Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere

Ayiti, Oluwatobi Esther; Babalola, Olubukola Oluranti

doi:10.1007/s00203-022-02857-2

Cited by 4 publications

(6 citation statements)

References 52 publications

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“…Regarding the functional profiles of rhizosphere microbial communities, PICRUSt and MG-RAST have been used in several studies to identify enzymatic activities involved in the metabolic processes in the rhizosphere bacterial communities [87][88][89]. Considering the top 50 most abundant enzymatic functions from both approaches, several common metabolic functions were identified, including some directly associated with genes/enzymes involved in various metabolic processes and biological functions related to lipid synthesis and degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis.…”

Section: Discussionmentioning

confidence: 99%

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

Muñoz-Ramírez,

González-Escobedo,

Avila-Quezada

et al. 2024

Agronomy

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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.

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Section: Discussionmentioning

confidence: 99%

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

Muñoz-Ramírez,

González-Escobedo,

Avila-Quezada

et al. 2024

Agronomy

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“…The sampling area and procedure are the same as described in Ayiti, et al [17]. The samples were collected from the 32-years old maize plantation of the North-West University, Molelwane, Mahikeng, South Africa (25 • 47 23.9604 S, 25 • 37 8.43348 E; altitude 1012 m Figure 1).…”

Section: Samplingmentioning

confidence: 99%

“…As reported by Ayiti, Ayangbenro, and Babalola [17], physical and chemical properties of the soils were measured using standard chemical analysis. The particle size (sand, silt, and clay) distribution was evaluated using the method of Kroetsch [18].…”

Section: Physio-chemical Analysis Of the Rhizosphere And Bulk Soilmentioning

confidence: 99%

“…The DNA extraction and 16S amplicon sequencing are the same as described by Ayiti, Ayangbenro and Babalola [17]. DNA was extracted using a Nucleospin soil DNA extraction kit (Macherey-Nagel, Duren, Germany) following the manufacturer's instructions.…”

Section: Dna Extraction and 16s Amplicon Sequencingmentioning

confidence: 99%

“…The data normalization tool was applied to reduce experimental error. Default parameters were used for the bioinformatics tools [17]. The abundance of bacterial and archaeal communities at different growth stages was evaluated.…”

Section: Metagenome Assembly and Gene Annotationmentioning

confidence: 99%

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16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors

Ayiti

Babalola

2022

Agriculture

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Nitrifying bacteria and archaea are ubiquitous and can transform ammonia locked up in soil or manure into nitrate, a more soluble form of nitrogen. However, nitrifying bacteria and archaea inhabiting maize rhizosphere have not been fully explored. This study evaluates the diversity and abundance of nitrifying bacteria and archaea across different growth stages of maize using 16S amplicon sequencing. Moreover, the influence of environmental factors (soil physical and chemical properties) on the nitrifying communities was evaluated. Rhizosphere soil DNA was extracted using Nucleospin Soil DNA extraction kit and sequenced on Illumina Miseq platform. MG-RAST was used to analyze the raw sequences. The physical and chemical properties of the soil were measured using standard procedure. The results revealed 9 genera of nitrifying bacteria; Nitrospira, Nitrosospira, Nitrobacter, Nitrosovibrio, Nitrosomonas, Nitrosococcus, Nitrococcus, unclassified (derived from Nitrosomonadales), unclassified (derived from Nitrosomonadaceae) and 1 archaeon Candidatus Nitrososphaera. The Nitrospirae phyla group, which had the most nitrifying bacteria, was more abundant at the tasselling stage (67.94%). Alpha diversity showed no significant difference. However, the Beta diversity showed significant difference (p = 0.01, R = 0.58) across the growth stages. The growth stages had no significant effect on the diversity of nitrifying bacteria and archaea, but the tasselling stage had the most abundant nitrifying bacteria. A correlation was observed between some of the chemical properties and some nitrifying bacteria. The research outcome can be put into consideration while carrying out a biotechnological process that involves nitrifying bacteria and archaea.

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Microbial regulation of aggregate stability and carbon sequestration under long-term conservation tillage and nitrogen application

Zhang,

Song,

et al. 2024

Sustainable Production and Consumption

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Relationship between nitrifying microorganisms and other microorganisms residing in the maize rhizosphere

Cited by 4 publications

References 52 publications

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

16S Amplicon Sequencing of Nitrifying Bacteria and Archaea Inhabiting Maize Rhizosphere and the Influencing Environmental Factors

Microbial regulation of aggregate stability and carbon sequestration under long-term conservation tillage and nitrogen application

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