Making phytoremediation work better: maximizing a plant's growth potential in the midst of adversity

While a number of different plants can either breakdown a variety of organic contaminants or hyperaccumulate metals from the environment, even the most efficient of those plants is typically inhibited by the presence of the toxicant(s). The plant stress that is induced by the presence of various environmental toxicants typically limits a plant's growth and ultimately its ability to phytoremediate the toxicant(s). Here, it is argued that the simple strategy of adding plant growth-promoting bacteria (preferably endophytes) that reduce plant ethylene levels by ACC deaminase activity and have the ability to synthesize the phytohoromone IAA, and are used to phytoremediate various toxicants can significantly (and often dramatically) increase both plant growth and phytoremediation activity in the presence of those toxicants.     

Using soil bacteria to facilitate phytoremediation

In the past twenty years or so, researchers have endeavored to utilize plants to facilitate the removal of both organic and inorganic contaminants from the environment, especially from soil. These phytoremediation approaches have come a long way in a short time. However, the majority of this work has been done under more controlled laboratory conditions and not in the field. As an adjunct to various phytoremediation strategies and as part of an effort to make this technology more efficacious, a number of scientists have begun to explore the possibility of using various soil bacteria together with plants. These bacteria include biodegradative bacteria, plant growth-promoting bacteria and bacteria that facilitate phytoremediation by other means. An overview of bacterially assisted phytoremediation is provided here for both organic and metallic contaminants, with the intent of providing some insight into how these bacteria aid phytoremediation so that future field studies might be facilitated.     

Bacteria with ACC deaminase can promote plant growth and help to feed the world

To feed all of the world's people, it is necessary to sustainably increase agricultural productivity. One way to do this is through the increased use of plant growth-promoting bacteria; recently, scientists have developed a more profound understanding of the mechanisms employed by these bacteria to facilitate plant growth. Here, it is argued that the ability of plant growth-promoting bacteria that produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase to lower plant ethylene levels, often a result of various stresses, is a key component in the efficacious functioning of these bacteria. The optimal functioning of these bacteria includes the synergistic interaction between ACC deaminase and both plant and bacterial auxin, indole-3-acetic acid (IAA). These bacteria not only directly promote plant growth, they also protect plants against flooding, drought, salt, flower wilting, metals, organic contaminants, and both bacterial and fungal pathogens. While a considerable amount of both basic and applied work remains to be done before ACC deaminase-producing plant growth-promoting bacteria become a mainstay of plant agriculture, the evidence indicates that with the expected shift from chemicals to soil bacteria, the world is on the verge of a major paradigm shift in plant agriculture.     

Tolerance of transgenic canola expressing 1-aminocyclopropane-1-carboxylic acid deaminase to growth inhibition by nickel.

Plant growth-promoting bacteria are useful to phytoremediation strategies in that they confer advantages to plants in contaminated soil. When plant growth-promoting bacteria contain the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, the bacterial cell acts as a sink for ACC, the immediate biosynthetic precursor of the plant growth regulator ethylene thereby lowering plant ethylene levels and decreasing the negative effects of various environmental stresses. In an effort to gain the advantages provided by bacterial ACC deaminase in the phytoremediation of metals from the environment two transgenic canola lines with the gene for this enzyme were generated and tested. In these transgenic canola plants, expression of the ACC deaminase gene is driven by either tandem constitutive cauliflower mosaic virus (CaMV) 35S promoters or the root specific rolD promoter from Agrobacterium rhizogenes. Following the growth of transgenic and non-transformed canola in nickel contaminated soil, it was observed that the rolD plants demonstrate significantly increased tolerance to nickel compared to the non-transformed control plants.     

Use of plant growth-promoting rhizobacteria to control stress responses of plant roots

Ethylene is a key gaseous hormone that controls various physiological processes in plants including growth, senescence, fruit ripening, and responses to abiotic and biotic stresses. In spite of some of these positive effects, the gas usually inhibits plant growth. While chemical fertilizers help plants grow better by providing soil-limited nutrients such as nitrogen and phosphate, over-usage often results in growth inhibition by soil contamination and subsequent stress responses in plants. Therefore, controlling ethylene production in plants becomes one of the attractive challenges to increase crop yields. Some soil bacteria among plant growth-promoting rhizobacteria (PGPRs) can stimulate plant growth even under stressful conditions by reducing ethylene levels in plants, hence the term “stress controllers” for these bacteria. Thus, manipulation of relevant genes or gene products might not only help clear polluted soil of contaminants but contribute to elevating the crop productivity. In this article, the beneficial soil bacteria and the mechanisms of reduced ethylene production in plants by stress controllers are discussed.     

