Metagenomic Analysis for Unveiling Agricultural Microbiome

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Farming Sustainability".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 24353

Special Issue Editors


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Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: plant microbiome; metagenomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation, University of Bonn, 53113 Bonn, Germany
Interests: maize; abiotic stress; root development; microbiome; rhizosphere
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The agricultural microbiome plays an important role in the nutrient absorption, disease resistance and stress resistance of crops, and it is the most important way to achieve sustainable agriculture. The purpose of this Special Issue is to promote the development of the field of agricultural microbiome; the scope of acceptance is for microbiome research related to agriculture, including crops, cash crops, oil crops, vegetables, fruits, agricultural products, animal husbandry and aquatic products. Research on amplicon sequencing is acceptable, and works on metagenome, metatranscriptome, metaproteome, metametabolome, bacterial genome, population association analysis, and multi-omics analysis are recommended, in order to more comprehensively use the meta-omics technology to analyze the role of the microbiome in agriculture, make the world a better place, and realize the harmonious development of science, technology and agriculture.

Dr. Yong-Xin Liu
Dr. Peng Yu
Guest Editors

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Keywords

  • plant microbiome
  • root microbiota, amplicon
  • metagenomics
  • metatranscriptome

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Published Papers (17 papers)

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Research

18 pages, 6796 KiB  
Article
Co-Ensiling Whole-Plant Cassava with Corn Stalk for Excellent Silage Production: Fermentation Characteristics, Bacterial Community, Function Profile, and Microbial Ecological Network Features
by Mao Li, Xuejuan Zi, Rong Sun, Wenjun Ou, Songbi Chen, Guanyu Hou and Hanlin Zhou
Agronomy 2024, 14(3), 501; https://doi.org/10.3390/agronomy14030501 - 28 Feb 2024
Viewed by 588
Abstract
The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage [...] Read more.
The objective of this study was to explore excellent silage production through co-ensiling whole-plant cassava and corn stalk, and different ratios of whole-plant cassava (0%, 10%, 20%, 30%, 40%, and 50%, fresh-matter basis) co-ensiled with corn stalk were analyzed based on the silage bacterial community, function profile, and microbial ecological network features. The results demonstrated that co-ensiling 30% whole-plant cassava with 70% corn stalk could be considered an efficient mode of production. The mixed silage showed great quality, as reflected by the reduced pH value and concentrations of acetic acid, butyric acid, and ammonia nitrogen and the enhanced lactic acid concentration, V-score, and nutritional value compared with corn stalk ensiled alone. Meanwhile, co-ensiling restricted the undesirable bacterial Acetobacter fabarum of corn stalk and Pseudomonas aeruginosa of whole-plant cassava and raised the abundance of lactic acid bacteria (LAB) such as Levilactobacillus brevis, Lactiplantibacillus plantarum, Lactobacillus harbinensis, etc. Besides that, the predicted functions of the bacterial community showed large differences in mixed silage compared with whole-plant cassava or corn stalk ensiled alone. Moreover, the analysis of co-occurrence networks showed that mixed silage affected microbial network features, module numbers, and bacterial relative abundances and weakened the complexity and stability of the networks compared with whole-plant cassava single silage. Furthermore, silage microbial community composition had a huge impact on the network properties, and undesirable Pseudomonas aeruginosa played a crucial role in the complexity and stability. Overall, this study revealed the characteristics of whole-plant cassava with corn stalk mixed-silage microbial communities and co-occurrence network modules, complexity, and stability and partly clarified the microbial mechanism of co-ensiling for producing high-quality silage. The findings of this study have important implications for deeply understanding the ensiling process and precisely regulating silage fermentation quality. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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17 pages, 4380 KiB  
Article
Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics
by Zilia Y. Muñoz-Ramírez, Román González-Escobedo, Graciela D. Avila-Quezada, Obed Ramírez-Sánchez, Victor M. Higareda-Alvear, Emiliano Zapata-Chávez, Alejandra Borrego-Loya and Laila N. Muñoz-Castellanos
Agronomy 2024, 14(2), 357; https://doi.org/10.3390/agronomy14020357 - 09 Feb 2024
Viewed by 1249
Abstract
The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple [...] Read more.
