Soil pH, nitrogen, phosphatase and urease activities in response to cover crop species, termination stage and termination method

Enhancing estimation of cover crop biomass using field-based high-throughput phenotyping and machine learning models

Incorporating cover crops into cropping systems offers numerous potential benefits, including the reduction of soil erosion, suppression of weeds, decreased nitrogen requirements for subsequent crops, and increased carbon sequestration. The aboveground biomass (AGB) of cover crops strongly influences their performance in delivering these benefits. Despite the significance of AGB, a comprehensive field-based high-throughput phenotyping study to quantify AGB of multiple cover crops in the U.S. Midwest has not been found. This study presents a two-year field experiment carried out in Eastern Nebraska, USA, to estimate AGB of five different cover crop species [canola (Brassica napus L.), rye (Secale cereale L.), triticale (Triticale × Triticosecale L.), vetch (Vicia sativa L.), and wheat (Triticum aestivum L.)] using high-throughput phenotyping and Machine Learning (ML) models. Destructive AGB sampling was performed three times during each spring season in 2022 and 2023. An array of morphological, spectral, thermal, and environmental features from the sensors were utilized as feature inputs of ML models. Moderately strong linear correlations between AGB and the selected features were observed. Four ML models, namely Random Forests Regression (RFR), Support Vector Regression (SVR), Partial Least Squares Regression (PLSR), and Artificial Neural Network (ANN), were investigated. Among the four models, PLSR achieved the highest Coefficient of Determination (R2) of 0.84 and the lowest Root Mean Squared Error (RMSE) of 892 kg/ha (Normalized RMSE (NRMSE) = 8.87%), indicating that PLSR could be the most appropriate method for estimating AGB of multiple cover crop species. Feature importance analysis ranked spectral features like Normalized Difference Red Edge (NDRE), Solar-induced Fluorescence (SIF), Spectral Reflectance at 485 nm (R485), and Normalized Difference Vegetation Index (NDVI) as top model features using PLSR. When utilizing fewer feature inputs, ANN exhibited better prediction performance compared to other models. Using morphological and spectral parameters as input features alone led to a R2 of 0.80 and 0.77 for AGB prediction using ANN, respectively. This study demonstrated the feasibility of high-throughput phenotyping and ML techniques for accurately estimating AGB of multiple cover crop species. Further enhancement of model performance could be achieved through additional destructive sampling conducted across multiple locations and years.

Cadmium-tolerant Bacillus cereus 2-7 alleviates the phytotoxicity of cadmium exposure in banana plantlets

Bananas are the world's important fruit and staple crop in the developing countries. Cadmium (Cd) contamination in soils results in the decrease of crop yield and food safety. Bioremediation is an environmental-friendly and effective measure using Cd-tolerant plant growth promoting rhizobacteria (PGPR). In our study, a Cd-resistant PGPR Bacillus cereus 2-7 was isolated and identified from a discarded gold mine. It could produce multiple plant growth promoting biomolecules such as siderophores, indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylate (ACC)-deaminase and phosphatase. The extracellular accumulation was a main manner of Cd removal. Surplus Cd induced the expression of Cd resistance/transport genes of B. cereus 2-7 to maintain the intracellular Cd homeostasis. The pot experiment showed that Cd contents decreased by 50.31 % in soil, 45.43 % in roots, 56.42 % in stems and 79.69 % in leaves after the strain 2-7 inoculation for 40 d. Bacterial inoculation alleviated the Cd-induced oxidative stress to banana plantlets, supporting by the increase of chlorophyll contents, plant height and total protein contents. The Cd remediation mechanism revealed that B. cereus 2-7 could remodel the rhizosphere bacterial community structure and improve soil enzyme activities to enhance the immobilization of Cd. Our study provides a Cd-bioremediation strategy using Cd-resistant PGPR in tropical and subtropical area.

