Research Article

The Role of Soil Microbes in Promoting Plant Growth  

Sheng Li1 , Mu Peng1 , Zhi  Liu1 , Syed Sadaqat Shah2
1 Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
2 Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, China
Author    Correspondence author
Molecular Microbiology Research, 2017, Vol. 7, No. 4   doi: 10.5376/mmr.2017.07.0004
Received: 09 Nov., 2017    Accepted: 09 Dec., 2017    Published: 15 Dec., 2017
© 2017 BioPublisher Publishing Platform
This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Li S., Peng M., Liu Z., and Shah S.S., 2017, The role of soil microbes in promoting plant growth, Molecular Microbiology Research, 7(4): 30-37 (doi: 10.5376/mmr.2017.07.0004)


More and more food is needed all over the world in order to meet rapidly growing population demands, while the modern agriculture on increasing output has already reached its limit. It is badly in need to cultivate new crop varieties for increase the yield and resistant to environmental stress and insects. However, crops are still need to provide the necessary fertilizer nutrients which is insufficient in soil. Recently, many evidences showed that soil microbes provide an opportunity for reducing agricultural demand in inorganic fertilizer. Microorganisms, due to their huge gene pool, are also used for a potential resource in biochemical reactions, which recycle nutrients for plant growth. Therefore, we need to modify and better use of soil microbiota to promote plant growth. In this review, we mainly summarized the role of soil microbiota by explaining the ecological balance, nitrogen fixation, nutrient elements, interactions and communication medium.

Plant; Soil microbiota; Interaction; Nitrogen fixation


Food is a key element to all life activities in the world (Haan and Velthuis, 2002). Both plants and soil microbiota must uptake nutrients to support their daily living activities. Along with the metabolism process, they absorb nutrients from soil and excrete metabolites to soil similarly. But, the influence between plants and soil microbiota is not clearly study. Plants are still provided the necessary fertilizer nutrients which is usually insufficient in soil (Caldwell et al., 1974).


Since Lorenz Hiltner first put forward the term of ‘rhizosphere’ to describe the effect of plant root secretion on edaphon, plant-microbe interactions have attracted growing interest from last century due to their critical role in promoting plant growth (Hütsch et al., 2002; Hartmann et al., 2008). The rhizosphere is a very special and narrow zone of soil that is influenced by plant root system (Giri et al., 2005). The physical, chemical and biological traits of rhizosphere are significant difference with their surrounding soil (Kim et al., 2010). Organic acids from the root exudates account for about 30% in the rhizosphere, and its compositions include simply carbohydrates, amino acid and complexity nutrients, which supply for plant growth (Sandnes et al., 2005). Thus, the number of microorganisms and invertebrates around rhizosphere are higher than that in bulk soil. Rhizosphere microbes are regarded as the second set of genome in plant and play key roles in promoting plant growth and development, nutrient acquisition, inhibition of fungal plant pathogens (Nihorimbere et al., 2011; Pérez et al., 2016).


It is noteworthy that the structure of bacterial microbiota is a heritable trait, which was verified in the rhizosphere of Arabidopsis and wheat, suggesting that its population could accelerate or suppress plant growth (Donaldson et al., 2016). Published findings widely confirmed that soil microorganisms play a crucial role in recycling of nutrients and organic compounds (Rai et al., 2016). Although fungal phytopathogens appear to be the cause of plant yield reduction, the richness of these pathogens could reduce in ‘suppressive soil’ (Löbmann et al., 2016). Note that in some edaphophyte that initially susceptible to fungal attack and suffer declined production might be able to resistant to these attacks in subsequent years. Therefore, a comprehensive study is needed to investigate whether soil microbe is responsible for the inhibition of pathogens.