Bacteria in the plant tissue culture environment

Bacteria and plants are joined in various symbiotic relationships that have developed over millennia and have influenced the evolution of both groups. Bacteria inhabit the surfaces of most plants and are also present inside many plant organs. These bacteria may have positive, neutral or negative impacts on their plant hosts. Probiotic effects may improve plant nutrition or increase resistance to biotic and abiotic stresses. Conversely pathogenic bacteria may kill or reduce the vigor of plant hosts. In addition some bacteria inhabit plants and profit from excess metabolites or shelter while not injuring the plant. Micropropagation of plants is based on the stimulation of organogenesis or embryogenesis from explants that are superficially decontaminated and placed into a sterile environment. If successful, this process removes bacteria from surfaces, but those inhabiting inner tissues and organs are usually not affected by these steriliants. In vitro conditions are designed for optimal plant growth and development, however these conditions are also often ideal for bacterial multiplication. The presence of bacteria in the in vitro environment was almost universally considered negative for plant culture, but more recently this view has been questioned. Certain bacteria appear to have a beneficial effect on the explants in culture; increasing multiplication and rooting, increasing explant quality, and organo- and embryogenesis of recalcitrant genotypes. The most important role of beneficial bacteria for micropropagated plants is likely to be during acclimatization, when growth is resumed under natural conditions. This review includes the role of bacterial interactions in plants, especially those grown in vitro.     

Bacterial endophytes and their interactions with hosts

Recent molecular studies on endophytic bacterial diversity have revealed a large richness of species. Endophytes promote plant growth and yield, suppress pathogens, may help to remove contaminants, solubilize phosphate, or contribute assimilable nitrogen to plants. Some endophytes are seedborne, but others have mechanisms to colonize the plants that are being studied. Bacterial mutants unable to produce secreted proteins are impaired in the colonization process. Plant genes expressed in the presence of endophytes provide clues as to the effects of endophytes in plants. Molecular analysis showed that plant defense responses limit bacterial populations inside plants. Some human pathogens, such as Salmonella spp., have been found as endophytes, and these bacteria are not removed by disinfection procedures that eliminate superficially occurring bacteria. Delivery of endophytes to the environment or agricultural fields should be carefully evaluated to avoid introducing pathogens.     

Endophytic and rhizospheric enterobacteria isolated from sugar cane have different potentials for producing plant growth-promoting substances

Background and aims

Endophytic and rhizospheric environments differ in many respects, leading to the presence of different bacterial communities at each site. However, microorganisms such as enterobacteria can be found both within plants and in the surrounding soil. Bacteria must present differences in the traits that affect such environments in order to successfully colonise them. The present study compared the plant growth-promoting potential of diazotrophic enterobacteria isolated from the rhizosphere and from within surface-disinfected plants.

Methods

A total of 46 diazotrophic enterobacterial strains (21 rhizospheric and 25 putatively endophytic) belonging to the Klebsiella and Enterobacter genera, which are prevalent in sugar cane plantations, were isolated from the rhizosphere and from surface-disinfected plants. Their ability to synthesise amino acids using combined nitrogen obtained from nitrogen fixation, and their ability to synthesise indole-3-acetic acid (IAA) were determined by high performance liquid chromatography. Endogenous ethylene production by the bacteria was measured using gas chromatography, and biocontrol of phytopathogenic fungi was determined qualitatively using a dual culture technique.

Results

The putative endophytes released significantly higher amounts of amino acids than the rhizospheric bacteria, whilst the latter produced higher quantities of ethylene and were more actively antagonistic to fungi. Both types of bacteria released similar amounts of IAA.

Conclusion

Endophytic and rhizospheric bacteria differ in their capacity to release plant growth-promoting substances, which may be a reflection of their adaptations and an indication of their potential impact on their natural environment.

