Organic pollutants released into the environment as a result of industrial and agricultural activity pose a serious threat to all living organisms [1]. Since traditional, physical and chemical methods for remediation of degraded environments are often costly and invasive, the methods of biological removal of this type of pollutants from the environment are garnering increasing attention. One of them is phytodegradation, based on the ability of plants to transform organic pollutants [5, 11, 75]. In recent years, studies on application of degradation potential of bacteria have been carried out to increase the efficiency of this method. Special attention of researchers is focused on endophytic bacteria. These bacteria can promote the growth and development of plants and, consequently, increase their biomass. They may also affect the bioavailability of organic pollutants in the soil. An important advantage resulting from the application of this group of microorganisms to support phytodegradation processes is also the fact that all toxic organic compounds collected by the plant undergo mineralization within its tissues [1, 20, 30].
Plant metabolism of xenobiotics sourced from the environment includes general transformations of these compounds into more water-soluble forms and the process of their sequestration [5, 75]. Photoautotrophic plants do not use organic compounds as a source of carbon and energy, and their role is limited to transformation of these compounds into less toxic forms, in order to protect sensitive enzyme systems and organelles. In the process of detoxification of xenobiotics in plant cells, three phases are distinguished: activation, conjugation and sequestration/compartmentalization. In the first phase of transformation, reactive polar functional groups are introduced into the lipophilic organic compounds. This leads to a reduction in their lipophilicity and increased solubility in the aqueous environment of the cell. The first phase reactions are usually catalysed by enzymes such as cytochrome P450 and carboxyl esterases. The second phase includes reactions catalysed by glutathione S-transferases (GST) and glucosyltransferases (GT), reactions of coupling the transformed compounds with endogenous molecules such as amino acids, sugars or glutathione to reduce their phytotoxicity. In the third phase, removal of inactivated xenobiotics from the cytosol into apoplastic cell compartments or vacuoles occurs [72].
The effectiveness of the phytodegradation process can be limited by plant sensitivity to excessively high concentrations of xenobiotics which can cause phytotoxic effects, inhibit plant growth and development [10]. It can also be limited by the bioavailability of pollutants [55]. The disadvantage of this process is also the – in many cases unknown – pathway of the transformation of compounds absorbed in plant tissues, which may lead to the formation of metabolites with significantly higher toxicity than the parent substance [36].
In contrast to plants, microorganisms, due to their comprehensive metabolic abilities, enable complete degradation of organic compounds, to CO2 and H2O [21]. In comparison with other organisms, they are characterised by a unique ability to adapt to new environmental conditions, including the treatment of compounds which are not products of their own metabolic transformations as an energy and carbon source [14]. Therefore, in recent years, a significant role in the treatment of degraded environments has been attributed to phytoremediation supported by microorganisms. A special role in this process is attributed to endophytic bacteria equipped with appropriate metabolic pathways, which increase the efficiency of organic compounds degradation, help plants to overcome the stress caused by pollution, and promote their growth [5].
Endophytic bacteria are defined mainly as bacteria colonizing internal plant tissues without causing disease symptoms or negative impact on their plant host [60]. In practice, the term defines microorganisms which can be isolated from surface-sterilised plant organs [18]. Many bacterial endophytes have been isolated from both dicotyledonous and monocotyledonous plants, from woody species such as oak and pear, to crop plants such as sugar beet and maize [60].
Population and diversity of endophytes present in plants is variable, mainly dependent on the plant genotype, type of tissue, plant development phase, amount of organic contaminants and physicochemical conditions of soil [28, 54]. A study by Phillips et al. [54] has proven that different plant species growing in hydrocarbon-contaminated soil maintain separate populations of endophytic microorganisms which may affect the ability of plants to promote the degradation of specific hydrocarbon groups.
The presence of endophytic bacteria capable of degrading organic pollutants has been demonstrated in many plant species characterised by high tolerance/resistance to contamination, such as the poplar (
It is worth noting that bacterial endophytes capable of degrading pollutants colonise specific plant tissues [1]. First of all, they can be found in xylem and/or root cortex [5]. The highest abundance of this group of bacteria has been observed in the roots of most plants [12, 59].
