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Agronomy
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Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition
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Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition

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

Deadline for manuscript submissions: closed (30 April 2025) | Viewed by 8294

Special Issue Editors

Prof. Dr. Yong-Xin Liu

E-Mail Website
Guest Editor
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
Interests: plant microbiome; metagenomics; bioinformatics
Special Issues, Collections and Topics in MDPI journals
Dr. Peng Yu

E-Mail Website
Guest Editor
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.

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

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Related Special Issues

Published Papers (7 papers)

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Research

15 pages, 4171 KiB  
Article
Integrated Microbiology and Metabolomics Analysis Reveal How Tolerant Soybean Cultivar Adapt to Continuous Cropping
by Xingdong Yao, Dexin He, Xiang Zhao, Zhuorui Tan, Hongtao Zhao, Futi Xie and Jingkuan Wang
Agronomy 2025, 15(2), 468; https://doi.org/10.3390/agronomy15020468 - 14 Feb 2025
Viewed by 589
Abstract
Soybean continuous cropping could alter soil microbial communities, leading to the development of continuous-cropping obstacles that negatively impacted yield. Different soybean cultivars exhibited varying degrees of resistance to these obstacles. However, the mechanisms underlying this resistance remain unclear. In this study, microbiology and [...] Read more.
Soybean continuous cropping could alter soil microbial communities, leading to the development of continuous-cropping obstacles that negatively impacted yield. Different soybean cultivars exhibited varying degrees of resistance to these obstacles. However, the mechanisms underlying this resistance remain unclear. In this study, microbiology and metabolomics were employed to explore the impacts of continuous cropping on rhizosphere microbial communities and metabolite profiles of two soybean cultivars. The results indicated that the cultivars did not reshape the bacterial and fungal community diversity but reshaped their community structures. The potentially pathogenic fungi of continuous-cropping-sensitive soybean cultivar (ACR) were higher than those of continuous-cropping-tolerant soybean cultivar (LCR), which suggested that disease resistance might be a crucial factor in mitigating continuous-cropping barriers. The metabolomic results showed that the rhizosphere soil metabolic profiles of the two soybean cultivars were significantly different, and some rhizosphere soil metabolites, which could promote the growth of pathogens, were higher in ACR than those in LCR. Correlation analysis showed that the differential microbes were closely related to the differential metabolites. All these results suggested that the rhizosphere metabolites of continuous-cropping-sensitive soybean cultivars could promote the growth of pathogens, alter rhizosphere microbial community structure, and subsequently lead to it being more sensitive to soybean continuous-cropping obstacles. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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10 pages, 2355 KiB  
Communication
Strigolactone and Karrikin Signaling Influence the Recruitment of Wild Tobacco’s Root Microbiome in the Desert
by Jie Cheng, Shuai Luo, Gundega Baldwin, Xu Cheng, Ian T. Baldwin and Suhua Li
Agronomy 2025, 15(1), 44; https://doi.org/10.3390/agronomy15010044 - 27 Dec 2024
Viewed by 847
Abstract
Survival in desert ecosystems poses significant challenges for plants due to harsh conditions. Plant microbiomes are thought to promote resilience; however, whether plant hormones, specifically strigolactones (SLs) and karrikins (KARs), shape plant microbiomes remains unknown. The recruitment of root-associated microbiomes in Nicotiana attenuata [...] Read more.
Survival in desert ecosystems poses significant challenges for plants due to harsh conditions. Plant microbiomes are thought to promote resilience; however, whether plant hormones, specifically strigolactones (SLs) and karrikins (KARs), shape plant microbiomes remains unknown. The recruitment of root-associated microbiomes in Nicotiana attenuata, a model desert plant, silenced in specific genes associated with SL biosynthesis (CCD7) and perception (D14), karrikin perception (KAI2), and in the shared receptor (MAX2), required for both pathways, was studied. SL and KAR signaling, with MAX2 as a co-regulator, fine-tuned the assembly of root-associated microbiomes, with unique and shared regulatory functions on bacterial microbiome recruitment, particularly in taproot. Significant variation among the different plant genotypes in bacterial diversity and composition in taproot and lateral roots provides a foundation for future research to explore how microbiomes function in plant resilience in these harsh environments. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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18 pages, 3634 KiB  