The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple trees were investigated through amplicon sequencing and shotgun metagenomics. The research was conducted at a location in the municipality of Cuauhtemoc, Chihuahua State, Mexico, and a total of 22 samples were collected, comprising 12 for amplicon sequencing and 10 for shotgun metagenomic sequencing. Symptomatic trees were identified based on reddish branches and internal necrosis in the trunk and root, while asymptomatic trees exhibited a healthy physiology. The findings showed that the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Bacteroidetes, with prevalent genera such as Streptomyces, Pseudomonas, and Rhodanobacter. The fungal communities featured Ascomycota, Mortierellomycota, and Basidiomycota, which were dominated by Fusarium, Penicillium, and Mortierella. In the fungal communities, Mortierellomycota, notably abundant in asymptomatic trees, holds potential as a biocontrol agent, as seen in other studies on the suppression of Fusarium wilt disease. The application of shotgun metagenomic sequencing revealed significant differences in alpha and beta diversities in bacterial communities, suggesting a health-dependent change in species composition and abundance. Functional profile analysis highlighted enzymatic activities associated with lipid synthesis/degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis, which have been documented to participate in symbiotic relationships between plants. These insights not only contribute to understanding the dynamics of rhizosphere microbial activity but also provide valuable perspectives on the potential application of microbial communities for tree health and implications for the management of apple orchards. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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15 pages, 2554 KiB  
Article
Paddy-Lilium Crop Rotation Improves Potential Beneficial Soil Fungi and Alleviates Soil Acidification in Lilium Cropping Soil
by Li Wen, Fengqiu Huang, Zhongxiu Rao, Kaikai Cheng, Yong Guo and Haiming Tang
Agronomy 2024, 14(1), 161; https://doi.org/10.3390/agronomy14010161 - 11 Jan 2024
Cited by 1 | Viewed by 693
Abstract
Lilium growth is severely impeded by continuous cropping, and crop rotation is essential to reducing the detrimental effects of monocultures. Soil (0–20 cm) was collected in three Lilium cropping patterns in Longshan County, Hunan Province, including continuous Lilium cropping (Lilium), corn upland rotation [...] Read more.
Lilium growth is severely impeded by continuous cropping, and crop rotation is essential to reducing the detrimental effects of monocultures. Soil (0–20 cm) was collected in three Lilium cropping patterns in Longshan County, Hunan Province, including continuous Lilium cropping (Lilium), corn upland rotation with Lilium (Corn), and paddy rotation with Lilium (Rice). Using Illumina high-throughput sequencing technology, the fungal ribosomal DNA internal-transcribed spacer 1 (ITS1) was examined to evaluate the features of soil fungi communities among three cropping patterns. Crop rotation has an impact on soil properties and the microbial community. Rice soil has a significantly higher pH than Lilium and corn soil, while corn and rice soil have a greater total nitrogen and total phosphorus content than Lilium soil. Rotation cropping clearly shifted the fungi community diversity based on the results of principal coordinate analysis (PCoA) and nonmetric multidimensional scaling (NMDS). Ascomycota was the most prevalent phylum, with the highest levels in Lilium soil. Genetic analysis revealed that paddy rotation led to a clear reduction in or non-detection of eight potentially pathogenic fungal genera and a noticeable accumulation of eight beneficial fungal genera compared to Lilium continuous cropping. Fungi communities and their abundant taxa were correlated with soil pH and nutrients. Altogether, we propose that rice rotation, with its ability to mitigate soil acidification, reducing pathogenic and accumulating beneficial communities, may be an effective strategy for alleviating the continuous cropping barrier. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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16 pages, 3105 KiB  
Article
The Preliminary Research on Shifts in Maize Rhizosphere Soil Microbial Communities and Symbiotic Networks under Different Fertilizer Sources
by Lidong Ji, Xing Xu, Fengju Zhang, Haili Si, Lei Li and Guilian Mao
Agronomy 2023, 13(8), 2111; https://doi.org/10.3390/agronomy13082111 - 11 Aug 2023
Cited by 2 | Viewed by 876
Abstract
The use of chemical fertilizer along with organic fertilizer is an important agricultural practice that improves crop yield but also affects soil biogeochemical cycles. In this study, a maize field experiment was conducted to investigate the effects of NPK fertilizer (NPK), organic fertilizer [...] Read more.
The use of chemical fertilizer along with organic fertilizer is an important agricultural practice that improves crop yield but also affects soil biogeochemical cycles. In this study, a maize field experiment was conducted to investigate the effects of NPK fertilizer (NPK), organic fertilizer (OF), and their combination (NPK+OF) on soil chemical properties, bacterial and fungal community structures, and diversity compared the control (CK, without any fertilizer). The results showed that the application of OF and NPK-combined OF increased soil organic matter (OM), total N, total P, available N, available P, and available K levels. For alpha diversity analyses, the application of fertilizers led to decreases in soil bacterial and fungal Shannon indices (except for NPK in fungi). Compared with CK, NPK, OF, and NPK+OF fertilization treatments significantly increased the abundances of Acidobacteriota, Gemmatimonadota, and Basidiomycota. Network analysis showed that fertilization produced fewer connections among microbial taxa, especially in the combination of NPK and OF. A redundancy analysis combined with Mantel test further found that the soil OM, available N and P were the main soil-fertility factors driving microbial community variations. Therefore, using organic fertilizer or biological fertilizer combined with chemical fertilizer to improve the status of soil C, N, and P is a promising method to maintain the balance of soil microorganisms in maize field. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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19 pages, 15569 KiB  
Article
Microbial Communities and Soil Respiration during Rice Growth in Paddy Fields from Karst and Non-Karst Areas
by Junbo Zhou, Zhenjiang Jin, Wu Yuan, Weijian Chen, Xuesong Li, Liyuan Xiong and Guanwen Cheng
Agronomy 2023, 13(8), 2001; https://doi.org/10.3390/agronomy13082001 - 28 Jul 2023
Cited by 1 | Viewed by 1355
Abstract
Soil microorganism and their relationships with soil respiration in paddy systems in karst areas (KA) of southern China is important for understanding the mechanisms of greenhouse gas emission reduction. Soils were collected from the tillage layer (0–20 cm) during the rice growing season [...] Read more.
