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A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms.

ABSTRACT: The effect of a microbial consortium-based (MCB) biocontrol product, composed of Bacillus subtilis, Trichoderma harzianum strain and diatomaceous earth as a carrier, on potato yield, and potential modes of action for its effect were investigated. The MCB product (300 kg ha^-1 ) was added to furrows in which the potato seed tubers each year for 3 years (2016, 2017 and 2018), while potato planting without the MCB product treatment served as the control. A metagenomic analysis indicated that bacterial phylotypes dominated the microbial community, with a relatively small contribution of archaea and fungal taxa. The relative abundance of beneficial bacterial taxa increased significantly in response to the MCB product treatment. Notably, a higher relative abundance of bacterial taxa with carbon fixation, carbon-degrading and nitrogen metabolism properties were observed in the MCB product-treated potato rhizosphere. This was also reflected in the identification of a greater abundance of genes encoding enzymes involved in nitrogen metabolism, carbon fixation and carbon degradation pathways in the conducted metagenomic analysis. The greater relative abundance of these beneficial bacterial taxa in the rhizosphere of MCB product-treated plots, as well as the higher abundance of genes associated with the indicated cellular processes, were associated with an increase in tuber yield. The observed changes in microbial community structure at an early stage of tuber development appears to have a beneficial impact on tuber yield.

SUBMITTER: Wang Z

PROVIDER: S-EPMC8449676 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Understanding the effectiveness and potential mechanism of action of agricultural biological products under different soil profiles and crops will allow more precise product recommendations based on local conditions and will ultimately result in increased crop yield. This study aimed to use bulk soil and rhizosphere microbial composition and structure to evaluate the potential effect of a Bacillus amyloliquefaciens inoculant (strain QST713) on potatoes and to explore its relationship with crop yield. We implemented next-generation sequencing (NGS) and bioinformatics approaches to assess the bacterial and fungal biodiversity in 185 soil samples, distributed over four different time points-from planting to harvest-from three different geographical locations in the United States. In addition to location and sampling time (which includes the difference between bulk soil and rhizosphere) as the main variables defining the microbiome composition, the microbial inoculant applied as a treatment also had a small but significant effect in fungal communities and a marginally significant effect in bacterial communities. However, treatment preserved the native communities without causing a detectable long-lasting effect on the alpha- and beta-diversity patterns after harvest. Using information about the application of the microbial inoculant and considering microbiome composition and structure data, we were able to train a Random Forest model to estimate if a bulk soil or rhizosphere sample came from a low- or high-yield block with relatively high accuracy (84.6%), concluding that the structure of fungal communities gives us more information as an estimator of potato yield than the structure of bacterial communities. IMPORTANCE Our results reinforce the notion that each cultivar on each location recruits a unique microbial community and that these communities are modulated by the vegetative growth stage of the plant. Moreover, inoculation of a Bacillus amyloliquefaciens strain QST713-based product on potatoes also changed the abundance of specific taxonomic groups and the structure of local networks in those locations where the product caused an increase in the yield. The data obtained, from in-field assays, allowed training a predictive model to estimate the yield of a certain block, identifying microbiome variables-especially those related to microbial community structure-even with a higher predictive power than the geographical location of the block (that is, the principal determinant of microbial beta-diversity). The methods described here can be replicated to fit new models in any other crop and to evaluate the effect of any agricultural input in the composition and structure of the soil microbiome.

Project description:Continuous potato cropping systems cause yield reduction, soil-borne disease aggravation, and soil degradation, but crop rotation can alleviate these negative effects. However, there are limited studies on the relationships between microbial community and other soil biochemical properties of continuous potato cropping at both pre-planting and harvest in North China. A 4-year study was conducted to explore the effects of different rotation system on soil biochemical properties, microbial community at pre-planting and harvest, and potato yield, tuber number and black scurf incidence at harvest in 2020 and 2021, which included 4 treatments vis. potato-potato-potato-potato (PC), potato-oat-faba bean-potato (PR), oat-faba bean-potato-oat (O), and faba bean-potato-oat-faba bean (B). The results showed that soil biochemical properties and microbial community among all treatments showed no significant difference at pre-planting after a long cold winter generally. At harvest, PC reduced tuber yield and number and significantly increased black scurf incidence relative to potato rotation systems. PC also reduced soil enzyme activities, the content of soil nutrients, and fungal community diversity, and increased bacterial community diversity compared with the other treatments, insignificantly when compared with PR. Relative abundance of microorganisms related to the degradation of organic residues, soil nitrogen cycling, and disease suppression, such as the genera Devosia, Aeromicrobium, Paraphoma, and Papiliotrema, were significantly higher in O or B than in PC and PR, while microorganisms related to disease infection such as the genera Pseudomonas, Colletotrichum, Plectosphaerella, Fusarium, and Verticillium exhibited increased in PC and PR. Principal Coordinates Analysis (PCoA) showed that there were significant differences in the microbial community structure of PC and PR at harvest compared with that of O and B. Redundancy analysis (RDA) revealed that soil available potassium (AK), acid phosphatase (ACP), available phosphorus (AP), sucrase (SUC) and pH were the dominant factors that significantly affected bacterial and fungal community structure. Partial least squares structural equation model indicated rotation system had significant negative effect on fungal community. It was concluded that growing oat or faba bean after potato can increase soil beneficial microorganisms and maintain the ecosystem healthy, thus reducing the incidence of tuber black scurf and increasing potato yield.