Article
Insights into the Driving Factors of Methane Emission from Double-Season Rice Field Under Different Fertilization Practices in South China
by Jin Zheng, Yusheng Lu, Peizhi Xu, Kaizhi Xie, Changmin Zhou, Yaying Li, Haoyang Geng, Qianyuan Wang and Wenjie Gu
Agronomy 2024, 14(12), 2767; https://doi.org/10.3390/agronomy14122767 - 21 Nov 2024
Viewed by 1068
Abstract
Paddy fields are the main agricultural source of greenhouse gas methane (CH4) emissions. To enhance rice yield, various fertilization practices have been employed in rice paddies. However, the key microbial and abiotic factors driving CH4 emissions under different fertilization practices [...] Read more.
Paddy fields are the main agricultural source of greenhouse gas methane (CH4) emissions. To enhance rice yield, various fertilization practices have been employed in rice paddies. However, the key microbial and abiotic factors driving CH4 emissions under different fertilization practices in paddy fields remain largely uncharted. This study conducted field experiments in a traditional double-cropping rice area in South China, utilizing five different fertilization practices to investigate the key factors influencing CH4 emissions. High-throughput sequencing and PICRUSt2 functional prediction were employed to investigate the contributions of soil physicochemical properties, CH4-metabolizing microorganisms (methanogens and methanotrophs), and key genes (mcrA and pmoA) on CH4 emissions. The results showed that CH4 emission fluxes exhibited seasonal variations, with consistent patterns of change observed across all treatments for both early- and late-season rice. Compared to the no-fertilization (NF) treatment, cumulative CH4 emissions were lower in early-season rice with green manure (GM) and straw returning (SR) treatments, as well as in late-season rice with GM treatment, while rice yields were maintained at higher levels. High-throughput sequencing analysis revealed that potential methanogens were primarily distributed among four orders: Methanobacteriales, Methanocellales, Methanomicrobiales, and Methanosarcinales. Furthermore, there was a significant positive correlation between the relative abundance of the CH4-related key gene mcrA and these microorganisms. Functional analysis indicated that these potential methanogens primarily produce methane through the acetoclastic and hydrogenotrophic pathways. Aerobic CH4-oxidizing bacteria, predominantly from the genus Methylocystis, were detected in all the treatments, while the CH4 anaerobic-oxidizing archaea ANME-1b was only detected in chemical fertilization (CF) and cow manure (CM) treatments. Our random forest analysis revealed that the relative abundance of two methanogens (Methanocellales and Methanosarcinales) and two environmental factors (pH and DOC) had significant impacts on the cumulative CH4 emissions. The variance decomposition analysis highlighted the CH4-metabolizing microorganisms explained 50% of the variance in the cumulative CH4 emissions, suggesting that they are the key microbial factors driving CH4 emissions. These findings provide guidance for the development of rational measures to reduce CH4 emissions in paddy fields. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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16 pages, 3068 KiB  
Article
Differential Effects of Sulfur Fertilization on Soil Microbial Communities and Maize Yield Enhancement
by Siqi Dong, Bing Zhang, Wenfeng Hou, Xue Zhou and Qiang Gao
Agronomy 2024, 14(10), 2251; https://doi.org/10.3390/agronomy14102251 - 29 Sep 2024
Cited by 1 | Viewed by 1236
Abstract
Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This [...] Read more.
Sulfur (S) is an essential nutrient for plant growth, influencing not only crop yields but also the composition and function of soil microbial communities. However, the differential effects of S fertilization on abundant and rare taxa in agricultural soils remain poorly understood. This study investigates the impact of different S fertilizer types on maize yield and the structure and stability of soil microbial communities, with a particular focus on abundant and rare taxa. S fertilization led to significant increases maize yield on two typical soils (black soil and sandy soil) (5.3–24.3%) and altered soil properties, including reducing pH (0.04–0.20) and increasing the available sulfur (AS) content (3.8–8.0 mg kg−1), with ammonium sulfate having a more pronounced effect than elemental sulfur. Microbial