Polycyclic aromatic hydrocarbons (PAH) constitute a group of toxic and persistent organic pollutants, which are widespread in the environment [53]. The presence of this type of compounds may be the result of both natural processes, such as forest fires and volcanic eruptions, as well as industrial and agricultural human activities [3]. Many endophytic bacteria are able to grow in the presence of PAHs, and some can degrade these compounds, using them as a source of carbon and energy. An example may be the endophytic strains
The presence of phenol and its derivatives in the environment is associated with the widespread use of these compounds, among others, for the production of dyes, paints, varnishes, detergents, herbicides and medicines. These compounds can also be formed as by-products of many industrial processes, such as: petroleum processing, hard coal coking and steel production. They may also arise from the biodegradation of aromatic polymers, such as lignin and tannins [40]. The ability to degrade phenols has been demonstrated, inter alia, in endophytic bacteria isolated from roots and stems of hemp (
Among all types of pollution, one of the main threats to the environment and human health are pesticides. Chlorpyrifos [O, O-Diethyl O- (3,5,6-trichloro-2-pyridinyl) phosphorothioate] (CP) is an insecticide widely used in agriculture. This compound accumulates in the environment, posing a threat to people and animals. It has been shown that CP can cause liver and kidney damage and negatively affect sperm activity. In addition, it is considered one of the factors responsible for the occurrence of breast cancer in women. The ability to degrade this insecticide has been demonstrated in the
2,4-dichlorophenoxyacetic acid (2,4-D) is one of the most widespread herbicides [37]. 2,4-D salts are easily absorbed by the roots of plants and undergo translocation into meristematic tissues of roots and shoots, where the compound acts as a plant hormone, causing their uncontrolled growth. The mobility of 2,4-D in soil often leads to the pollution of surface and groundwater. Although the herbicide is biodegradable, it may persist in soil and water [16]. The use of 2,4-D on a large scale poses a threat to both human health and the environment [37]. The ability of endophytic bacteria to degrade 2,4-D has been demonstrated in an experiment carried out by Germaine et al. [16]. In these studies, the endophytic strain
Production and processing of ammunition led to environmental pollution with compounds such as: 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or octa-hydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). These toxic and mutagenic compounds are characterised by high durability and resistance to chemical agents, biological oxidation and hydrolysis [52]. A study by Van Aken et al. [73] has demonstrated that the endophytic strain of
Selected bacterial species isolated from roots, shoots and rhizosphere of sycamore maple (
Currently, many studies focus on the possibility of using endophytic methanotrophs in the bioremediation of greenhouse gases, in particular methane and carbon dioxide. These bacteria contribute to the efficient capture of methane produced in peat bogs, thus limiting its emission into the atmosphere [67]. Methanotrophic bacteria are capable of using methane as the sole source of carbon and energy. The key enzyme responsible for oxidation of methane is methane monooxygenase. This enzyme can exist in two forms, as sMMO and pMMO. The sMMO form is present in the cytosol, whereas pMMO is associated with the cell membrane. Both forms of this enzyme have been shown to oxidise a number of aliphatic and aromatic compounds [64] and may be present in the cell simultaneously, but their activity is directly dependent on the concentration of copper ions (Cu2+) in the biomass [68]. It has been demonstrated that endophyte methanotrophs,
In the genomes of the majority of isolated endophytic bacteria capable of degrading hydrocarbons, the gene encoding the alkane monooxygenase (
Differences in the expression of genes encoding degradation enzymes in endophytic bacteria were also demonstrated by Yousaf et al. [82] in the studies on the expression of the
Genetic information encoding the synthesis of enzymes involved in the degradation of organic compounds is most often located in mobile genetic elements such as plasmids or transposons which enable HTG between bacteria [21]. HTG is the main mechanism by means of which microorganisms acquire new metabolic pathways, thanks to which they adapt quickly to the changes which occur in the environment [74]. It allows for increasing the population and the activity of indigenous endophytic bacteria capable of decomposing organic compounds [1]. Moreover, HTG enables the acquisition of endophytic bacteria with new catabolic pathways and heterologous gene expression, especially when the donor and recipient belong to related species [18, 65].