Likewise, many researches demonstrated that mixed cropping leaded to an improvement in the fertility of the soil and increased in crop yield (Iijima et al., 2016; Syakir et al., 2016). The possible reason for this advantage is that the different root exudates year after year weaken the specific plant host pathogens in crop rotation. Interestingly, even though monoculture shows a decline in crop yield, Hilton et al. still detected an increase in the abundance of two fungi pathogens, Olpidium brassicae and Pyrenochaeta lycopersici, which possibly arising a soil suppressiveness effect. In forestry, mixed forest not only has obvious economic and social benefits, but also has hidden ecological benefits (Hilton et al., 2013). Although supply sufficient fertilizer and the same cultivation measure, crop yield is still annual decline with long-term monoculture caused by the accumulation of harmful substance in rhizosphere (Lampurlanés et al., 2016).


It is an important target in the study of plant rhizosphere microbes to providing the necessary microelement and macroelement for plant using the ability of microbes. Therefore, we mainly summarized the nitrogen, phosphorus and iron fixations by microbes.


1 Ecological Balance between Plant and Microbe

Microbial metabolism accelerates the decomposition of organic matter, promotes the mineralization of nutrients, and stimulates nutrients absorbed by plant. Carbon dioxide efflux from the soil derived from two distinct aspects, including rhizosphere respiration that contains root and microbial respirations, and microbial decomposition of soil organic matter (Cheng et al., 2005). The decomposer activity of soil microbial biomass is an important ecosystem trait to maintain the recycling and stabilization of nutrients.


The curious relationship between plant and microbe is helping and competing based on ecological balance level. Some microbes could promote plant growth. For example, rhizosphere microbes provide soluble phosphate through dissolving phosphate in mineral, enhancing the uptake of phosphate by plant (Pingale and Virkar, 2017). Synthesizing a variety of auxin and plant hormone, which promote plant growth and expedite seed germination and roots development (Li et al., 2016). The secreted antibiotics by bacteria prevent plant to avoid being harmed by pathogens infection or directly kill pathogens and also to establish a collaborative relationship with other microbes. Or helping transfer radiation material and harmful substances such as heavy metals in plants. Additionally, rhizosphere microbes produce carbon dioxide, increasing calcium solubility (Gschwendtner et al., 2016; Huang et al., 2017). Importantly, nirtogen-fixing bacteria in rhizosphere could fix nitrogen to provide plants with organic and inorganic nitrogen (Zheng et al., 2016).


However, microbes also compete mineral nutrition with plant, for a certain period of time, leading reduced nutrient supply for plant and nutrient losses as denitrifying bacteria convert nitrogenous substance into nitrogen (Bonnet et al., 2016). Due to the different selectivity of rhizosphere, some pathogenic bacteria in the corresponding plant rhizosphere gradually accumulate, resulting in the occurrence of disease.


2 The Ability of Endophytic Bacteria on Nitrogen Fixation

In the course of life activity process, microbes transform the inert atmosphere of nitrogen into ionic nitrogen, which could be directly absorbed by plant, ensuring the nitrogen nutrition for plant growth. Nodules as a very effective method for nitrogen assimilation have been widely researched in recently years (Coruzzi et al., 2016). However, it is only confined to a small number of plants such as leguminous and actinorhizal plants.


Legume nodulation is regarded as a complex plant microbial exchange, which explains that why only a limited number of bacterial species nodule in some plant species. The interaction of endogenous bacteria does not seem to be very stringent, therefore, nitrogen-fixing endophytes could widely colonize in plant hosts (Chen et al., 2017). This feature makes it possible to play a special value on the study of endophytic bacteria and model plants, but it can also be applied to crop plants. For example, Rhizobium IRBG74 and nitrogen-fixing rhizobia are isolated from wetland plants, but also can infect rice roots (Mitra et al., 2016).