Soil microorganism and their relationships with soil respiration in paddy systems in karst areas (KA) of southern China is important for understanding the mechanisms of greenhouse gas emission reduction. Soils were collected from the tillage layer (0–20 cm) during the rice growing season from KA and non-karst areas (NKA) (red soils) from the Guilin Karst Experimental Site in China. Community structures and inferred functionalities of bacteria and fungi were analyzed using the high-throughput sequencing techniques, FAPROTAX and FUNGuild. A bacterial–fungal co-occurrence network was constructed and soil respiration was measured using dark box-gas chromatography and built their relationships. The results indicated that soil respiration was significantly lower in KA than in NKA. Principal component analysis indicated that bacterial and fungal community structures significantly differed between KA and NKA. The OTU ratio of fungi to bacteria (F/B) was positively correlated with soil respiration (p = 0.044). Further, the key network microorganisms were OTU69 and OTU1133 and OTU1599 in the KA. Soil respiration negatively correlated with Acidobacteria Gp6, dung saprotroph-endophyte-litter saprotroph-undefined saprotroph, aerobic nitrite oxidizers and nitrifier in KA (p < 0.05). Overall, this study demonstrated that soil respiration was reduced when soil microorganisms shifted from bacterial to fungal dominance during the rice growing season in KA. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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19 pages, 3720 KiB  
Article
Effects of Transplantation and Microhabitat on Rhizosphere Microbial Communities during the Growth of American Ginseng
by Fan Chang, Feng-An Jia, Min Guan, Qing-An Jia, Yan Sun and Zhi Li
Agronomy 2023, 13(7), 1876; https://doi.org/10.3390/agronomy13071876 - 16 Jul 2023
Cited by 1 | Viewed by 918
Abstract
Transplanting has been widely used in American ginseng (Panax quinquefolium L.) cultivation in Northwest China to mitigate the negative effects of continuous cropping obstacles. Because of the accumulation of pathogenic microorganisms and the change in soil properties, transplanting American ginseng to newly [...] Read more.
Transplanting has been widely used in American ginseng (Panax quinquefolium L.) cultivation in Northwest China to mitigate the negative effects of continuous cropping obstacles. Because of the accumulation of pathogenic microorganisms and the change in soil properties, transplanting American ginseng to newly cultivated fields after two years of growth has become a major planting pattern. Despite transplanting improving the quality of American ginseng, the effects of soil properties and microbiota on growth during the transplanting process are poorly understood. In the present study, microbial communities, soil physico-chemical properties and morpho-physiological parameters were analyzed to investigate the effects of microbiota and soil characteristics on American ginseng growth in both soil and ginseng root microhabitats. Results indicated that the structure and species of bacterial and fungal communities changed significantly in different microhabitats before and after transplantation. Moreover, the assemblage process of the bacterial community was dominated by deterministic processes. The stochastic process ratio increased and niche breadth decreased significantly after transplanting. While the assembly of the fungal community was dominated by stochastic process, and there was no significant difference in NST, βNTI or niche breadth before and after transplanting. Bacterial co-occurrence networks demonstrated a higher connectivity but a lower aggregation in soil microhabitat, while the fungal community networks remained stable before and after transplantation. Gammaproteobacteria was the biomarker in the soil microhabitat, while Alphaproteobacteria, Betaproteobacteria and Gemmatimonadetes were biomarkers in the ginseng root microhabitat. Sordariomycetes was a biomarker with high relative abundance in the fungal community before and after transplanting. The bacterial functional and important ASVs were significantly correlated with pH, organic matter, total nitrogen, available phosphorus, total potassium root fresh weight, taproot diameter and stem height of American ginseng. Partial least squares path modeling showed that soil properties significantly affected the formation of different microbial specific ASVs. The important functional ASVs in ginseng root microhabitat had a positive effect on American ginseng growth, while the rare taxa had a negative effect. Our results provide a good starting point for future studies of microbial community succession in different microhabitats influenced by the transplantation pattern of American ginseng. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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17 pages, 3475 KiB  
Article
A Meta-Analysis in Nine Different Continuous Cropping Fields to Find the Relationship between Plant Species and Rhizosphere Fungal Community
by Qiuling Pang, Mohammad Murtaza Alami, Weilong Yu, Zhen Ouyang, Shaohua Shu, Daiqun Tu, Mohammad Jawad Alami and Xuekui Wang
Agronomy 2023, 13(7), 1827; https://doi.org/10.3390/agronomy13071827 - 10 Jul 2023
Viewed by 860
Abstract
Plant species and cropping systems influence rhizospheric fungal communities’ composition, diversity, and structure. The fungus community is one of the main factors behind soil health and quality. Yet, there is insufficient evidence and research on the effect of plant species with continuous cropping [...] Read more.
