Decoding the mojo of plant-growth-promoting microbiomes

https://doi.org/10.1016/j.pmpp.2021.101687Get rights and content

Highlights

  • Soil Microbiome include microbes of Caulosphere, rhizosphere, Phyllosphere and endosphere.

  • Rhizosphere and Phyllospheric microorganisms enhance plant productivity.

  • Actinobacteria, Bacteroidetes, Firmicutes and proteobacteria as PGPR.

  • Role of PGPR in combating environmental stresses experienced by plants.

Abstract

Farmers, so-called the father of land, have a tremendous responsibility to feed the world. The demand for agricultural yield is constantly surging, and the resources that provide this agricultural yield is limited. This imbalance has forced farmers to treat their crops with chemicals to improve yield. These chemical substances are broadly classified as chemical fertilizers and chemical pesticides. A century ago, these chemicals were thought to be a boon for farmers, and the golden age of chemistry was parallel being witnessed in agriculture. The constant use of these chemicals in soil over several years has ultimately exposed its dark side, as its detrimental impact is well spread from diminishing farmer-friendly nematodes like earth warms to a culprit in causing cancer in vertebrates. Therefore, an alternative to these chemicals is inevitable to be provided in the agriculture system for sustainable development. The answer to this hurdle is obtained in the form of the microbiome of soil that interacts with plants and helps it by symbiotic associations. Some members of microbes found in this microbiome are to be identified that has a positive impact on plant growth and is apotheosized to be used as a biological alternative to chemical fertilizers. Such microbes are broadly classified as Plant-Growth-Promoting Rhizobacteria (PGPR) and Plant-Growth-Promoting Fungi (PGPF) microbiome. The association of such Phyto-friendly microbes is well characterized by researchers globally and is depicted in this review.

Introduction

The Food and Agriculture Organization of the United Nations (FAO) has recently estimated the world's population to reach 10 billion by 2050 [1]. The potential consequences of this may affect the food prices, as the population is expected to grow by 34% over the next three decades. On the other hand, agriculture production is not expected to rise at this pace. Henceforth, there is a dire need to increase agricultural productivity to balance the socio-economic disturbances that may arise due to the population boom [2]. Moreover, the high population explosion is recorded in the developing countries with less per capita income like India, Pakistan, Bangladesh, and China, while in the developed countries, the rise in population is steady but sluggish (U.S, countries of Europe and Japan). Since developed countries consume more protein and meat, it would be essential to produce twice as much food [3]. The possible solution to satisfy increasing agricultural demands will be the use of transgenic crops, improved fertilizers, increasing soil fertility, minimizing disease and seed infections [4]. Many of the mentioned solutions have inherent limitations that are difficult to overcome. Transgenic crops in various countries are banned due to ethical concerns. Likewise, all artificial inventions can deliver positive and negative effects. Biotic and abiotic factors are a major concern that decline global agronomic productivity. Reducing fertile land availability and human population expansion are the two crucial intimidation for agronomic sustainability [5].

The fundamental cause for a major decline in crop yield globally is environmental stress. Abiotic stress like high winds, drought, extreme temperatures, soil salinity, solidification, pH, and acid rain affect the yield and tillage of agronomic plants. Soil salinity and soil solidification are the most devastating environmental stress, which causes major reductions in agriculture land area, plant yield, and panegyric [6]. It is estimated that 50% of arable land will be salinized due to abiotic cause by 2050 [5].

Plants can overcome abundant environmental compression and hostile conditions. They react to these adverse situations through many morphological, biochemical, and molecular mechanisms and interaction among their respective signalling pathways [7]. Phyto-pathogens, pests, parasites, fungi, bacteria, nematodes, and viruses are the pathogens primarily responsible for the plant diseases [8]. In arable land, the constant exposure of the plants to biotic stress leads to changes in plants anabolic and catabolic processes, which eventually results in yield loss and physiological disruption. In such a scenario, a sustainable and effective biotechnological technique that induces interaction between plant root exudates and soil microflora is needed to increase crop productivity and enhance soil health [9]. Epiphytes, endocellular and exocellular microorganisms colonize plants in their natural environment. Microorganisms of the rhizosphere and rhizoplane, especially beneficial bacteria, and fungi, may boost plant response in a stressful environment and improve productivity [10]. Ambient environments, soil characteristics, and microbial composition may have an effect on the rhizospheric microbiota [11].

