, but how resource availability modifies biodiversity effects in grass–legume mixtures composed of highly productive spe- cies is yet to be explicitly tested. We addressed this ques- tion by choosing two grasses (Arrhenatherum elatius and Dactylis glomerata) and two legumes (Medicago × varia and Onobrychis viciifolia) which are highly productive in Monocultures and dominant in mixtures (the Jena Experi- ment). We established Monocultures, all possible two- and three-species mixtures, and the four-species mixture under three different resource supply conditions (control, fertili- zation, and shading). Compared to the control, community biomass production decreased under shading (−56 %) and increased under fertilization (+12 %). Net diversity effects (i.e., mixture minus mean Monoculture biomass) were positive in the control and under shading (on average +15 and +72 %, respectively) and negative under fertilization (−10 %). Positive complementarity effects in the control suggested resource partitioning and facilitation of growth through symbiotic N2 fixation by legumes. Positive com- plementarity effects under shading indicated that resource partitioning is also possible when growth is carbon-limited. Negative complementarity effects under fertilization sug- gested that external nutrient supply depressed facilitative grass–legume interactions due to increased competition for light. Selection effects, which quantify the dominance of species with particularly high Monoculture biomasses in the mixture, were generally small compared to complemen- tarity effects, and indicated that these species had compara- ble competitive strengths in the mixture. Our study shows that resource availability has a strong impact on the occur- rence of positive diversity effects among tall and highly productive grass and legume species.
William R Harcombe - One of the best experts on this subject based on the ideXlab platform.
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weakest link dynamics predict apparent antibiotic interactions in a model cross feeding community
Antimicrobial Agents and Chemotherapy, 2020Co-Authors: Elizabeth M Adamowicz, William R HarcombeAbstract:With the growing global threat of antimicrobial resistance, novel strategies are required for combatting resistant pathogens. Combination therapy, in which multiple drugs are used to treat an infection, has proven highly successful in the treatment of cancer and HIV. However, this practice has proven challenging for the treatment of bacterial infections due to difficulties in selecting the correct combinations and dosages. An additional challenge in infection treatment is the polymicrobial nature of many infections, which may respond to antibiotics differently than a Monoculture pathogen. This study tests whether patterns of antibiotic interactions (synergy, antagonism, or independence/additivity) in Monoculture can be used to predict antibiotic interactions in an obligate cross-feeding coculture. Using our previously described weakest-link hypothesis, we hypothesized antibiotic interactions in coculture based on the interactions we observed in Monoculture. We then compared our predictions to observed antibiotic interactions in coculture. We tested the interactions between 10 previously identified antibiotic combinations using checkerboard assays. Although our antibiotic combinations interacted differently than predicted in our Monocultures, our Monoculture results were generally sufficient to predict coculture patterns based solely on the weakest-link hypothesis. These results suggest that combination therapy for cross-feeding multispecies infections may be successfully designed based on antibiotic interaction patterns for their component species.
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weakest link dynamics predict apparent antibiotic interactions in a model cross feeding community
bioRxiv, 2020Co-Authors: Elizabeth M Adamowicz, William R HarcombeAbstract:Abstract With the growing global threat of antimicrobial resistance, novel strategies are required for combatting resistant pathogens. Combination therapy, wherein multiple drugs are used to treat an infection, has proven highly successful in the treatment of cancer and HIV. However, this practice has proven challenging for the treatment of bacterial infections due to difficulties in selecting the correct combinations and dosages. An additional challenge in infection treatment is the polymicrobial nature of many infections, which may respond to antibiotics differently than a Monoculture pathogen. This study tests whether patterns of antibiotic interactions (synergy, antagonism, or independence/additivity) in Monoculture can be used to predict antibiotic interactions in an obligate cross-feeding co-culture. Using our previously described weakest link hypothesis, we hypothesized antibiotic interactions in co-culture based on the interactions we observed in Monoculture. We then compared our predictions to observed antibiotic interactions in co-culture. We tested the interactions between ten previously identified antibiotic combinations using checkerboard assays. Although our antibiotic combinations interacted differently than predicted in our Monocultures, our Monoculture results were generally sufficient to predict co-culture patterns based solely on the weakest link hypothesis. These results suggest that combination therapy for cross-feeding multispecies infections may be successfully designed based on antibiotic interaction patterns for their component species.