analysis revealed distinct impacts on the diversity and community structure of both abundant and rare taxa. Elemental sulfur reduced the alpha diversity of abundant taxa more than ammonium sulfate, while NMDS indicated significant shifts in community structures, particularly among abundant taxa. Network analysis showed that S fertilization decreased the complexity of microbial interactions among rare taxa, with ammonium sulfate leading to simpler networks and elemental sulfur resulting in higher modularity. SEM highlighted that the diversity of rare taxa played a crucial role in influencing maize yield, alongside direct effects from soil properties such as AS and SAR (aryl sulfatase). Functional predictions demonstrated that amino acid metabolism and xenobiotic biodegradation and metabolism pathways were enriched in rare taxa, suggesting significant implications for soil health and crop productivity. This study provides new insights into the roles of abundant and rare bacterial taxa under S fertilization, emphasizing their importance in optimizing fertilization strategies for enhanced crop yield in specific soil types. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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19 pages, 8108 KiB  
Article
Grape Endophytic Microbial Community Structures and Berry Volatile Components Response to the Variation of Vineyard Sites
by Ruihua Ren, Maoyu Zeng, Yunqi Liu, Jingjing Shi, Zhuowu Wan, Miaomiao Wang, Shibo Zhang, Zhenwen Zhang and Qingqing Zeng
Agronomy 2024, 14(10), 2186; https://doi.org/10.3390/agronomy14102186 - 24 Sep 2024
Cited by 1 | Viewed by 975
Abstract
Vitis vinifera L. is a commercially important horticultural plant with abundant microbial resources. However, the impact of grape-associated microbiota on grape quality and flavor has been largely overlooked. We integrated volatomics and microbiomics to explore temporal variations in berry volatiles and microbial diversity [...] Read more.
Vitis vinifera L. is a commercially important horticultural plant with abundant microbial resources. However, the impact of grape-associated microbiota on grape quality and flavor has been largely overlooked. We integrated volatomics and microbiomics to explore temporal variations in berry volatiles and microbial diversity of ‘Cabernet Sauvignon’ in Ningxia (NX) and Shanxi (SX), and the correlation between microbial communities and volatiles. A total of 38 and 35 free and bound aroma compounds, respectively, were identified in NX berries and SX berries. For free aroma, these 38 compounds were classified into aldehydes (69%), alcohols (22%), acids (4%), aromatics (4%), terpenes (0.6%), esters (0.37%), and norisoprenoids (0.3%). Similarly, the 35 bound aromas were attributed to aromatics (58%), acids (29%), terpenes (4%), esters (3%), alcohols (2.82%), aldehydes (2.78%), and norisoprenoids (0.4%). Additionally, a total of 616 bacterial genera and 254 fungal genera were detected in all samples from both regions. The results demonstrated that vineyard sites significantly shaped the characteristics of berry volatiles and microbial biogeographic patterns. SX berries exhibited more abundant free aroma and higher microbial diversity than NX berries, with three key taxa (Sphingomonas, Massilia, and Bacillus) identified in the bacterial network. Correlation analysis results highlighted that these key taxa might play an important role in berry-free aroma. This study reveals the crucial role of microbes in shaping grape flavor and uncovers the link between microbial diversity and the regional attributes of grapes and wine. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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17 pages, 4555 KiB  
Article
Community Diversity of Endophytic Bacteria in the Leaves and Roots of Pea Seedlings
by Junjie Hao, Quanlan Liu, Fengjing Song, Xiao Cui, Lu Liu, Liping Fu, Shouan Zhang, Xingbo Wu and Xiaoyan Zhang
Agronomy 2024, 14(9), 2030; https://doi.org/10.3390/agronomy14092030 - 5 Sep 2024
Cited by 1 | Viewed by 1437
Abstract
Endophytic bacteria from pea (Pisum sativum L.) plants play important roles in regulating plant growth, health, and nutrition. To enhance the understanding of endophytic bacteria in peas, twenty pea cultivars, two chickpeas, and two broad bean cultivars were planted into artificial soils [...] Read more.