Project description:Sweetpotato can be cultivated in the reclaimed rocky soil in Sichuan Basin, China, which benefits from the release of mineral nutrients in the rocky soil by microorganisms. Shortage of nitrogen (N) in the rocky soil limits sweetpotato yield, which can be compensated through N fertilization. Whereas high N fertilization inhibits biological N fixation and induces unintended environmental consequences. However, the effect of low N fertilization on microorganism community and sweetpotato yield in the N-deficient rocky soil is still unclear. We added a low level of 1.5 g urea/m2 to a rocky soil cultivated with sweetpotato, and measured rocky soil physiological and biochemical properties, rhizosphere microbial diversity, sweetpotato physiological properties and transcriptome. When cultivating sweetpotato in the rocky soil, low N fertilization (1.5 g urea/m2) not only improved total N (TN) and available N (AN) in the rocky soil, but also increased available phosphorus (AP), available potassium (AK), and nitrogenase and urease activity. Interestingly, although low N fertilization could reduce bacterial diversity through affecting sweetpotato root exudates and rocky soil properties, the relative abundance of P and K-solubilizing bacteria, N-fixing and urease-producing bacteria increased under low N fertilization, and the relative abundance of plant pathogens decreased. Furthermore, low N fertilization increased the phytohormones, such as zeatin riboside, abscisic acid, and methyl jasmonate contents in sweetpotato root. Those increases were consistent with our transcriptome findings: the inhibition of the lignin synthesis, the promotion of the starch synthesis, and the upregulated expression of Expansin, thus resulting in promoting the formation of tuberous roots and further increasing the sweetpotato yield by half, up to 3.3 kg/m2. This study indicated that low N fertilization in the N-deficient rocky soil improved this soil quality through affecting microorganism community, and further increased sweetpotato yield under regulation of phytohormones pathway.

Project description:BackgroundIn this study, we assessed the actively metabolizing bacteria in the rhizosphere of potato using two potato cultivars, i.e. the genetically-modified (GM) cultivar Modena (having tubers with altered starch content) and the near-isogenic non-GM cultivar Karnico. To achieve our aims, we pulse-labelled plants at EC90 stage with (13)C-CO2 and analysed their rhizosphere microbial communities 24 h, 5 and 12 days following the pulse. In the analyses, phospholipid fatty acid/stable isotope probing (PLFA-SIP) as well as RNA-SIP followed by reverse transcription and PCR-DGGE and clone library analysis, were used to determine the bacterial groups that actively respond to the root-released (13)C labelled carbonaceous compounds.Methodology/principal findingsThe PLFA-SIP data revealed major roles of bacteria in the uptake of root-released (13)C carbon, which grossly increased with time. Gram-negative bacteria, including members of the genera Pseudomonas and Burkholderia, were strong accumulators of the (13)C-labeled compounds at the two cultivars, whereas Gram-positive bacteria were lesser responders. PCR-DGGE analysis of cDNA produced from the two cultivar types showed that these had selected different bacterial, alpha- and betaproteobacterial communities at all time points. Moreover, an effect of time was observed, indicating dynamism in the structure of the active bacterial communities. PCR-DGGE as well as clone library analyses revealed that the main bacterial responders at cultivar Karnico were taxonomically affiliated with the genus Pseudomonas, next to Gluconacetobacter and Paracoccus. Cultivar Modena mainly attracted Burkholderia, next to Moraxella-like (Moraxellaceae family) and Sphingomonas types.Conclusions/significanceBased on the use of Pseudomonas and Burkholderia as proxies for differentially-selected bacterial genera, we conclude that the selective forces exerted by potato cultivar Modena on the active bacterial populations differed from those exerted by cultivar Karnico.

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A microbial consortium-based product promotes potato yield by recruiting rhizosphere bacteria involved in nitrogen and carbon metabolisms.

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