Plant species and cropping systems influence rhizospheric fungal communities’ composition, diversity, and structure. The fungus community is one of the main factors behind soil health and quality. Yet, there is insufficient evidence and research on the effect of plant species with continuous cropping histories on the rhizospheric fungal community. In order to investigate how the fungal community responds to the various plant species and cropping systems, we have chosen one field that is left fallow along with eight continuously farmed areas to research. Among the eight phyla, the relative abundance of Ascomycota was significantly higher in Polygonum multiflorum, which was continuously cropped in fields for two years (P2). Basidiomycota was considerably higher in the fallow field (CK). Among the 1063 genera, the relative abundance of Fusarium was significantly higher in maize continuous-cropped fields for six years (M6), followed by Fritillaria thunbergii continuous-cropped fields for two years (F2), and found lower Fusarium abundance in CK. The alpha diversity observed in taxa, Chao1, and phylogenetic diversity indices were significantly higher in M2. β-diversity found that the fungal communities in the samples clustered from the fields in the same year were quite similar. In all the soil samples, the saprotrophic trophic type was the most common among the OTUs that had been given a function. Our studies have proved that continuous cropping and plant species changed the fungal community’s composition, diversity, and structure. This research may serve as a guide for overcoming significant agricultural challenges and advancing the industry’s sustainable growth. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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19 pages, 4575 KiB  
Article
Effect of Root-Knot Nematode Disease on Bacterial Community Structure and Diversity in Peanut Fields
by Lijun Wu, Yan Ren, Xiangsong Zhang, Guanghui Chen, Chuantang Wang, Qi Wu, Shuangling Li, Fudong Zhan, Li Sheng, Wenliang Wei and Mei Yuan
Agronomy 2023, 13(7), 1803; https://doi.org/10.3390/agronomy13071803 - 06 Jul 2023
Viewed by 1199
Abstract
The root-knot nematode (RKN) disease is a highly destructive soilborne disease that significantly affects peanut yield in Northern China. The composition of the soil microbiome plays a crucial role in plant disease resistance, particularly for soilborne diseases like RKN. However, the relationship between [...] Read more.
The root-knot nematode (RKN) disease is a highly destructive soilborne disease that significantly affects peanut yield in Northern China. The composition of the soil microbiome plays a crucial role in plant disease resistance, particularly for soilborne diseases like RKN. However, the relationship between the occurrence of RKN disease and the structure and diversity of bacterial communities in peanut fields remains unclear. To investigate bacterial diversity and the community structure of peanut fields with severe RKN disease, we applied 16S full-length amplicon sequencing based on the third high-throughput sequencing technology. The results indicated no significant differences in soil bacterial α-diversity between resistant and susceptible plants at the same site. However, the Simpson index of resistant plants was higher at the site of peanut-wheat-maize rotation (Ro) than that at the site of peanut continuous cropping (Mo), showing an increase of 21.92%. The dominant phyla identified in the peanut bulk soil included Proteobacteria, Acidobacteria, Actinobacteria, Planctomycetes, Chloroflexi, Firmicutes, and Bacteroidetes. Further analysis using LEfSe (Linear discriminant analysis effect size) revealed that Sulfuricellaceae at the family level was a biomarker in the bulk soil of susceptible peanut compared to resistant peanut. Additionally, Singulisphaera at the genus level was significantly more enriched in the bulk soil of resistant peanut than that of susceptible peanut. Soil properties were found to contribute to the abundance of bacterial operational taxonomic units (OTUs). Available phosphorus (AP), available nitrogen (AN), organic matter (OM), and pH made a positive contribution to the bacterial OTUs, while available potassium (AK) made a negative contribution. The metabolic pathway of novobiocin biosynthesis was only enriched in soil samples from resistant peanut plants. Eleven candidate beneficial bacteria and ten candidate harmful strains were identified in resistant and susceptible peanut, respectively. The identification of these beneficial bacteria provides a resource for potential biocontrol agents that can help improve peanut resistance to RKN disease. Overall, the study demonstrated that severe RKN disease could reduce the abundance and diversity of bacterial communities in peanut bulk soil. The identification of beneficial bacteria associated with resistant peanut offered the possibility for developing biocontrol strategies to enhance peanut resistance to RKN disease. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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15 pages, 1660 KiB  
Article
The Nitrogen Cycling Key Functional Genes and Related Microbial Bacterial Community α−Diversity Is Determined by Crop Rotation Plans in the Loess Plateau
by Rui Liu, Yang Liu, Yuan Gao, Fazhu Zhao and Jun Wang
Agronomy 2023, 13(7), 1769; https://doi.org/10.3390/agronomy13071769 - 29 Jun 2023
Cited by 2 | Viewed by 1724
Abstract
Soil nitrogen cycling microbial communities and functional gene α−diversity indicate soil nitrogen cycling ecological functions and potentials. Crop rotation plans affect soil nitrogen fractions and these indicators. We sequenced soil samples from four crop rotation plans (fallow, winter wheat monoculture, pea-winter wheat-winter wheat-millet [...] Read more.