Although there is direct evidence that endogenous N-fixers provide nitrogen compounds for their hosts, this is not enough. However, it is generally accepted that the process of offering is very possible. For example, a non-immobilized nitrogen can not promote the growth of its plant host (sugarcane) compared to wild type (Li et al., 2017). Sugarcane is a nutrient-demanding, fast-growing, C4 photosynthetic plant. Due to its high biomass growth rate and sugar content, it has become an important biofuel crop. Acetobacter pylori Pal5, an endophytic bacterium in sugarcane roots, stems and leaves, is the same bacterial subfamily as Alphaproteobacteria-rhizobia, but it is a different species (Rhodospirillum) (Bontemps et al., 2016). This strain not only fixes atmospheric nitrogen, but also with the ability of anti-fungal and anti-bacterial to plant pathogens, such as Fusarium and Xanthomonas. Genome sequencing confirmed that Acetobacter sp. Pal5 was able to promote plant growth (Oliveira et al., 2016). Possibly due to its relatively small genome size, it has to dependent on its plant host closely to sustain life.


Many researchers are interested in endophytic bacteria and their function in plants (Fidalgo et al., 2016). These organisms may help to increase plant biomass and nutrient uptake. However, we still need to know more detailed information about them, and select the most promising microbial strains, which may be specific for plants and soils. In addition, in order to commercialize the use of endophytic bacteria, it is vital to determine its impact on the environment. Using them to enhance crop growth also requires detailed understanding of its potential impact on human health.


3 Releasing Nutrient Elements in Insoluble Mineral Substance

The limiting factors in plant growth are phosphorus, nitrogen and, to a lesser extent, iron (Zhonglian et al., 2016). These are nutrients acquired by plants from soil directly or using microorganisms as fixer or soil scavengers. The most common and important example is the symbiotic interactions between mycorrhizal fungi and plant roots, in which fungi is especially important in providing phosphorus for plant host, in return for carbon for fungus. Although phosphorus is rich in soil, it is still a limiting factor in plant growth, because it is associated with aluminum and iron (form strengite and varescite, respectively), or form apatite with calcium under acidic or alkaline conditions. However, plants require soluble phosphate with the form of H2PO4 or HPO4 (Ponomareva et al., 2017). Some bacteria could release organic acids that chelate cation to form phosphoric acid releasing into soil. However, it is not enough for plants to achieve all the necessary phosphate (especially in acid soils), therefore, phosphate supplied by mycorrhizal fungi is particularly crucial. In addition to nitrogen and phosphorus, iron as another element that plant absorb depending on soil microbes. Arthrobacterium, Azospirillum, Pseudomonas and Bacillus, which termed ‘plant growth promoting rhizobacteria’ (PGPR), produce some organic matter and stimulate the growth of plant (Rodríguez and Fraga, 1999). A group of PGPR strains sequestrate insoluble Fe3+ from rhizosphere by siderophores, which improve the plant growing condition and then promote plant growth. Plants absorb iron by bacterial siderophores, even though bacteria secrete iron cells, while these cells with iron-binding capacity are very weak.


Microbes in soil can dissolve insoluble mineral complexes into soluble compounds during its lifetime, so as to help plant uptake various mineral elements. Soils were found a lot of potassium-solubilizing bacteria (PSB) and phosphobacteria with the ability of releasing ineffective phosphorus and potassium. The number of PSB and phosphobacteria is affected by soil physical properties, organic content, soil type and fertility, and tillage methods (Shao et al., 2016). To date, PSB were mainly found in those species of Bacillus, Pseudomonas, Escherichia, Erwinia and Thiobacillus. Published findings demonstrated that the mechanism of phosphate-solubilizing microorganisms was reported to dissolve insoluble phosphates by the production of organic acids which both reduced pH value in soil and combined iron and aluminum (Deb et al., 2016). Additionally, previous experiments showed conclusively that phosphate solubilization using bacteria was one of the most important ways for promoting plant growth under a low-fertility soil. Arbuscular mycorrhizal fungi (AMF) together with soil bacteria could synergistically facilitate the uptake of phosphorus in plants. Zhang et al. (Zhang et al., 2014) proved the hyphosphere interactions between an AM fungus (Rhizophagus irregularis) and PSB (Pseudomonas alcaligenes) on phytate mineralization using nylon mesh barrier. Sole inoculation with AM fungus or PSB increased acid phosphatase activity in soil. Their results indicated that the mineralization of soil phytate was promoted by the interaction between the AM fungus and its hyphosphere PSB.