Examples of endophytic bacteria, in whose genomes the presence of genes involved in the degradation of organic pollutants has been found
Bacterial endophyte | Host plant(s) | Gene | Coded enzyme | References |
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alkane monooxygenase | [4] |
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alkane hydroxylase | [29] |
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cytochrome P450 hydroxylase | [82] |
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catechol 2,3-dioxygenase | [74] |
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naphthalene dioxygenase | [15] |
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naphthalene dioxygenase | [54] |
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phenanthrene dioxygenase | [54] |
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alpha subunit of the PAH-ring |
[29] |
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organophosphorus hydrolase | [44] |
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toluene monooxygenase | [70] |
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glutathione-S-transferase | [41] |
Due to the presence of organic pollutants, the availability of minerals, including nitrogen, phosphorus and iron in the soil may be limited, which leads to limitation of plant growth [27]. The bioavailability of minerals in contaminated soils is one of the main factors limiting the effectiveness of phytoremediation [1]. Among bacterial endophytes promoting the growth of plants, it is possible to find such that have the ability to fix free atmospheric nitrogen (diazotrophic bacteria). Recent studies have shown that some bacterial endophytes capable of degrading organic compounds also demonstrate the capability of fixing free nitrogen [27]. Dashti et al. [9] report that bacteria capable of degrading organic pollutants and fixing free nitrogen increase the degradation of hydrocarbons in soils contaminated with petroleum and low in nitrogen. Bacterial endophytes are also able to synthesise specific organic compounds, siderophores, which enable the reduction of Fe3+ to Fe2+ ions, more easily available to plants [27]. Another macro-component, important for the growth and development of organisms is phosphorus [30]. Bacteria associated with plants may increase the solubility of inorganic phosphates through the synthesis of organic acids and phosphatases [27]. In addition to the minerals discussed above, endophytic bacteria supply essential vitamins [60] to plants, including vitamin B1 [39] and B12 [67].
One of the most important phytohormones produced by bacterial endophytes is indole-3-acetic acid (IAA), belonging to the group of auxins. This phytohormone stimulates root growth, activates cell division, and induces formation of lateral roots [56]. In addition, IAA can serve as a signal molecule in the communication between bacterial cells [18]. Bacterial IAA also indirectly impacts the regulation of ethylene level in the plant. It may increase the transcription and activity of the plant enzyme of ACC synthase, catalysing the formation of 1-aminocyclopropane-1-carboxylic acid (ACC), a direct precursor of ethylene [17]. Research by Sheng et al. [65] conducted on
Ethylene (C2H4) is an important phytohormone, which modulates the growth and metabolism of plant cells. However, its surplus, produced by plants in response to environmental stress, may inhibit root growth, lateral root formation and root hairs [30]. In the ethylene biosynthesis pathway, S-adenosylmethionine (SAM) is converted by ACC synthase to 1-aminocyclopropane-1-carboxylic acid (ACC), which is then converted to ethylene by ACC oxidase. Bacteria exhibit the capability of synthesising ACC deaminase, an enzyme which catalyses the decomposition of ACC into ammonia and α-ketobutyric acid, thus lowering the level of ethylene in the plant [17]. Recent studies have shown that bacterial endophytes, which both produce ACC deaminase and exhibit the capability of hydrocarbon degradation, significantly contribute to the production of plant biomass, as opposed to bacteria that have only one of these features [27]. For example, Yousaf et al. [82] demonstrated a positive correlation between the activity of ACC deaminase present in
Bacterial endophytes may also indirectly stimulate plant growth in soils contaminated with organic compounds by inhibiting the growth and the activity of phytopathogens, induction of the plant resistance mechanisms, synthesis of hydrolytic enzymes, and the distribution of organic pollutants [27].