Soil nitrogen cycling microbial communities and functional gene α−diversity indicate soil nitrogen cycling ecological functions and potentials. Crop rotation plans affect soil nitrogen fractions and these indicators. We sequenced soil samples from four crop rotation plans (fallow, winter wheat monoculture, pea-winter wheat-winter wheat-millet rotation, and corn-wheat-wheat-millet rotation) in a long-term field experiment. We examined how microbial communities and functional gene α−diversity changed with soil nitrogen fractions and how nitrogen fractions regulated them. Planting crops increased the abundance and richness of nitrogen cycling key functional genes and bacterial communities compared with fallow. The abundance and richness correlated positively with nitrogen fractions, while Shannon index did not. The abundance increased with soil total nitrogen (STN) and potential nitrogen mineralization (PNM), while Shannon index showed that nitrogen cycling key functional genes increased and then decreased with increasing STN and PON. Introducing legumes into the rotation improved the α−diversity of nitrogen cycling key functional genes. These results can guide sustainable agriculture in the Loess Plateau and clarify the relationship between nitrogen fractions and nitrogen cycling key functional genes. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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14 pages, 8013 KiB  
Article
High-Throughput Sequencing Reveals the Effect of the South Root-Knot Nematode on Cucumber Rhizosphere Soil Microbial Community
by Fan Yang, Huayan Jiang, Shen Liang, Gaozheng Chang, Kai Ma, Lili Niu, Guoquan Mi, Yanling Tang, Baoming Tian and Xuanjie Shi
Agronomy 2023, 13(7), 1726; https://doi.org/10.3390/agronomy13071726 - 27 Jun 2023
Viewed by 940
Abstract
Due to long-term cultivation in greenhouses, cucumbers are susceptible to root-knot nematode (RKN), resulting in reduced yield and quality. The objective of this study was to investigate the effect of RKN on the rhizosphere microbial community of cucumber. Understanding the composition of rhizosphere [...] Read more.
Due to long-term cultivation in greenhouses, cucumbers are susceptible to root-knot nematode (RKN), resulting in reduced yield and quality. The objective of this study was to investigate the effect of RKN on the rhizosphere microbial community of cucumber. Understanding the composition of rhizosphere bacterial and fungal communities and the possible interaction between microorganisms and RKN is expected to provide a reference for the eco-friendly control of M. incognita in the future. Three different groups were selected for sampling based on the RKN incidence and root galling scale (NHR, 0%, no root galling; NR, 5–15%, root galling scale 1–2; NS, 60–75%, root galling scale 4–5). Soil properties were determined to evaluate the effect of M. incognita on rhizosphere soil. High-throughput sequencing was used to examine the bacterial and fungal communities in rhizosphere soil. The results showed that the contents of soil nutrients and enzyme activities were significantly lower in the NS than in the NHR. The alpha diversity showed that M. incognita had a greater effect on rhizosphere soil bacteria than on fungi. In beta diversity, there were significant differences among the three groups by PCoA (p = 0.001). Furthermore, bacteria and fungi with significant differences in relative abundance were screened at the genus level for a correlation analysis with soil factors, and a correlation analysis between the bacteria and fungi was performed to study their relationships. A redundancy analysis (RDA) of rhizosphere microorganisms and soil properties showed a negative correlation between nematode contamination levels and soil nutrient content. Finally, we predicted the interaction among RKN, soil factors, and the rhizosphere microbial community, which provided evidence for the prevention of RKN via microecological regulation in the future. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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15 pages, 4716 KiB  
Article
Long-Term Chemical Fertilization Drove Beneficial Bacteria for Rice Soil to Move from Bulk Soil to the Rhizosphere
by Jian Xiao, Jianglin Zhang, Yajie Gao, Yanhong Lu, Xue Xie, Changyu Fang, Yulin Liao and Jun Nie
Agronomy 2023, 13(6), 1645; https://doi.org/10.3390/agronomy13061645 - 19 Jun 2023
Cited by 2 | Viewed by 1324
Abstract
Overuse of chemical fertilizer (CF) causes damage to soil and the environment. To reveal the process of the response of crop rhizospheric and bulk soil fertility and the bacterial community to long-term CF conditions, CF application and nonfertilization (CK, control) treatments were used [...] Read more.