Juanying Wang - One of the best experts on this subject based on the ideXlab platform.
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rhizosphere fungal community dynamics associated with rehmannia glutinosa replant disease in a consecutive Monoculture regime
Phytopathology, 2018Co-Authors: Linkun Wu, Jun Chen, Zhigang Xiao, Juanying Wang, Hongmiao Wu, Muhammad Umar Khan, Zhongyi ZhangAbstract:: Consecutive Monoculture of Rehmannia glutinosa in the same field leads to a severe decline in both quality and yield of tuberous roots, the most useful part in traditional Chinese medicine. Fungi are an important and diverse group of microorganisms in the soil ecosystem and play crucial roles in soil health. In this study, high-throughput pyrosequencing of internal transcribed spacer 2 ribosomal DNA amplicons was applied to gain insight into how consecutive Monoculture practice influence and stimulate R. glutinosa rhizosphere and bulk soil fungal communities. The results from nonmetric multidimensional scaling ordination and clustering analysis revealed distinctive differences between rhizosphere and bulk soil fungal communities. However, longer-term Monocultured bulk soils were more similar to the rhizosphere soils in comparison with the shorter-term Monocultured bulk soils. Moreover, consecutive Monoculture caused a gradual shift in the composition and structure of the soil fungal community. The cultivation of this plant led to the appearance of some exclusive operational taxonomic units in rhizosphere or bulk soils that were assigned to the genera Fusarium, Rhizoctonia, and so on. Furthermore, the sum of the relative abundance of species of Fusarium, Cylindrocarpon, and Gibberella (belonging to the family Nectriaceae); Rhizoctonia, Thanatephorus, and Ceratobasidium (belonging to the family Ceratobasidiaceae); and Lectera and Plectosporium (belonging to the family Plectosphaerellaceae) was significantly higher in consecutively Monocultured (CM) than in newly planted (NP) soil in both rhizosphere and bulk soils. In particular, Fusarium abundance was significantly higher in CM than in NP in the rhizosphere, and higher in rhizosphere soils than in bulk soils for each treatment. A pathogenicity test showed that both Fusarium strains isolated were pathogenic to R. glutinosa seedlings. In addition, the culture filtrate and mycotoxins produced by Fusarium oxysporum significantly repressed the growth of the antagonistic bacterium, Pseudomonas aeruginosa. In conclusion, consecutive Monoculture of R. glutinosa restructured the fungal communities in both rhizosphere and bulk soils but bulk effects developed more slowly over time in comparison with rhizosphere effects. Furthermore, microbial interactions might lead to a reduction in the abundance of beneficial microbes.
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Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture
MDPI AG, 2018Co-Authors: Jun Chen, Zhigang Xiao, Xiaocheng Zhu, Juanying Wang, Zhongyi Zhang, Wenxiong LinAbstract: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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Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture
MDPI AG, 2018Co-Authors: Juanying Wang, Jun Chen, Zhigang Xiao, Zhongyi Zhang, Xianjin Qin, Wenxiong LinAbstract:Consecutive Monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive Monoculture. The results showed R. glutinosa Monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year Monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year Monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive Monoculture
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effects of consecutive Monoculture of pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing
Scientific Reports, 2016Co-Authors: Jun Chen, Juanying Wang, Zhongyi Zhang, Muhammad Umar Khan, Sheng Lin, Wenxiong LinAbstract:Under consecutive Monoculture, the biomass and quality of Pseudostellaria heterophylla declines significantly. In this study, a three-year field experiment was conducted to identify typical growth inhibition effects caused by extended monoculturing of P. heterophylla. Deep pyrosequencing was used to examine changes in the structure and composition of soil fungal community along a three-year gradient of Monoculture. The results revealed a distinct separation between the newly planted plot and the two-year, three-year Monocultured plots. The Shannon and Simpson diversity indices were significantly higher in the two-year and three-year Monoculture soils than in the newly planted soil. Consecutive Monoculture of this plant led to a significant increase in relative abundance of Fusarium, Trichocladium and Myrothecium and Simplicillium, etc., but a significant decrease in the relative abundance of Penicillium. Quantitative PCR analysis confirmed a significant increase in Fusarium oxysporum, an agent known to cause wilt and rot disease of P. heterophylla. Furthermore, phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth of pathogenic F. oxysporum. Overall, this study demonstrated that consecutive Monoculture of P. heterophylla can alter the fungal community in the rhizosphere, including enrichment of host-specific pathogenic fungi at the expense of plant-beneficial fungi.