The plant microbiome refers to the diverse range of beneficial microorganisms associated with plants [12]. In this context, plants can be viewed as superorganisms that rely on their microbiome for specific functions and traits. However, we have limited knowledge about plant-associated microbiome and their effect on crop productivity, growth, health and disease [13]. Plants can exploit the rhizospheric microbiome according to their benefit by selectively inducing microorganisms with the traits that aid development and survival [14]. Whether plants produced secondary metabolites as exudates to ‘cry for help’ or are not ‘just crying’ remains to be addressed [15].

Section snippets

Microbiome

Soil fertility, plant health, growth, production, carbon sequestration, and phytoremediation are all aided by the microbiome colonizing the soil and the plant's surface [16]. Numerous experimental studies suggested that the plant and genotypes of the same crop reports minimal variation in plant microbiome [17]. Interaction among plant-soil microbiome is complex. Recent studies have focused on the pathogenicity of microbial agents like biofertilizer and bioaugmentor, as well as how they use and

Plant growth promotion by microbiome

Abundant microorganisms present in the soil environment. The preliminary focus is given to the rhizospheric microorganisms. The rhizosphere is derived from the Greek word “rhiza”, meaning root. The word rhizosphere is coined by Hiltner. The rhizosphere is the region that connects the plant root, tiny hair, root surrounding soil area, and numerous microbial communities. It is a zone of intensive microbial development following nutrient concentrations in which important macro-micronutrients and

Genetic base of plant-growth-promoting traits

Numbers of Plant-Growth-Promoting rhizobacteria and fungi showing plant helpful properties, genome interpretation showed several genes contributing to plant beneficial functions including nitrogen fixation, phosphate solubilization, siderophore production phytohormones production and induced systemic resistance. According to Ref. [91] analyzed and identified the effect of 23 genes involved in direct and indirect PGPR mechanisms, based on genome sequence identification of 304 different group of

Commercialization of PGPR and PGPF

Preparation of bioformulation should be cautious with microbes because certain variables such as, ageing, price, use, ease in purchase, marketing, compatibility for agronomic use are responsible for damaging their potential. In addition to this, toxigenicity, pathogenicity, allergic nature, sustainability in any environmental condition and gene transfer process should be taken into consideration. Interestingly, the use of rhizobacteria to produce bacterial bioformulation is dependent on the

Conclusion and future prospective

Plant microbiome and their interaction are exceptionally diverse and there are numerous factors that impart its effect on plant health. Scientific evidence emphasizes the significance of the rhizospheric microbiota, such as plant growth-promoting bacteria and fungi, which is beneficial for plant development and yield. According to our knowledge, if we apply bio-formulation and biofertilizer in good proportion, it may help to reduce the loss in crop production and enable pest-free crops with no

Author's contributions

RM and DG contribute to the conception and design of the manuscript. RM and KM compiled the literature and wrote the manuscript. DG and MS reviewed the manuscript.

Funding

We are also thankful for UGC-BSR Research Start-Up-Grant No. F.30-521/2020(BSR) for providing funding.

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

We acknowledge the support provided by Department of Microbiology and Biotechnology, School of Sciences, Gujarat University, DST- FIST sponsored department for providing necessary facilities and research support.

References (159)

  • A. Sumbul et al.

    Azotobacter: a potential bio-fertilizer for soil and plant health management

    Saudi J. Biol. Sci.

    (2020)
  • H. Vainio

    Public health and evidence-informed policy-making: the case of a commonly used herbicide

    Scand. J. Work. Environ. Health

    (2020)
  • P. Adhikari et al.

