Abstract
Resistant cultivars have played important roles in controlling Fusarium wilt disease, but the roles of rhizosphere interactions among different levels of resistant cultivars are still ...unknown. Here, two phenotypes of cucumber, one resistant and one with increased susceptibility to
Fusarium oxysporum
f.sp.
cucumerinum
(Foc), were grown in the soil and hydroponically, and then 16S rRNA gene sequencing and nontargeted metabolomics techniques were used to investigate rhizosphere microflora and root exudate profiles. Relatively high microbial community evenness for the Foc-susceptible cultivar was detected, and the relative abundances of
Comamonadaceae
and
Xanthomonadaceae
were higher for the Foc-susceptible cultivar than for the other cultivar. FishTaco analysis revealed that specific functional traits, such as protein synthesis and secretion, bacterial chemotaxis, and small organic acid metabolism pathways, were significantly upregulated in the rhizobacterial community of the Foc-susceptible cultivar. A machine-learning approach in conjunction with FishTaco plus metabolic pathway analysis revealed that four organic acids (citric acid, pyruvate acid, succinic acid, and fumarate) were released at higher abundance by the Foc-susceptible cultivar compared with the resistant cultivar, which may be responsible for the recruitment of
Comamonadaceae
, a potential beneficial microbial group. Further validation demonstrated that
Comamonadaceae
can be “cultured” by these organic acids. Together, compared with the resistant cultivar, the susceptible cucumber tends to assemble beneficial microbes by secreting more organic acids.
Plant pathogen invasions are often associated with changes in physical environmental conditions and the composition of host-associated rhizosphere microbiome. It is however unclear how these factors ...interact and correlate with each other in determining plant disease dynamics in natural field conditions. To study this, we temporally sampled the rhizosphere of tomato plants that were exposed to moderate to aggressive Ralstonia solanacearum pathogen invasions over one crop season. We found that physiochemical soil properties correlated weakly with the severity of pathogen invasion apart from the water-soluble nitrogen concentration, which increased more clearly during the aggressive invasion. Instead, a much stronger link was found between pathogen invasion and reduced abundance and diversity of various rhizosphere bacterial taxa, simplification of bacterial interaction networks and loss of several predicted functional genes. We further verified our results in a separate greenhouse experiment to show that pathogen invasion causally drives similar changes in rhizosphere microbiome diversity and composition under controlled environmental conditions. Our results suggest that R. solanacearum invasion disrupts rhizosphere bacterial communities leading to clear reduction in the diversity and abundance of non-pathogenic bacteria. These changes could potentially affect the likelihood of secondary pathogen invasions during following crop seasons as less diverse microbial communities are also often less resistant to invasions. Strong negative correlation between pathogen and non-pathogenic bacterial densities further suggest that relative pathogen abundance could better predict the severity of bacterial wilt disease outbreaks compared to absolute pathogen abundance. Monitoring the dynamics of whole microbiomes could thus open new avenues for more accurate disease diagnostics in the future.
•Ralstonia solanacearum (RS) invasion changes rhizobacterial community composition.•These changes include lowered rhizobacterial density, diversity and functioning.•The relative RS abundance is a key predictor of bacterial wilt disease severity.
Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms ...(i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers.
To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B. amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen.
Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function. Video Abstract.
•A nationwide survey of animal manure-based composts was carried out in China.•As was present mainly as AsⅤ, with DMA and MMA as the minor species in composts.•Zn, Cu, As, Cd and Hg were the most ...cautionary elements with composts application.
A nationwide survey of animal manure-based composts was carried out in China. Two hundred and twelve samples were collected and analyzed for the concentrations of 9 heavy metals or metalloids and arsenic (As) speciation. The concentrations of heavy metals vary widely (Zn 11.8–3692, Cu 3.6–916, Cr 0.7–6603, Ni 0.7–73, Pb 0.05–189, As 0.4–72, Co 0.1–94, Cd 0.01–8.7 and Hg 0.01–1.9mgkg−1 dry weight). Compared with the maximum permissible values of the Chinese standard for organic fertilizers, 13.7% and 2.4% of the composts exceeded the limits for As (15mgkg−1) and Cd (3mgkg−1), respectively. Some samples contained very high concentrations of Zn and Cu, although no limits have been set for these two metals in China. Further analysis showed that As was present mainly as arsenate (AsⅤ), with dimethylarsenate (DMA) and monomethylarsenate (MMA) as the minor species in composts. There were significant correlations between the concentrations of Zn, Cu and As, suggesting co-contamination of these elements in some composts. Monte Carlo simulations based on the distributions of metal concentrations and application rate showed that repeated applications of compost likely increase the concentrations of Zn, Cu, Cd and Hg in soil significantly compared with the soil background levels. This study highlights a need to minimize the concentrations of Zn, Cu, Cd, Hg and As in animal manures to ensure their safe recycling to agricultural soils.
The relationship between biodiversity and soil microbiome stability remains poorly understood. Here, we investigated the impacts of bacterial phylogenetic diversity on the functional traits and the ...stability of the soil microbiome. Communities differing in phylogenetic diversity were generated by inoculating serially diluted soil suspensions into sterilized soil, and the stability of the microbiome was assessed by detecting community variations under various pH levels. The taxonomic features and potential functional traits were detected by DNA sequencing.