A lot of nitrogen ion is needed to synthesize compounds in plant during their growth and development process. It was hard for scientists to understand where is the source of nitrogen ion. This problem cannot be illuminated until 1886 when scientists detected nitrogen-fixing microorganism from the extract of soybean root nodules. The families of nitrogen-fixing bacteria (NFB) consist of more than one hundred of prokaryotes (Semenov et al., 2016). Generally, the symbiotic relationship between NFB and its host belongs to one-to-many relationship (Boya P et al., 2017). The initial product of assimilation with carbon dioxide is malic acid or aspartic acid in symbiotic NFB related to C4 plants, which the fixation efficiency was higher than that in C3 plant with the 3-phosphoglyceric acid. These NFB metabolized atmospheric nitrogen into absorbable nitrogen ion, and improved the ion content in soil, providing a large number of nitrogen for plant growth and development. In addition, the content of potassium and phosphorus in soil is far from the demand for plant growth. Plant, therefore, absorb these elements from mineral substance with the help of phosphate- and potassium-solubilizing bacteria. It is worth mentioning that these bacteria not only have position effects on plant growth, but also a positive influence in soil property. Manganese is an irreplaceable element and absolutely necessary for life activities, metabolism, compounds synthesis in plant. Scientists found that PGPR could promote plant absorption in manganese, and also produce IAA and ABA to lose the cell wall and increase cell volume after a series of action (Sakurai and Masuda, 1977).


The interaction between bacteria and AMF is important regulating effect in soil nitrogen cycle. AMF colonization might alter root exudates and indirectly affect soil bacterial community structure. Ammoxidation is a clean and environmentally benign process in regulating soil N cycling and involved by autotrophic ammonia-oxidizing bacteria (AOB). Previous findings demonstrated that AOB were weak competitors for ammonium compared with AMF (Juliette et al., 1993). This could partly explain that AMF inhibited AOB growth and limited ammonia oxidation, thus, reducing the content of NO3- (Bollmann et al., 2002). The published paper also showed that AMF could induce a reduction in N2O emissions in soil by increasing N immobilization into plant biomass, reducing the concentrations of mineral soil N (Bender et al., 2014). In addition, the abundance of N2O production was negatively correlated with AMF abundance, whereas N2O consumption was positively, indicating that the regulation of N2O emissions influenced by AMF changes in soil microbial community.


4 Interactions between Plants and Mycorrhizal Fungi

It is estimated that the majority of land plants have been found the mutualistic associations with AMF, a dominant group of soil fungi, in which donate carbon for plants and, in return, receive benefits such as phosphate and other nutrient uptake. AMF thrive in the form of spores in soil until they attach plant as they are incapable of completing their life cycle independently (Tkacz and Poole, 2015). They germinated and released hyphae in the vicinity of host roots, and then hyphal branching stimulated in response to plant strigolactones. After detected plant, they formed the appressorium which used to penetrate the plant root using sulphated and non-sulphated lipochitooligosaccharides signal, then formed nutrient exchange structures (Akiyama et al., 2005; Maillet et al., 2011). Eventually, AMF formed branched hyphae in cortical cell, which were surrounded by plant plasma membrane.