Full-Length Transcriptome Sequencing Analysis and Characterization of WRKY Transcription Factors Responsive to Cadmium Stress in Arabis paniculata

Arabis paniculata is a newly discovered hyperaccumulator known for its ability to accumulate multiple metals. WRKY proteins play a significant role in plant responses to various stresses, including cadmium (Cd) stress. However, there is limited research on the molecular biology of Arabis paniculata, especially regarding the WRKY family. In this study, we conducted third-generation sequencing for functional annotation and structural analysis of Arabis paniculata. We obtained 41,196 high-quality isoforms from the full-length transcriptome, with an average length of 1043 bp. A total of 26,670 genes were predicted against NR, Swissprot, KOG, and KEGG databases. Functional comparison using the KOG database revealed excellent annotation in 25 functional categories, with general function prediction (1822 items) being the most predominant. MISA analysis identified 12,593 SSR loci, with single nucleotide repeats being the largest category (44.83% of the total). Moreover, our predictions provide insights into 20,022 coding sequences (CDS), 811 transcription factors, and 17,963 LncRNAs. In total, 34 WRKY gene sequences were identified in Arabis paniculata. Bioinformatics analysis revealed diverse numbers of amino acids in these WRKYs (113 to 545 aa), and a conserved WRKYGQK sequence within the N-terminus of the WRKY protein. Furthermore, all WRKYs were found to be localized in the nucleus. Phylogenetic analysis classified the WRKY genes into three categories: I (14 members), II (17 members), and III (3 members). Category II was subsequently divided into four sub-categories: II-a (8 members), II-b (1 member), II-c (1 member), and II-d (7 members). Our quantitative real-time polymerase chain reaction (qRT-PCR) experiments revealed that ApWRKY23 and ApWRKY34 exhibited the highest expression levels at the 24-h time point, suggesting their potential role as the candidate genes for Cd stress response. These findings contribute to our understanding of the genomic information of Arabis paniculata and provide a basis for the analysis of its genetic diversity. Additionally, this study paves the way for a comprehensive exploration of the molecular mechanisms underlying the WRKY genes in Arabis paniculata under Cd stress conditions.

Sub-micron microplastics affect nitrogen cycling by altering microbial abundance and activities in a soil-legume system

Recently, the environmental and agricultural impact of plastic waste has attracted considerable attention. Here, we investigated the impact of sub-micron polyethylene (PE) and polypropylene (PP) microplastics (MPs) on nitrogen cycling, with emphasis on bacterial abundance and diversity in a soil-soybean (Glycine max) system. Exposure to soil containing MPs (50 and 500 mg kg-1) did not affect soybean growth, but significantly increased plant nitrogen uptake, which was confirmed by increased activities of nitrogenase in the soil and glutamine synthetase in soybean root. Additionally, there was an increase in 16S gene copy number and carbon and nitrogen substrate utilization, indicating increased abundance and activity of rhizosphere microbial communities. Moreover, MP contamination affected the taxonomic profile of rhizosphere bacteria, especially the abundance of symbiotic and free-living bacteria involved in nitrogen cycling. Furthermore, qPCR analysis of nitrogen-related genes and Kyoto Encyclopedia of Genes and Genomes analysis of 16S rRNA gene sequencing data revealed an increased abundance of functional genes associated with nitrogen fixation and nitrification. However, the concentration and polymer type of MPs did not have a significant impact in our system. Overall, these results provide insights into the interactions between MPs and rhizosphere bacterial communities in the soil-legume system.

Potential application of novel cadmium-tolerant bacteria in bioremediation of Cd-contaminated soil

With the increase in cadmium (Cd) release into the environment, it is necessary to find appropriate solutions to reduce soil Cd pollution. Microorganisms are a green and effective means for the remediation of Cd-contaminated soil. In this study, in a Cd-contaminated farmland, we screened and identified novel Cd-resistant strains, Paenarthrobactor nitroguajacolicus, Lysinibacillus fusiformis, Bacillus licheniformis, and Methyllobacium brachiatum, with minimum inhibitory concentrations of 100, 100, 50, and 50 mg/L, respectively, and added them each to pots containing Cd-contaminated rape plants to explore their remediation ability. The results showed that treatment with each of the four strains significantly increased the abundance of Nitrospirae, Firmicutes, Verrucomicrobia, and Patescibacterium in the rhizosphere soil of the plants. This led to changes in soil physical and chemical indices; pH; and available phosphorus, urease, and catalase activities, which were significantly negatively correlated with bioavailable Cd, reducing 28.74-58.82 % Cd enrichment to plants and 23.72-43.79 % Cd transport within plants, and reducing 5.52-10.68 % available cadmium in soil, effectively reducing the biotoxicity of Cd. Thus, this study suggests microbial remediation as a reliable option, forming a basis for the remediation of Cd-contaminated soil.