Overuse of chemical fertilizer (CF) causes damage to soil and the environment. To reveal the process of the response of crop rhizospheric and bulk soil fertility and the bacterial community to long-term CF conditions, CF application and nonfertilization (CK, control) treatments were used in a long-term (12-year) fertilization experiment. Long-term CF application significantly increased the soil organic matter, total nitrogen, and available phosphorus contents (p < 0.05), increased the available nitrogen (AN) and potassium (AK) contents to varying degrees, and decreased the soil pH in both rice rhizospheric soil and bulk soil. In addition, the bacterial Shannon and Ace indices in rice rhizospheric soil under the CF treatment were all higher than those under the control (CK) treatment, and the bulk soil bacteria showed the opposite trend. The LEfSe results showed that unidentified_Gammaproteobacteria and Geobacter (genera) were significantly enriched in the rhizospheric and bulk soil of rice under the CK treatment, respectively. Gemmatimonadetes (phylum) and Nitrospirae (phylum) + Thiobacillus (genus) were significantly enriched in the rice rhizospheric and bulk soil under the CF treatment. Only AK and AN had strong positive correlations with soil bacteria. Long-term CF application accelerated the migration of soil bacteria from the bulk soil to the rhizosphere, thus improving soil fertility and nutrient cycling. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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17 pages, 3901 KiB  
Article
Dodder Parasitism Leads to the Enrichment of Pathogen Alternaria and Flavonoid Metabolites in Soybean Root
by Wen Luo, Yuanli Li, Ruiping Luo, Gehong Wei, Yongxin Liu and Weimin Chen
Agronomy 2023, 13(6), 1571; https://doi.org/10.3390/agronomy13061571 - 09 Jun 2023
Viewed by 1508
Abstract
Dodders (Cuscuta chinensis) are rootless and holoparasitic herbs that can infect a variety of host plants, including the vitally important economic and bioenergy crop soybean (Glycine max). Although dodder parasitism severely affects the physiology of host plants, little is [...] Read more.
Dodders (Cuscuta chinensis) are rootless and holoparasitic herbs that can infect a variety of host plants, including the vitally important economic and bioenergy crop soybean (Glycine max). Although dodder parasitism severely affects the physiology of host plants, little is known about its effects on fungal communities and root secondary metabolites in hosts. In this study, variations in root-associated fungal communities and root metabolites of soybean under different parasitism conditions were investigated using ITS rRNA gene sequencing and UPLC–MS/MS metabolome detection technologies. The results showed that dodder parasitism significantly altered the composition and diversity of the fungal communities in the rhizosphere and endosphere of soybean. The relative abundance of the potential pathogenic fungus Alternaria significantly increased in the root endosphere of dodder-parasitized soybean. Furthermore, correlation analysis indicated that the fungal community in the root endosphere was susceptible to soil factors under dodder parasitism. Meanwhile, the content of soil total nitrogen was significantly and positively correlated with the relative abundance of Alternaria in the rhizosphere and endosphere of soybean. Metabolomic analysis indicated that dodder parasitism altered the accumulation of flavonoids in soybean roots, with significant upregulation of the contents of kaempferol and its downstream derivatives under different parasitism conditions. Taken together, this study highlighted the important role of dodder parasitism in shaping the fungal communities and secondary metabolites associated with soybean roots, providing new insights into the mechanisms of multiple interactions among dodder, soybean, microbial communities and the soil environment. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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16 pages, 2059 KiB  
Article
Variations in Methanogenic and Methanotrophic Communities Resulted in Different Methane Emissions from Paddy Soil Applied with Two Types of Manure
by Beibei Zhou, Ruirui Chen, Shuang Peng, Jianwei Zhang, Xiangui Lin and Yiming Wang
Agronomy 2023, 13(5), 1268; https://doi.org/10.3390/agronomy13051268 - 28 Apr 2023
Cited by 1 | Viewed by 1087
Abstract
Organic manure application is crucial for the maintenance and improvement of soil fertility. However, it inevitably results in increased paddy CH4 emissions, restricting the use of organic manure in the rice fields. In the present study, two kinds of manures, rapidly composted [...] Read more.