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correction corrigendum plant microbe rhizosphere interactions mediated by rehmannia glutinosa root exudates under consecutive Monoculture
Scientific Reports, 2016Co-Authors: Linkun Wu, Jun Chen, Juanying Wang, Hongmiao Wu, Weimin Huang, Yanqiu Yang, Zhongyi ZhangAbstract:Under consecutive Monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive Monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under Monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the Monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during Monoculture. Prolonged Monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended Monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended Monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
Wenxiong Lin - One of the best experts on this subject based on the ideXlab platform.
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Barcoded Pyrosequencing Reveals a Shift in the Bacterial Community in the Rhizosphere and Rhizoplane of Rehmannia glutinosa under Consecutive Monoculture
MDPI AG, 2018Co-Authors: Jun Chen, Zhigang Xiao, Xiaocheng Zhu, Juanying Wang, Zhongyi Zhang, Wenxiong LinAbstract: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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Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture
MDPI AG, 2018Co-Authors: Juanying Wang, Jun Chen, Zhigang Xiao, Zhongyi Zhang, Xianjin Qin, Wenxiong LinAbstract:Consecutive Monoculture of Rehmannia glutinosa, highly valued in traditional Chinese medicine, leads to a severe decline in both quality and yield. Rhizosphere microbiome was reported to be closely associated with the soil health and plant performance. In this study, comparative metagenomics was applied to investigate the shifts in rhizosphere microbial structures and functional potentials under consecutive Monoculture. The results showed R. glutinosa Monoculture significantly decreased the relative abundances of Pseudomonadaceae and Burkholderiaceae, but significantly increased the relative abundances of Sphingomonadaceae and Streptomycetaceae. Moreover, the abundances of genera Pseudomonas, Azotobacter, Burkholderia, and Lysobacter, among others, were significantly lower in two-year Monocultured soil than in one-year cultured soil. For potentially harmful/indicator microorganisms, the percentages of reads categorized to defense mechanisms (i.e., ATP-binding cassette (ABC) transporters, efflux transporter, antibiotic resistance) and biological metabolism (i.e., lipid transport and metabolism, secondary metabolites biosynthesis, transport and catabolism, nucleotide transport and metabolism, transcription) were significantly higher in two-year Monocultured soil than in one-year cultured soil, but the opposite was true for potentially beneficial microorganisms, which might disrupt the equilibrium between beneficial and harmful microbes. Collectively, our results provide important insights into the shifts in genomic diversity and functional potentials of rhizosphere microbiome in response to R. glutinosa consecutive Monoculture
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effects of consecutive Monoculture of pseudostellaria heterophylla on soil fungal community as determined by pyrosequencing
Scientific Reports, 2016Co-Authors: Jun Chen, Juanying Wang, Zhongyi Zhang, Muhammad Umar Khan, Sheng Lin, Wenxiong LinAbstract:Under consecutive Monoculture, the biomass and quality of Pseudostellaria heterophylla declines significantly. In this study, a three-year field experiment was conducted to identify typical growth inhibition effects caused by extended monoculturing of P. heterophylla. Deep pyrosequencing was used to examine changes in the structure and composition of soil fungal community along a three-year gradient of Monoculture. The results revealed a distinct separation between the newly planted plot and the two-year, three-year Monocultured plots. The Shannon and Simpson diversity indices were significantly higher in the two-year and three-year Monoculture soils than in the newly planted soil. Consecutive Monoculture of this plant led to a significant increase in relative abundance of Fusarium, Trichocladium and Myrothecium and Simplicillium, etc., but a significant decrease in the relative abundance of Penicillium. Quantitative PCR analysis confirmed a significant increase in Fusarium oxysporum, an agent known to cause wilt and rot disease of P. heterophylla. Furthermore, phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth of pathogenic F. oxysporum. Overall, this study demonstrated that consecutive Monoculture of P. heterophylla can alter the fungal community in the rhizosphere, including enrichment of host-specific pathogenic fungi at the expense of plant-beneficial fungi.