Many bacterial endophytes exhibit antagonistic effect against numerous fungi and bacteria [56]. They can inhibit the activity of enzymes or degrade toxins produced by pathogens [75]. Some of them are capable of producing lytic enzymes degrading fungal cell walls [39], others produce hydrogen cyanide [7, 29, 50] or many secondary metabolites, including antibiotics [56]. Research by Bisht et al. [7] demonstrated that the endophytic strain of
Examples of endophytic bacteria promoting the growth of plants and exhibiting the ability to degrade organic pollutants
Bacterial endophyte | Host plant(s) | Plant growth-promoting traits | Degraded organic pollutants | References |
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production of IAA, production of siderophores, production of HCN | diesel oil | [29] |
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production of ACC deaminase, production of IAA, production of HCN, production of NH3 | diesel oil | [50] |
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production of ACC deaminase, production of IAA, production of siderophores | diesel oil | [51] |
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production of ACC deaminase | alkanes | [82] |
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production of ACC deaminase, production of IAA, production of siderophores, production of lytic enzymes | anthracene, naphthalene, benzene, toluene, xylene | [7] |
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production of IAA, production of siderophores, phosphate solubilization | pyrene | [65] |
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production of IAA, nitrogen fixation | toluene | [19] |
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production of siderophores, phosphate solubilization | toluene | [74] |
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production of ACC deaminase | textile wastewaters | [2] |
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production of IAA | fenpropathrin | [75] |
Some endophytic bacteria useful in phytoremediation are able to produce surface-active agents – biosurfactants [12, 29, 48, 83]. These intracellular, extracellular metabolites or ones associated with the cell wall of microorganisms can be divided into two groups. The first group includes compounds of relatively low molecular weight (glycolipids, phospholipids, lipopeptides), the second group is formed by high molecular weight substances, such as emulsan, liposan or polysaccharide-protein complexes. Low molecular weight biosurfactants generally strongly reduce interphase and surface tension. On the other hand, high molecular weight biosurfactants are mostly effective emulsifiers [47, 48]. The biosurfactants, as well as microorganisms that produce them, play a special role in the bioremediation of environments contaminated with petroleum hydrocarbons [32]. The remediation of such environments is limited due to the high hydrophobicity of this type of contaminants and their low solubility in water. These compounds are adsorbed on soil particles or trapped in soil pores and thus become inaccessible to microorganisms and plants [12, 83]. The presence of biosurfactants produced by microorganisms contributes to the increased bioavailability of organic pollutants and facilitates their uptake by plants [12]. By interacting directly with hydrocarbons, biosurfactants increase their solubility in water, and by interacting with the surface of bacterial cells degrading these substances, they contribute to their hydrophobicity [5, 12]. Moreover, the presence of biosurfactants in the environment may impact both individual cells and entire microbial populations. For example, some cyclic lipopeptides produced by the bacteria of the genus
Biosurfactants produced by endophytes can be a good alternative to the increasingly controversial synthetic surface-active agents used to support bioremediation processes [31]. The use of synthetic surfactants raises concerns, especially due to their toxicity and resistance to biodegradation, which may lead to an increase in environmental pollution with this type of compounds [8, 23, 42]. The ability to degrade anionic surfactants has been demonstrated in soil bacteria
The use of endophytic bacteria in the remediation of organic pollutants is currently one of the most important research directions in environmental biotechnology. Numerous studies confirm that the relationship between plants and their internal symbiotes clearly contributes to the effective course of bioremediation. Therefore, it is worth exploring these interactions in order to develop methods and strategies to make better use of these interactions. Newly isolated endophytic bacteria may become a starting point for further studies on their ability to degrade organic pollutants or support plant growth. Identification and understanding of the genetic basis of interactions between plants and endophytes, using the latest molecular biology techniques, will allow the full potential of this group of microorganisms to be exploited.