Living grass mulching improves soil enzyme activities through enhanced available nutrients in citrus orchards in subtropical China

Living grass mulching (LGM) is an important orchard floor management that has been applied worldwide. Although LGM can effectively enhance soil nutrient availability and fertility, its effects on microbial-mediated soil nutrient cycling and main drivers are unclear. Meanwhile, the variation of enzyme activities and soil nutrient availability with LGM duration have been rarely studied. This study aims to explore the effects of mulching age and soil layer on enzyme activities and soil nutrients in citrus orchards. In this study, three LGM (Vicia villosa) treatments were applied, i.e., mulching for eight years, mulching for four years, and no mulching (clean tillage). Their effects on the enzyme activities and soil nutrients were analyzed in different soil layers of citrus orchards in subtropical China, i.e., 0-10, 10-20, and 20-40 cm. Compared to clean tillage, mulching for four years had fewer effects on enzyme activities and soil nutrients. In contrast, mulching for eight years significantly increased available nitrogen (N), phosphorus (P) nutrients, β-glucosidase, and cellobiohydrolase activities in the soil layer of 0-20 cm. In the soil layer of 0-40 cm, microbial biomass carbon (C), N, P, N-acetylglucosaminidase, leucine aminopeptidase, and acid phosphatase activities also increased (P < 0.05). Mulching for eight years significantly promoted C, N, and P-cycling enzyme activities and total enzyme activities by 2.45-6.07, 9.29-54.42, 4.42-7.11, and 5.32-14.91 times, respectively. Redundancy analysis shows that mulching treatments for eight and four years had soil layer-dependent positive effects on soil enzyme activities. Microbial C and P showed the most significant positive correlation with enzyme activities, followed by moisture content, organic C, and available N (P < 0.05). Available nutrients contributed almost 70% to affect enzyme activities significantly and were the main drivers of the enzyme activity variation. In summary, LGM could improve soil enzyme activities by increasing available nutrients. The promotion effect was more significant under mulching for eight years. Therefore, extending mulching age and improving nutrient availability are effective development strategies for sustainable soil management in orchard systems. Our study can provide valuable guidelines for the design and implementation of more sustainable management practices in citrus orchards.

Regulating Root Fungal Community Using Mortierella alpina for Fusarium oxysporum Resistance in Panax ginseng

Plant-associated microbes play important roles in plant health and disease. Mortierella is often found in the plant rhizosphere, and its possible functions are not well known, especially in medical plants. Mortierella alpina isolated from ginseng soil was used to investigate its effects on plant disease. The promoting properties and interactions with rhizospheric microorganisms were investigated in a medium. Further, a pot experiment was conducted to explore its effects on ginseng root rot disease. Physicochemical properties, high-throughput sequencing, network co-occurrence, distance-based redundancy analysis (db-RDA), and correlation analysis were used to evaluate their effects on the root rot pathogen. The results showed that Mortierella alpina YW25 had a high indoleacetic acid production capacity, and the maximum yield was 141.37 mg/L at 4 days. The growth of M. alpina YW25 was inhibited by some probiotics (Bacillus, Streptomyces, Brevibacterium, Trichoderma, etc.) and potential pathogens (Cladosporium, Aspergillus, etc.), but it did not show sensitivity to the soil-borne pathogen Fusarium oxysporum. Pot experiments showed that M. alpina could significantly alleviate the diseases caused by F. oxysporum, and increased the available nitrogen and phosphorus content in rhizosphere soil. In addition, it enhanced the activities of soil sucrase and acid phosphatase. High-throughput results showed that the inoculation of M. alpina with F. oxysporum changed the microbial community structure of ginseng, stimulated the plant to recruit more plant growth-promoting bacteria, and constructed a more stable microbial network of ginseng root. In this study, we found and proved the potential of M. alpina as a biocontrol agent against F. oxysporum, providing a new idea for controlling soil-borne diseases of ginseng by regulating rhizosphere microorganisms.