We found that bacterial communities with higher phylogenetic diversity tended to be more stable, implying that microbiomes with higher biodiversity are more resistant to perturbation. Functional gene co-occurrence network and machine learning classification analyses identified specialized metabolic functions, especially "nitrogen metabolism" and "phosphonate and phosphinate metabolism," as keystone functions. Further taxonomic annotation found that keystone functions are carried out by specific bacterial taxa, including Nitrospira and Gemmatimonas, among others.
This study provides new insights into our understanding of the relationships between soil microbiome biodiversity and ecosystem stability and highlights specialized metabolic functions embedded in keystone taxa that may be essential for soil microbiome stability. Video abstract.
Grafting is a basic technique which is widely used to increase yield and enhance biotic and abiotic stress tolerance in plant production. The diversity and interactions of rhizobacterial assemblages ...shaped by grafting are important for the growth of their hosts but remain poorly understood. To test the hypothesis that plant grafting shapes complexity and co-occurrence of rhizobacterial assemblage, four types of plants, including ungrafted bottle gourd (B), ungrafted watermelon (W), grafted watermelon with bottle gourd rootstock (W/B), and grafted bottle gourd with watermelon rootstock (B/W), were cultivated in two soil types in a greenhouse, and the rhizosphere bacterial communities were analyzed by 16S rRNA gene high-throughput sequencing. Both the soil type and grafting significantly influenced the bacterial community composition. Grafting increased bacterial within-sample diversity in both soils. Core enriched operational taxonomic units (OTUs) in the W/B rhizosphere compared with the other three treatments (B, W, and B/W) were mainly affiliated with Alphaproteobacteria, Deltaproteobacteria, and Bacteroidetes, which are likely related to methanol oxidation, methylotrophy, fermentation, and ureolysis. Co-occurrence network analysis proved that grafting increased network complexity, including the number of nodes, edges, and modules. Moreover, grafting strengthened the structural robustness of the network in the rhizosphere, while ungrafted watermelon had the lowest network robustness. Homogeneous selection played a predominant role in bacterial community assembly, and the contribution of dispersal limitation was increased in grafted watermelon with bottle gourd rootstock. Grafting increased the diversity and transformed the network topology of the bacterial community, which indicated that grafting could improve species coexistence in the watermelon rhizosphere.
Cellular pH homeostasis is fundamental for life, and all cells adapt to maintain this balance. In plants, the chemical form of nitrogen supply, nitrate and ammonium, is one of the cellular pH ...dominators. We report that the rice nitrate transporter OsNRT2.3 is transcribed into two spliced isoforms with a natural variation in expression ratio. One splice form, OsNRT2.3b is located on the plasma membrane, is expressed mainly in the phloem, and has a regulatory motif on the cytosolic side that acts to switch nitrate transport activity on or off by a pH-sensing mechanism. High OsNRT2.3b expression in rice enhances the pH-buffering capacity of the plant, increasing N, Fe, and P uptake. In field trials, increased expression of OsNRT2.3b improved grain yield and nitrogen use efficiency (NUE) by 40%. These results indicate that pH sensing by the rice nitrate transporter OsNRT2.3b is important for plant adaption to varied N supply forms and can provide a target for improving NUE.
Drought stress is a major global issue limiting agricultural productivity. Plants respond to drought stress through a series of physiological, cellular, and molecular changes for survival. The ...regulation of water transport and photosynthesis play crucial roles in improving plants' drought tolerance. Nitrogen (N, ammonium and nitrate) is an essential macronutrient for plants, and it can affect many aspects of plant growth and metabolic pathways, including water relations and photosynthesis. This review focuses on how drought stress affects water transport and photosynthesis, including the regulation of hydraulic conductance, aquaporin expression, and photosynthesis. It also discusses the cross talk between N, water transport, and drought stress in higher plants.
The continuous cropping of banana in the same field may result in a serious soil-borne Fusarium wilt disease and a severe yield decline, a phenomenon known as soil sickness. Although soil ...microorganisms play key roles in maintaining soil health, the alternations of soil microbial community and relationship between these changes and soil sickness under banana monoculture are still unclear. Bacterial and fungal communities in the soil samples collected from banana fields with different monoculture spans were profiled by sequencing of the 16S rRNA genes and internal transcribed spacer using the MiSeq platform to explore the relationship between banana monoculture and Fusarium wilt disease in the present study. The results showed that successive cropping of banana was significantly correlated with the Fusarium wilt disease incidence. Fungal communities responded more obviously and quickly to banana consecutive monoculture than bacterial community. Moreover, a higher fungal richness significantly correlated to a higher banana Fusarium wilt disease incidence but a lower yield. Banana fungal pathogenic genus of Fusarium and Phyllosticta were closely associated with banana yield depletion and disease aggravation. Potential biocontrol agents, such as Funneliformis, Mortierella, Flavobacterium, and Acidobacteria subgroups, exhibited a significant correlation to lower disease occurrence. Further networks analysis revealed that the number of functionally interrelated modules decreased, the composition shifted from bacteria-to fungi-dominated among these modules, and more resources-competitive interactions within networks were observed after banana long-term monoculture. Our results also showed that bacterial and fungal communities were mainly driven by soil organic matter. Overall, the findings indicated that the bacterial and fungal community structures altered significantly after banana long-term monoculture, and the fungal richness, abundance of Fusarium, interactions between and within bacteria and fungi in ecological networks, and soil organic matter were associated with banana soilborne Fusarium wilt disease.
Plants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by ...plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants.
Plants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response.
Collectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.
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