Organic manure application is crucial for the maintenance and improvement of soil fertility. However, it inevitably results in increased paddy CH4 emissions, restricting the use of organic manure in the rice fields. In the present study, two kinds of manures, rapidly composted manure (RCM) and non-composted manure (NCM), were investigated through a 19-week greenhouse experiment, during which the dynamics of CH4 emission, soil parameters (DOC, acetate, NH4+, NO3, and SO42−), and communities of methanogens and methanotrophs were simultaneously measured. The results showed that NCM significantly enhanced CH4 emission, while RCM decreased CH4 emission by 65.03%; there was no significant difference with the manure-free treatment. In order to well understand the methanogenic process, the seasonal CH4 flux was divided into two periods, namely Stage 1 (before drainage) and Stage 2 (after drainage), on the basis of CH4 emission intensity. The different CH4 production abilities among the three treatments could contribute to the varied CH4 emissions at Stage 1. The much higher soil DOC concentrations were observed in the manure-amended soils (NCM- and RCM-treatments), which could correspondingly lead to the relative higher CH4 emissions compared to the control during Stage 1. Furthermore, the increased methanogenic abundance and the shifted methanogenic archaeal community characterized by the functionally stimulated growth of Methanosarcina genus were observed in the NCM-treated soils, which could consequently result in a higher CH4 emission from the NCM treatment relative to the RCM treatment. As for Stage 2, apart from the significant decrease in soil DOC, the increased contents of soil NO3 and SO42−, especially with the RCM-treated soils, were also detected following the drainage, which might retard CH4 production. The lower CH4 emission at Stage 2 could also be attributed to the vigorous aerobic CH4 oxidations, especially in the RCM-treated soils. As a support, the amount of methanotrophs revealed an increasing trend during the late rice growth period, as did the predominance of the methylotrophy of Methylophilaceae species, which showed robust co-occurrence with methanotrophs, inferring interspecies cooperation in methane oxidation. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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17 pages, 2100 KiB  
Article
Changes in Soil Rhizobia Diversity and Their Effects on the Symbiotic Efficiency of Soybean Intercropped with Maize
by Zeyu Cheng, Lingbo Meng, Tengjiao Yin, Ying Li, Yuhang Zhang and Shumin Li
Agronomy 2023, 13(4), 997; https://doi.org/10.3390/agronomy13040997 - 28 Mar 2023
Cited by 4 | Viewed by 1832
Abstract
It has been established that maize/soybean intercropping can improve nitrogen use efficiency. However, few studies have addressed how maize/soybean intercropping affects nitrogen-fixing bacterial diversity and N fixation efficiency of intercropped soybean. In this study, nitrogen-fixing bacterial communities, N fixation efficiency, and their relationships [...] Read more.
It has been established that maize/soybean intercropping can improve nitrogen use efficiency. However, few studies have addressed how maize/soybean intercropping affects nitrogen-fixing bacterial diversity and N fixation efficiency of intercropped soybean. In this study, nitrogen-fixing bacterial communities, N fixation efficiency, and their relationships with soil properties under three nitrogen fertilization application rates (N0 0 kg/ha, N1 40 kg/ha, N2 80 kg/ha) were explored through field experiments. Nitrogen fixation and nitrogen-fixing bacteria diversity were assessed using 15N natural abundance, Illumina high-throughput sequencing, and nifH (nitrogen fixation) gene copies quantification in the rhizosphere soil of intercropped soybean. The results showed that nitrogen application rates significantly decreased the nitrogen-fixing bacteria diversity, nitrogen fixation efficiency, and nifH gene copies in the rhizosphere soil. Nitrogen fixation efficiency, nodule number, and dry weight of intercropped soybean were highest in the N0 treatment, and nitrogen fixation was the highest in the N1 treatment. The nitrogen-fixing efficiency in N0, N1, and N2 treatments increased by 69%, 59%, and 42% and the nodule number of soybean was 10%, 22%, and 21%, respectively, compared with monocultures. The soybean nitrogen-fixing bacteria diversity in intercropping under N0 and N1 treatments significantly increased compared with monocultures. There was a significant positive correlation between soil nifH gene copies and N fixation efficiency and a negative correlation with soil available nitrogen. Bradyrhizobium abundance in soybean rhizosphere soil decreased significantly with the increase in nitrogen application rates and was significantly correlated with soil AN (available nitrogen) and pH content in the soybean rhizosphere. These results help us to understand the mechanisms by which nitrogen use efficiency was improved, and nitrogen fertilizer could be reduced in legume/Gramineae intercropping, which is important to improve the sustainability of agricultural production. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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16 pages, 1677 KiB  
Article
Rhizosphere Microbiomes of Amaranthus spp. Grown in Soils with Anthropogenic Polyelemental Anomalies
by Anna Muratova, Svetlana Gorelova, Sergey Golubev, Dilyara Kamaldinova and Murat Gins
Agronomy 2023, 13(3), 759; https://doi.org/10.3390/agronomy13030759 - 06 Mar 2023
Cited by 4 | Viewed by 1609
Abstract
Study of rhizospheric microbial communities of plants growing under different environmental conditions is important for understanding the habitat-dependent formation of rhizosphere microbiomes. The rhizosphere bacterial communities of four amaranth cultivars were investigated in a laboratory pot experiment. Amaranthus tricolor cv. Valentina, A. cruentus [...] Read more.