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plant microbe rhizosphere interactions mediated by rehmannia glutinosa root exudates under consecutive Monoculture
Scientific Reports, 2015Co-Authors: Juanying Wang, Jun Chen, Zhongyi Zhang, Weimin Huang, Yanqiu Yang, Wenxiong LinAbstract:Under consecutive Monoculture, the biomass and quality of Rehmannia glutinosa declines significantly. Consecutive Monoculture of R. glutinosa in a four-year field trial led to significant growth inhibition. Most phenolic acids in root exudates had cumulative effects over time under sterile conditions, but these effects were not observed in the rhizosphere under Monoculture conditions. It suggested soil microbes might be involved in the degradation and conversion of phenolic acids from the Monocultured plants. T-RFLP and qPCR analysis demonstrated differences in both soil bacterial and fungal communities during Monoculture. Prolonged Monoculture significantly increased levels of Fusarium oxysporum, but decreased levels of Pseudomonas spp. Abundance of beneficial Pseudomonas spp. with antagonistic activity against F. oxysporum was lower in extended Monoculture soils. Phenolic acid mixture at a ratio similar to that found in the rhizosphere could promote mycelial growth, sporulation, and toxin (3-Acetyldeoxynivalenol, 15-O-Acetyl-4-deoxynivalenol) production of pathogenic F. oxysporum while inhibiting growth of the beneficial Pseudomonas sp. W12. This study demonstrates that extended Monoculture can alter the microbial community of the rhizosphere, leading to relatively fewer beneficial microorganisms and relatively more pathogenic and toxin-producing microorganisms, which is mediated by the root exudates.
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assessment of shifts in microbial community structure and catabolic diversity in response to rehmannia glutinosa Monoculture
Applied Soil Ecology, 2013Co-Authors: Zhongyi Zhang, Weimin Huang, Muhammad Azam Khan, Wenxiong LinAbstract:Abstract Rehmannia glutinosa, a widely used Chinese medicinal herb, has been shown to suffer from serious consecutive Monoculture problems that cause significant decline in both yield and quality. The objective of this study was to evaluate the response of the soil microbial community and the effect on catabolic diversity to consecutive Monoculture regime using three different techniques: substrate-induced respiration (SIR), phospholipid fatty acid (PLFA) and community-level physiological profiles (CLPP) analyses. We found that basal soil respiration (BSR) was significantly higher in the control and newly planted soils than in the second and third year consecutive Monoculture soils. However, no significant difference was observed in SIR among the newly planted, second and third year consecutive Monoculture soils. The PLFA signatures indicated that the bacterial biomass was larger than the fungal biomass in all four treatments and both enhanced with the increasing years of Monoculture and attained the peak in SM. The ratio of cyclopropyl PLFAs to their metabolic precursors (cy/pre), a measure of physiological stress in microbial communities, in the second and third year consecutive Monoculture soils was significantly greater than that in the control and newly planted soils. Biolog analysis results revealed that the consumption of carboxylic acids, phenolic acids and amines, especially acid carbon substrates, in the consecutively Monocultured soil was significantly greater than that in the newly planted soil. Both PLFA- and CLPP-based principal component analysis (PCA) and cluster analysis revealed the distinct separation between the control, newly planted plots and the second, third year consecutive Monoculture plots. Through our PLFA-based and Biolog analysis, together with microbial respiration determination, we were able to reveal characteristic differences in the microbial community composition and activities in the rhizosphere following R. glutinosa Monoculture.
