The fungal and archaeal community within plant rhizosphere: a review on their contribution to crop safety

Akinola, Saheed Adekunle; Babalola, Olubukola Oluranti

doi:10.1080/01904167.2020.1845376

Cited by 27 publications

(26 citation statements)

References 123 publications

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“…Compared to fungi and bacteria, little is known regarding the ecological roles of archaea inhabiting plant microbiomes, because most of them remain undetectable when using conventional culture-based methods. In the last few years, next-generation sequencing methods, as well as omics (i.e., metabolomics, metatranscriptomics, and metagenomics), have greatly increased the number of studies assessing archaeal communities, as well as their roles in plant proximity [17]. Consequently, the archaeal community is now considered as an important component of the plant rhizosphere microbiome [16][17][18].…”

Section: Archaeal Communitiesmentioning

confidence: 99%

“…In the last few years, next-generation sequencing methods, as well as omics (i.e., metabolomics, metatranscriptomics, and metagenomics), have greatly increased the number of studies assessing archaeal communities, as well as their roles in plant proximity [17]. Consequently, the archaeal community is now considered as an important component of the plant rhizosphere microbiome [16][17][18]. Although the relationships between archaea and plants remain largely unclear, their ubiquitous occurrence on healthy plants has been suggested to reflect positive interactions between both partners [16].…”

Section: Archaeal Communitiesmentioning

confidence: 99%

“…Induced systemic resistance (ISR) would also enhances plant resistance against trace elements (TEs) and organic pollutants [15]. Archaea are now considered as other important components of the plant microbiome [16][17][18]. Although less is known about their relations with plants, it is assumed that they would interact positively due to their ubiquitous occurrence within the microbiome of healthy plants [16].…”

Section: Introductionmentioning

confidence: 99%

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Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

Faubert

Labrecque

Hijri

2022

JoF

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There is a growing interest in plant microbiome’s engineering to optimize desired functions such as improved phytoremediation. This study is aimed at examining the microbial communities inhabiting the roots and rhizospheres of two Salix miyabeana cultivars that had been grown in a short-rotation intensive culture (SRIC) system for six years in a soil contaminated with the discharge from a petrochemical factory. DNA was extracted from roots and rhizospheric soils, and fungal ITS and bacterial and archaeal 16S rDNA regions were amplified and sequenced using Illumina MiSeq technology. Cultivars ‘SX61’ and ‘SX64’ were found to harbor a similar diversity of fungal, bacterial, and archaeal amplicon sequence variants (ASVs). As expected, a greater microbial diversity was found in the rhizosphere biotope than in the roots of both cultivars, except for cultivar ‘SX64’, where a similar fungal diversity was observed in both biotopes. However, we found that microbial community structures were cultivar- and biotope-specific. Although the implication of some identified taxa for plant adaptability and biomass production capacity remains to be explored, this study provides valuable and useful information regarding microbes that could potentially favor the implantation and phytoremediation efficiency of Salix miyabeana in mixed contamination sites in similar climatic environments.

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Section: Archaeal Communitiesmentioning

confidence: 99%

Section: Archaeal Communitiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

Faubert

Labrecque

Hijri

2022

JoF

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“…Rhizobium bacteria form a symbiotic relationship with roots of legume crop that results in N fixation, as well as increased uptake of P and macronutrients by the plant and reduced impact of stress factors ( Nadeem et al., 2009 ). Symbiotic bacteria may also promote plant growth by supplying additional N through atmospheric N 2 fixation, producing phytohormones (auxins, cytokinins, and gibberellins), and releasing anti-microbial molecules to shield crops from diseases ( Afkhami et al., 2021 ; Akinola and Babalola, 2020 ; Barka et al., 2016 ; Díez-Méndez and Menéndez, 2021 ; Flores-Félix et al., 2019 ; Khan, 2005 ; Lindstrom and Mousavi, 2019 ; Menendez and Paço, 2020 ; Mupambwa et al., 2018 ; Murali et al., 2021 ; Siqueira et al., 2020 ). In the past, farmers have widely used earthworms and organic fertilizers to boost soil productivity ( Rashid et al., 2013 , 2014a , 2014b , 2016 ; Shah et al., 2013 ), and these practices have proven to be beneficial to agro-ecosystems.…”

Section: Importance Of Microbial Community To Soil Fertility and Sustainabilitymentioning

confidence: 99%

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Lahlali

Ibrahim

Belabess

et al. 2021

Heliyon

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Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.

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“…Despite the tiny nature of fungi, for example, Penicillium notatum has been used as an invaluable source of novel metabolite compounds and broad-spectrum antibiotics, as credited to Alexander Fleming in the discovery of penicillin [ 4 ]. Since then, this antibiotic has continued to dominate the market and has also awakened the consciousness of scientists in the search for bioactive metabolites from fungi inhabiting the soil (rhizosphere) or plant endosphere [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Pharmacological Potential of Fungal Endophytes Associated with Medicinal Plants: A Review

Adeleke

Babalola

2021

JoF

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Endophytic microbes are microorganisms that colonize the intracellular spaces within the plant tissues without exerting any adverse or pathological effects. Currently, the world population is facing devastating chronic diseases that affect humans. The resistance of pathogens to commercial antibiotics is increasing, thus limiting the therapeutic potential and effectiveness of antibiotics. Consequently, the need to search for novel, affordable and nontoxic natural bioactive compounds from endophytic fungi in developing new drugs with multifunction mechanisms to meet human needs is essential. Fungal endophytes produce invaluable bioactive metabolic compounds beneficial to humans with antimicrobial, anticancer, antidiabetic, anti-inflammatory, antitumor properties, etc. Some of these bioactive compounds include pestacin, taxol, camptothecin, ergoflavin, podophyllotoxin, benzopyran, isopestacin, phloroglucinol, tetrahydroxy-1-methylxanthone, salidroside, borneol, dibenzofurane, methyl peniphenone, lipopeptide, peniphenone etc. Despite the aforementioned importance of endophytic fungal metabolites, less information is available on their exploration and pharmacological importance. Therefore, in this review, we shall elucidate the fungal bioactive metabolites from medicinal plants and their pharmacological potential.

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The fungal and archaeal community within plant rhizosphere: a review on their contribution to crop safety

Cited by 27 publications

References 123 publications

Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

Ectomycorrhizal Fungi Dominated the Root and Rhizosphere Microbial Communities of Two Willow Cultivars Grown for Six-Years in a Mixed-Contaminated Environment

High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects

Pharmacological Potential of Fungal Endophytes Associated with Medicinal Plants: A Review

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