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

Deadline for manuscript submissions: 30 June 2023 | Viewed by 5039

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Special Issue Editors

Prof. Dr. Yong-Xin Liu

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Guest Editor

Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Interests: plant microbiome; metagenomics; bioinformatics

Dr. Peng Yu

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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 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

Published Papers (5 papers)

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Research

Open AccessArticle

Variations in Methanogenic and Methanotrophic Communities Resulted in Different Methane Emissions from Paddy Soil Applied with Two Types of Manure

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Agronomy 2023, 13(5), 1268; https://doi.org/10.3390/agronomy13051268 - 28 Apr 2023

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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 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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Open AccessArticle

Changes in Soil Rhizobia Diversity and Their Effects on the Symbiotic Efficiency of Soybean Intercropped with Maize

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Agronomy 2023, 13(4), 997; https://doi.org/10.3390/agronomy13040997 - 28 Mar 2023

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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 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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Open AccessFeature PaperArticle

Rhizosphere Microbiomes of Amaranthus spp. Grown in Soils with Anthropogenic Polyelemental Anomalies

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Agronomy 2023, 13(3), 759; https://doi.org/10.3390/agronomy13030759 - 06 Mar 2023

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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 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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Open AccessArticle

Can Sugarcane Yield and Health Be Altered with Fully Mechanized Management?

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Agronomy 2023, 13(1), 153; https://doi.org/10.3390/agronomy13010153 - 03 Jan 2023

Cited by 1 | Viewed by 675

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 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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Open AccessFeature PaperArticle

Maize Rotation Combined with Streptomyces rochei D74 to Eliminate Orobanche cumana Seed Bank in the Farmland

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Agronomy 2022, 12(12), 3129; https://doi.org/10.3390/agronomy12123129 - 09 Dec 2022

Cited by 1 | Viewed by 1356

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 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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