    Plant growth promotion at low temperature by phosphate-solubilizing Pseudomonas spp. Isolated from high-altitude Himalayan soil

    Microb. Ecol.

    (2021)
  • N.M. Duran et al.

    Bean seedling growth enhancement using magnetite nanoparticles

    J. Agric. Food Chem.

    (2018)
  • S. Pattnaik et al.

    Improvement of rice plant productivity by native Cr(VI) reducing and plant growth promoting soil bacteria Enterobacter cloacae

    Chemosphere

    (2020)
  • P. Shrivastava et al.

    Soil salinity: a serious environmental issue and plant growth promoting bacteria as one of the tools for its alleviation

    Saudi J. Biol. Sci.

    (2015)
  • L. Sharma et al.

    Plant growth-regulating molecules as thermoprotectants: functional relevance and prospects for improving heat tolerance in food crops

    J. Exp. Bot.

    (2020)
  • R. Mushtaq et al.

    Isolation of biotic stress resistance genes from cotton (Gossypium arboreum) and their analysis in model plant tobacco (Nicotiana tabacum) for resistance against cotton leaf curl disease complex

    J. Virol Methods

    (2020)
  • X. Liang et al.

    Proline mechanisms of stress survival

    Antioxidants Redox Signal.

    (2013)
  • B.J.J. Lugtenberg et al.

    Microbe-plant interactions: principles and mechanisms. Antonie van Leeuwenhoek

    Int. J. Gen. Mol .Microbiol.

    (2002)
  • C. Dimkpa et al.

    Plant-rhizobacteria interactions alleviate abiotic stress conditions

    Plant Cell Environ.

    (2009)
  • J.K. Guo et al.

    Prospects and applications of plant growth promoting rhizobacteria to mitigate soil metal contamination: a review

    Chemosphere

    (2020)
  • S. Compant et al.

    A review on the plant microbiome: ecology, functions, and emerging trends in microbial application

    J. Adv. Res.

    (2019)
  • M.M. Howard et al.

    Soil microbiome transfer method affects microbiome composition, including dominant microorganisms, in a novel environment

    FEMS Microbiol. Lett.

    (2017)
  • R. Gupta et al.

    Plant-microbe interactions endorse growth by uplifting microbial community structure of Bacopa monnieri rhizosphere under nematode stress

    Microbiol. Res.

    (2019)
  • H. Alzubaidy et al.

    Rhizosphere microbiome metagenomics of gray mangroves (Avicennia marina) in the Red Sea

    Gene

    (2016)
  • M. Adamczyk et al.

    The soil microbiome of Gloria Mountain summits in the Swiss Alps

    Front. Microbiol.

    (2019)
  • T.Y. Akyol et al.

    Impact of introduction of arbuscular mycorrhizal fungi on the root microbial community in agricultural fields

    Microb. Environ.

    (2019)
  • Y. Fang et al.

    Microbial mechanisms of carbon priming effects revealed during the interaction of crop residue and nutrient inputs in contrasting soils

    Global Change Biol.

    (2018)
  • R. Lal

    The new science of metagenomics: fourth domain of life

    Indian J. Microbiol.

    (2011)
  • S. Bruisson et al.

    Endophytes and epiphytes from the grapevine leaf microbiome as potential biocontrol agents against phytopathogens

    Front. Microbiol.

    (2019)
  • Z. Wei et al.

    The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China

    PLoS One

    (2017)
  • D. Püschel et al.

    Arbuscular mycorrhiza stimulates biological nitrogen fixation in two Medicago spp. through improved phosphorus acquisition

    Front. Plant Sci.

    (2017)
  • G. Berg et al.

    The plant microbiome and its importance for plant and human health

    Front. Microbiol.

    (2014)
  • R. Mendes et al.

    The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms

    FEMS Microbiol. Rev.

    (2013)
  • A.D. Koricha et al.

    Occurrence and molecular identification of wild yeasts from Jimma zone, South west Ethiopia

    Microorganisms

    (2019)
  • R. de Souza et al.

