Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Babalola, Olubukola Oluranti; Emmanuel, Obianuju Chiamaka; Adeleke, Bartholomew Saanu; Odelade, Kehinde Abraham; Nwachukwu, Blessing Chidinma; Ayiti, Oluwatobi Esther; Adegboyega, Taofeek T.; Igiehon, Nicholas O.

doi:10.1007/s00284-021-02375-2

Cited by 45 publications

(25 citation statements)

References 175 publications

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“…Therefore, the taxonomic composition of soil organisms reflects the environmental conditions of soils. Soil biota, especially microbiome, is influenced by plants (crops) [ 2 , 3 ]. Thus, quantitative information on the taxa of soil organisms is useful for assessing soil environments, including agricultural soils.…”

Section: Introductionmentioning

confidence: 99%

Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

et al. 2021

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Nematodes are abundant metazoans that play crucial roles in nutrient recycle in the pedosphere. Although high-throughput amplicon sequencing is a powerful tool for the taxonomic profiling of soil nematodes, polymerase chain reaction (PCR) primers for amplification of the 18S ribosomal RNA (SSU) gene and preparation of template DNAs have not been sufficiently evaluated. We investigated nematode community structure in copse soil using four nematode-specific (regions 1–4) and two universal (regions U1 and U2) primer sets for the SSU gene regions with two DNAs prepared from copse-derived mixed nematodes and whole soil. The major nematode-derived sequence variants (SVs) identified in each region was detected in both template DNAs. Order level taxonomy and feeding type of identified nematode-derived SVs were distantly related between the two DNA preparations, and the region U2 was closely related to region 4 in the non-metric multidimensional scaling (NMDS) based on Bray-Curtis dissimilarity. Thus, the universal primers for region U2 could be used to analyze soil nematode communities. We further applied this method to analyze the nematodes living in two sampling sites of a sweet potato-cultivated field, where the plants were differently growing. The structure of nematode-derived SVs from the two sites was distantly related in the principal coordinate analysis (PCoA) with weighted unifrac distances, suggesting their distinct soil environments. The resultant ecophysiological status of the nematode communities in the copse and field on the basis of feeding behavior and maturity indices was fairly consistent with those of the copse- and the cultivated house garden-derived nematodes in prior studies. These findings will be useful for the DNA metabarcoding of soil eukaryotes, including nematodes, using soil DNAs.

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Section: Introductionmentioning

confidence: 99%

Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

et al. 2021

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“…Studies have shown that plants release bioactive compounds into the rhizospheres to modulate the soil environ in their favor, and also to attract rhizosphere microbial community required for their fitness in the ecosystem (Hu et al, 2018;Zhalnina et al, 2018). Some of the released metabolites attract antibiotic-producing microorganisms needed as weapons against existing plant pathogens (Babalola et al, 2021;Hu et al, 2018;Schulz-Bohm et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Antibiotic-producing bacteria isolated from some natural habitats in the Federal Capital Territory (FCT), Nigeria

Olasinbo¹,

Sylvanus²,

Peters³

2022

Afr. J. Microbiol. Res.

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High global prevalence of multidrug-resistant bacteria due to antibiotics misuse has prompted the need for novel antibacterial compounds to replace the failing antibiotics. This study investigated some natural habitats in Abuja, Nigeria, for antibiotics-producing bacteria. Thirty-six soil samples from termite mounds, river banks and rhizospheres of Anacardium occidentale L. (cashew tree), Gmelina arborea Roxb. ex Sm. (beechwood), Ageratum conyzoides L. (goat weed) including Cymbopogon citratus (DC) Stapf. (lemon grass) were cultured on nutrient media. Twelve potential antibiotic-producing isolates were identified by crowded plates method and characterized using Bergey's manual. The antimicrobial activities of the filtrates from the isolates against some pathogenic strains namely Streptococcus pneumonia, Salmonella typhi, Escherichia coli (ATCC 25922), Proteus mirabilis, Staphylococcus aureus (ATCC 25923), Candida albicans, Bacillus subtilis and Pseudomonas aeruginosa (ATCC 27853) were determined by agar-well diffusion method. Only 5 eventually inhibited at least 1 test microorganism; 4 showed activities against both Gram-positive and Gram-negative bacteria (broad spectrum) and 2 among the 4 also inhibited Candida albicans, while the remaining 1 inhibited only 1 Gram-positive bacterium (narrow spectrum). The 5 potent antibiotics-producers were Bacillus spp. In conclusion, some natural habitats in the FCT are important sources of antibiotic-producing bacteria. Their antimicrobial lead compounds could be extracted and developed locally for pharmaceutical applications.

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“…17 different genera have been identified by this study, and the high genetic diversity is probably due to multitude elements ( Macdonald and Singh, 2014 , Nwachukwu and Babalola, 2021 ). PGPR are agriculture bioresources that enhance both plant growth and productivity, these Plant microbiomes have a direct impact on noxious microbes in the rhizosphere, and many beneficial microorganisms isolated from soil could boost the defensive capacity of the plant ( Zamioudis and Pieterse, 2012 , Babalola et al, 2021 ). The studies of bacteria strains naturally associated with dried fruit are limited ( Nyanga et al, 2007 , Ribeiro et al, 2014 ) and the fruit flora commonly includes yeasts and molds ( Qadri et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

Abid

Smiri

Federici

et al. 2022

Saudi Journal of Biological Sciences

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Rhizosphere Microbiome Cooperations: Strategies for Sustainable Crop Production

Cited by 45 publications

References 175 publications

Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

Use of universal primers for the 18S ribosomal RNA gene and whole soil DNAs to reveal the taxonomic structures of soil nematodes by high-throughput amplicon sequencing

Antibiotic-producing bacteria isolated from some natural habitats in the Federal Capital Territory (FCT), Nigeria

Diversity of rhizospheric and endophytic bacteria isolated from dried fruit of Ficus carica

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