Endophytic bacteria from pea (Pisum sativum L.) plants play important roles in regulating plant growth, health, and nutrition. To enhance the understanding of endophytic bacteria in peas, twenty pea cultivars, two chickpeas, and two broad bean cultivars were planted into artificial soils for 4 weeks. Leaves and roots were collected from plants and sterilized. Endophytic bacterial DNAs were isolated from sterilized materials (leaves, roots, and seeds) and used as templates to detect the bacterial diversity by amplifying the 16S V3–V4 region. The Remel Tryptose Soya Agar (TSA) medium, the aluminum sec-butoxide (ASb) medium, and the yeast extract mannitol agar (YMA) medium were used to isolate bacteria from sterilized leaves and roots, respectively. The plant growth-promoting (PGP) properties of these isolated bacteria, such as the solubilization of phosphorus and potassium and the production of Indole-3-acetic acid (IAA), 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, nitrogenase, pectinase, and cellulose, were studied in vitro. Bacterial isolates were processed for 16S rDNA gene sequencing and performed molecular identification by reconstruction of the phylogenetic tree using the neighborhood association approach in the software MEGA X. Results indicated that the majority of the bacterial communities were shared among leaves, roots, and seeds of pea plants. In both the leaves and roots of pea plants, the prominent phyla identified were Pseudomonadota, Bacteroidota, and Bacillota, with dominant genera such as Rhizobium, Bacteroides, Blautia, and Prevotella prevailing at the genus level. The samples from leaves and roots had unique dominant bacterial genera. In total, 48 endophytic bacteria strains were isolated from leaves and roots, of which 16 strains were from roots and 32 strains were from leaves. The majority of the isolates from leaves (78.13%) and roots (75%) had the ability to produce indole-3-acetic acid (IAA). Moreover, isolates from roots also had greater ability to produce 1-amino-cyclopropane-1-carboxylic acid (ACC) deaminase (81.25%) than those from leaves (62.5%). This study demonstrated the unique distribution of endophytes in leaves and roots of pea, which can have great potential in pea production. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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21 pages, 6241 KiB  
Article
Microbiome Analysis Revealed the Effects of Environmental Factors on the Presence of Toxigenic Fungi and Toxin Production in Rice Grains
by Fengmin Zhang, Zhenzhen Cao, Xiaohua Zhao, Qing Yan, Meiyan Guan, Mingxue Chen and Xiaoyan Lin
Agronomy 2024, 14(8), 1681; https://doi.org/10.3390/agronomy14081681 - 30 Jul 2024
Viewed by 1150
Abstract
Fungal contamination in rice and mycotoxins present significant challenges to both rice quality and food safety. However, there is a dearth of comprehensive research on the compositional and structural changes within fungal colonies in rice, particularly in typical rice-producing regions, as well as [...] Read more.
Fungal contamination in rice and mycotoxins present significant challenges to both rice quality and food safety. However, there is a dearth of comprehensive research on the compositional and structural changes within fungal colonies in rice, particularly in typical rice-producing regions, as well as their underlying influencing factors. In this study, a comprehensive analysis of fungal taxa in rice grains was conducted using amplicon sequencing and bioinformatics methods on 99 rice samples collected in three major rice-producing regions in China: Northeast Plain (NP), Yangtze River Basin (YR), and Southeast Coastal Area (SC). A total of 6,019,722 fungal ITS sequences were obtained with an average sequence length of 235 base pairs, and effective ASVs (2014) accounted for approximately 97.58% of the total ASVs (2064). The fungal community diversity in rice grains exhibited significant variations across the three regions, with deterministic processes playing a predominant role in shaping the ecological dynamics of fungal taxa. Among the core microbiota (92 shared ASVs), the first five species (Alternaria, Fusarium, Curvularia, Epicoccum, and Ustilaginoidea) accounting for a proportion greater than 5% had been reported as potential pathogens for plants. Geographical variations in fungal community composition were evident, with a significantly higher number of shared populations observed between YR and CS regions compared to those in the NP region. Nutrient elements and climatic conditions were the internal and external driving factors of rice fungal community composition. Additionally, notable regional variations in fungal functionality were observed. The findings have significant implications for gaining a comprehensive understanding of the distribution patterns of fungal communities in the major rice-producing regions in China. Additionally, it provides valuable insights into controlling key influencing factors to effectively reduce the occurrence of toxin-producing fungi and mitigate the associated risks related to mycotoxin contamination, thereby contributing to improved risk management and assessment. Full article
(This article belongs to the Special Issue Metagenomic Analysis for Unveiling Agricultural Microbiome—2nd Edition)
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