Study of rhizospheric microbial communities of plants growing under different environmental conditions is important for understanding the habitat-dependent formation of rhizosphere microbiomes. The rhizosphere bacterial communities of four amaranth cultivars were investigated in a laboratory pot experiment. Amaranthus tricolor cv. Valentina, A. cruentus cv. Dyuimovochka, and A. caudatus cvs. Bulava and Zelenaya Sosulka were grown for six months in three soils with different anthropogenic polyelemental anomalies and in a background control soil. After the plant cultivation, the rhizosphere soils were sampled and subjected to metagenomic analysis for the 16S rRNA gene. The results showed that the taxonomic structure of the amaranth rhizosphere microbiomes was represented by the dominant bacterial phyla Actinobacteriota and Proteobacteria. A feature of the taxonomic profile of the rhizobiomes of A. tricolor cv. Valentina and A. cruentus cv. Dyuimovochka was a large abundance of sequences related to Cyanobacteria. The formation of the amaranth rhizosphere microbiomes was largely unaffected by soils, but cultivar differences in the formation of the amaranth rhizosphere microbial structure were revealed. Bacterial taxa were identified that are possibly selected by amaranths and that may be important for plant adaptation to various habitat conditions. The targeted enrichment of the amaranth rhizosphere with members of these taxa could be useful for improving the efficacy of amaranth use for agricultural and remediation purposes. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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13 pages, 5007 KiB  
Article
Can Sugarcane Yield and Health Be Altered with Fully Mechanized Management?
by Jian Xiao, Tian Liang, Shangdong Yang and Hongwei Tan
Agronomy 2023, 13(1), 153; https://doi.org/10.3390/agronomy13010153 - 03 Jan 2023
Cited by 4 | Viewed by 1361
Abstract
At present, fully mechanized cultivation (FMC) has begun to be utilized in commercial sugarcane production in China. To provide new insights into whether cane yield and health are altered by fully mechanized cultivations, the cane yield and endophytic microbial community structure in stems [...] Read more.
At present, fully mechanized cultivation (FMC) has begun to be utilized in commercial sugarcane production in China. To provide new insights into whether cane yield and health are altered by fully mechanized cultivations, the cane yield and endophytic microbial community structure in stems of sugarcane that underwent fully mechanized cultivation (FMC) and conventional artificial cultivation (CAC) were compared. The results showed that the diversity and richness of endophytic microorganisms, except for the bacterial richness in the stems of sugarcane, could be significantly increased by using FMC. Meanwhile, in comparison with CAC, the relative abundance of Proteobacteria and Ascomycota increased under FMC. Moreover, some dominant endophytic bacterial genera, such as Acidovorax, Microbacterium, and Paenibacillus, and some dominant endophytic fungal genera, such as Scleroramularia, Tetraplosphaeria, and Dinemasporium, were found to be significantly enriched in cane stems under FMC treatments. Additionally, the endophytic microbial functions in sugarcane stems were not significantly altered by FMC treatments. Our results suggest that cane growth, yield, and health are not significantly altered by FMC. The results also indicate that fully mechanized management can be developed as a sustainable method in sugarcane production. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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16 pages, 4401 KiB  
Article
Maize Rotation Combined with Streptomyces rochei D74 to Eliminate Orobanche cumana Seed Bank in the Farmland
by Jiao Xi, Zanbo Ding, Tengqi Xu, Wenxing Qu, Yanzhi Xu, Yongqing Ma, Quanhong Xue, Yongxin Liu and Yanbing Lin
Agronomy 2022, 12(12), 3129; https://doi.org/10.3390/agronomy12123129 - 09 Dec 2022
Cited by 3 | Viewed by 2244
Abstract
Orobanche cumama wallr. is the sunflower root parasitic weed with special life stage in which seed germination and parasitism take place in the soil. In practice, applying microbial agents and trapping crop rotation are utilized separately, or just one of them is selected [...] Read more.
Orobanche cumama wallr. is the sunflower root parasitic weed with special life stage in which seed germination and parasitism take place in the soil. In practice, applying microbial agents and trapping crop rotation are utilized separately, or just one of them is selected to control O. cumana. The development of the sunflower industry is severely constrained on the farmland, where there is high density of O. cumana’s seed banks. In this study, two biological control methods were combined to solve the problem of O. cumana parasitism. The bioassay experiment showed that the high concentration fermentation filtrates of Streptomyces rochei D74 could effectively inhibit the germination and growth of the germ tube of O. cumana seeds. As the concentration was increased to 3.1 mg/mL, O. cumana was almost unable to sprout. A two-year pot experiment revealed that the use of D74 agents and sunflower–maize–sunflower rotation together promoted sunflower growth, as shown by the biomass accumulation, plant height, and denser root systems. The combined method resulted in a significant decrease in the number of O. cumana parasitism, compared to one method alone. Additionally, it affected the bacterial community composition of sunflower rhizosphere, mostly leading to an increase in Streptomyces and Brevibacterium and a decrease in Arthrobacter. This experiment, combined with multiple biological control, means significantly reducing the parasitism of O. cumana, which provides an effective foundation for practical application. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome)
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