    Plant growth-promoting bacteria as inoculants in agricultural soils

    Genet. Mol. Biol.

    (2015)
  • M. Hernández et al.

    Different bacterial populations associated with the roots and rhizosphere of rice incorporate plant-derived carbon

    Appl. Environ. Microbiol.

    (2015)
  • A. Canarini et al.

    Root exudation of primary metabolites: mechanisms and their roles in plant responses to environmental stimuli

    Front. Plant Sci.

    (2019)
  • U. Vik et al.

    Different bacterial communities in ectomycorrhizae and surrounding soil

    Sci. Rep.

    (2013)
  • J.A. Edwards et al.

    Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice

    PLoS Biol.

    (2018)
  • M. Lang et al.

    Rhizoplane bacteria and plant species Co-determine phosphorus-mediated microbial legacy effect

    Front. Microbiol.

    (2019)
  • G. Wieland et al.

    Variation of microbial communities in soil, rhizosphere, and rhizoplane in response to crop species, soil type, and crop development

    Appl. Environ. Microbiol.

    (2001)
  • J. Mercado-Blanco et al.

    Belowground microbiota and the health of tree crops

    Front. Microbiol.

    (2018)
  • C.M. Timm et al.

    Abiotic stresses shift belowground populus-associated bacteria toward a core stress microbiome

    mSystems

    (2018)
  • C.H. Goh et al.

    The impact of beneficial plant-associated microbes on plant phenotypic plasticity

    J. Chem. Ecol.

    (2013)
  • A. Beneduzi et al.

    Plant growth-promoting rhizobacteria (PGPR): their potential as antagonists and biocontrol agents

    Genet. Mol. Biol.

    (2012)
  • M. Perazzolli et al.

    Resilience of the natural phyllosphere microbiota of the grapevine to chemical and biological pesticides

    Appl. Environ. Microbiol.

    (2014)
  • F. Bringel et al.

    Pivotal roles of phyllosphere microorganisms at the interface between plant functioning and atmospheric trace gas dynamics

    Front. Microbiol.

    (2015)
  • P.A.H.M. Bakker et al.

    The rhizosphere revisited: root microbiomics

    Front. Plant Sci.

    (2013)
  • D. Goswami et al.

    Portraying mechanics of plant growth promoting rhizobacteria (PGPR): a review

    Cogent Food Agric.

    (2016)
  • B.R. Glick

    Plant growth-promoting bacteria: mechanisms and applications

    Scientifica (Cairo)

    (2012)
  • S. Farhangi-Abriz et al.

    How can salicylic acid and jasmonic acid mitigate salt toxicity in soybean plants?

    Ecotoxicol. Environ. Saf.

    (2018)
  • S. Liu et al.

    Influence of biochar application on potassium-solubilizing Bacillus mucilaginosus as potential biofertilizer

    Prep. Biochem. Biotechnol.

    (2017)
  • D. Patel et al.

    Phosphorus Solubilization and Mobilization: Mechanisms, Current Developments, and Future Challenge

    (2020)
  • M. Ahemad et al.

    Alleviation of fungicide-induced phytotoxicity in greengram [Vigna radiata (L.) Wilczek] using fungicide-tolerant and plant growth promoting Pseudomonas strain

    Saudi J. Biol. Sci.

    (2012)
  • G. Kudoyarova et al.

    Phytohormone mediation of interactions between plants and non-symbiotic growth promoting bacteria under edaphic stresses

    Front. Plant Sci.

    (2019)
  • D.A. Korasick et al.

    Auxin biosynthesis and storage forms

    J. Exp. Bot.

    (2013)
  • D. Goswami et al.

    Screening of PGPR from saline desert of Kutch: growth promotion in Arachis hypogea by Bacillus licheniformis A2

    Microbiol. Res.

    (2014)
  • D. Patel et al.

    Profiling indolic auxins produced by the strains of Aspergillus using novel HPTLC technique

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