AMF include a member of soil fungi belonging to Glomeromycota. However, up to now, Geosiphon pyriformis is the only known member of a fungus living in endocytobiotic association with a cyanobacterium, Nostoc punctiforme, on the surface and in the upper layer of wet soils with inorganic nutrients. Thus, the Geosiphon endocyanosis could serve as a model system for AM research. When this fungal hypha detected with free-living Nostoc cells, and incorporated together at the hyphal tip. At the junction, swell parts gradually formed the irregular structure, and thereafter transformed into a unicellular ‘bladder’ on the soil surface (Schüßler and Kluge, 2001). However, none of these fungi has been cultivated without their plant hosts in laboratory test, leading to slow progress in the research of phylogenies (Redecker and Raab, 2006).


Plant growth-promoting rhizobacteria (PGPR) were termed firstly by Klopepper and Schroch in 1978, which have the ability to improve plant growth, diseases resistance, and improvement in yields. Inoculation with both Pseudomonas putida and versicular-arbuscular mycorrhizal (VAM) fungi in subterranean clover (Trifolium subterraneum L.), plant growth, root dry weight and nodulation significantly increased after 12 weeks, compared to PGPR or VAM fungi alone (Meyer and Linderman, 1986). However, must but not all interactions between mycorrhizal fungi were mutualistic. Their interactions might be inhibitory or stimulatory (Fitter and Garbaye, 1994). Domenech et al. co-inoculated Pisolithus tinctorius and Bacillus spp. with oak, and their findings illustrated that only B. licheniformis promoted the growth of oak seedlings, and inhibited fungal growth using ergosterol/chitin analysis, suggesting that B. licheniformis has a positive effect on oak growth. However, the co-inoculation of either bacterial strain with P. tinctorius had a negative effect on plant growth, indicating no synergistic effect in those microbes. As shown by phospholipid fatty acid profiles, the inoculation caused a slight alteration in the microbial community structure of rhizosphere, both in the total community and the culturable populations (Domenech et al., 2004). The interactions between different PGPR in rhizosphere and mycorrhiza fungi were significant difference, in which regularities of population distribution was not consistent. Previous evidence suggested that AMF could inhibit other fungi or stimulate synergistic effect in combination with specific fungi. For example, the microbial co-inoculation effect with Glomus mosseae and Penicillium thomii was positive on English mint (Mentha piperita L.) growth (Cabello et al., 2005).


5 Communication Medium between Plants and Soil Microbes

Plant secretions are a platform for communication between plants and soil microbes. Up to 21% of carbon fixation secrete by plant roots, indicating that plant may supply resources for the plant-microbial interactions. Thus, plant can actively secrete compounds and modify rhizosphere microbes.


When the Arabidopsis ABC transporter is mutated, the bacterial and fungal microbial populations of its rhizosphere microbes will be changed when compared with wild type (Badri et al., 2009). However, the other comprehensive study showed that the exudate of Arabidopsis, such as phenolic compounds, amino acids, sugar alcohols and sugars, could also change the soil microbes (Dayakar et al., 2013). This may be the reason that plant utilize metabolic secretions to recruit beneficial microbes and inhibit pathogens. For example, tomato can conditionally change their secretions if the pathogen is Fusarium oxysporum (a natural biological control of fungi) (Bao and Lazarovits, 2001).


Many studies have focused on comparative analysis of rhizosphere microbes in different plants. Therefore, the detailed rhizosphere microbial population structure has been obtained in potatoes, rice, maize, wheat, oats, peas and some important economically significant plants. Different plants specifically chose different soil microbes (Grayston et al., 1998). As we know, β-mycobacteria and Pseudomonas are selected in the potato rhizosphere, while rice is selected for actinomycetes, and maize is Burkholderia, Helicobacter and Shingobacteriales. In addition to that, wheat is closely related with Dyadobacter, Fibrobacteriaceae, Verrucomicrobium and Firmicutes.


Authors’ contributions

SL, MP, ZL, SSS drafted the manuscript. All authors read and approved the final manuscript.



This study was supported by the Fundamental Research Funds for the Central Universities (2572017AA23).



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Molecular Microbiology Research
• Volume 7
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