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Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield.

ABSTRACT: 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.

SUBMITTER: Imam N

PROVIDER: S-EPMC8386434 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Intercropping is an efficient land use and sustainable agricultural practice widely adopted worldwide. However, how intercropping influences the structure and function of soil bacterial communities is not fully understood. Here, the effects of five cropping systems (sole sorghum, sole millet, sole peanut, sorghum/peanut intercropping, and millet/peanut intercropping) on soil bacterial community structure and function were investigated using Illumina MiSeq sequencing. The results showed that integrating peanut into intercropping systems increased soil available nitrogen (AN) and total nitrogen (TN) content. The alpha diversity index, including Shannon and Chao1 indices, did not differ between the five cropping systems. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) illustrated a distinct separation in soil microbial communities among five cropping systems. Bacterial phyla, including Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi, were dominant across all cropping systems. Sorghum/peanut intercropping enhanced the relative abundance of phyla Actinobacteriota and Chloroflexi compared to the corresponding monocultures. Millet/peanut intercropping increased the relative abundance of Proteobacteria, Acidobacteriota, and Nitrospirota. The redundancy analysis (RDA) indicated that bacterial community structures were primarily shaped by soil organic carbon (SOC). The land equivalent ratio (LER) values for the two intercropping systems were all greater than one. Partial least squares path modeling analysis (PLS-PM) showed that soil bacterial community had a direct effect on yield and indirectly affected yield by altering soil properties. Our findings demonstrated that different intercropping systems formed different bacterial community structures despite sharing the same climate, reflecting changes in soil ecosystems caused by interspecific interactions. These results will provide a theoretical basis for understanding the microbial communities of peanut-based intercropping and guide agricultural practice.

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.

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Dataset Information

Local Network Properties of Soil and Rhizosphere Microbial Communities in Potato Plantations Treated with a Biological Product Are Important Predictors of Crop Yield.

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