     

Comparative structural bioinformatics analysis of <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> chemotaxis proteins within <Emphasis Type="Italic">Bacillus subtilis</Emphasis> group

Chemotaxis is a process in which bacteria sense their chemical environment and move towards more favorable conditions. Since plant colonization by bacteria is a multifaceted process which requires a response to the complex chemical environment, a finely tuned and sensitive chemotaxis system is needed. Members of the Bacillus subtilis group including Bacillus amyloliquefaciens are industrially important, for example, as bio-pesticides. The group exhibits plant growth-promoting characteristics, with different specificity towards certain host plants. Therefore, we hypothesize that while the principal molecular mechanisms of bacterial chemotaxis may be conserved, the bacterial chemotaxis system may need an evolutionary tweaking to adapt it to specific requirements, particularly in the process of evolution of free-living soil organisms, towards plant colonization behaviour. To date, almost nothing is known about what parts of the chemotaxis proteins are subjected to positive amino acid substitutions, involved in adjusting the chemotaxis system of bacteria during speciation. In this novel study, positively selected and purified sites of chemotaxis proteins were calculated, and these residues were mapped onto homology models that were built for the chemotaxis proteins, in an attempt to understand the spatial evolution of the chemotaxis proteins. Various positively selected amino acids were identified in semi-conserved regions of the proteins away from the known active sites.     

Promotion of Plant Growth by Bacterial ACC Deaminase

To date, there has been only limited commercial use of plant growth-promoting bacteria in agriculture, horticulture, and silviculture. However, with recent progress toward understanding the mechanisms that these organisms utilize to facilitate plant growth, the use of plant growth-promoting bacteria is expected to continue to increase worldwide. One of the key mechanisms employed by plant growth-promoting bacteria to facilitate plant growth is the lowering of plant ethylene levels by the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase. This article reviews the published work on this enzyme, with an emphasis on its biochemistry, protein structure, genes, and regulation. In addition, this article provides some initial insights into the changes in both plants and ACC deaminase-containing plant growth-promoting bacteria as a consequence of plant-microbe interactions. Finally, a brief discussion of how bacterial ACC deaminase and indoleacetic acid (IAA) together modulate plant growth and development is included.     

Understanding the development of roots exposed to contaminants and the potential of plant-associated bacteria for optimization of growth

Background and Scope

Plant responses to the toxic effects of soil contaminants, such as excess metals or organic substances, have been studied mainly at physiological, biochemical and molecular levels, but the influence on root system architecture has received little attention. Nevertheless, the precise position, morphology and extent of roots can influence contaminant uptake. Here, data are discussed that aim to increase the molecular and ecological understanding of the influence of contaminants on root system architecture. Furthermore, the potential of plant-associated bacteria to influence root growth by their growth-promoting and stress-relieving capacities is explored.

Methods

Root growth parameters of Arabidopsis thaliana seedlings grown in vertical agar plates are quantified. Mutants are used in a reverse genetics approach to identify molecular components underlying quantitative changes in root architecture after exposure to excess cadmium, copper or zinc. Plant-associated bacteria are isolated from contaminated environments, genotypically and phenotypically characterized, and used to test plant root growth improvement in the presence of contaminants.

Key Results

The molecular determinants of primary root growth inhibition and effects on lateral root density by cadmium were identified. A vertical split-root system revealed local effects of cadmium and copper on root development. However, systemic effects of zinc exposure on root growth reduced both the avoidance of contaminated areas and colonization of non-contaminated areas. The potential for growth promotion and contaminant degradation of plant-associated bacteria was demonstrated by improved root growth of inoculated plants exposed to 2,4-di-nitro-toluene (DNT) or cadmium.

Conclusions

Knowledge concerning the specific influence of different contaminants on root system architecture and the molecular mechanisms by which this is achieved can be combined with the exploitation of plant-associated bacteria to influence root development and increase plant stress tolerance, which should lead to more optimal root systems for application in phytoremediation or safer biomass production.     

Bacterial endophytes from seeds of Norway spruce (Picea abies L. Karst)

Endophytic bacteria from wooden plants and especially seed-associated endophytes are not well studied. Fresh seeds collected from four Norway spruce trees (Picea abies) from different locations in the Slovene subalpine region were surface-sterilised and dissected into a seed coat, embryo and endosperm. The presence of endophytes was detected by culturing methods and by direct amplification of the eubacterial 16S rDNA gene. Both approaches identified bacteria from genera Pseudomonas and Rahnella in the Norway spruce seeds. Both are known plant-associated bacteria with growth-promoting properties and biological control potential. We suggest that plant seeds could serve as a vector for transmission of beneficial bacteria.     

转基因植物在环境污染监测中的应用

在通常情况下,污染物的存在很难被发现。它们对环境和人类的潜在危害就更加难以估计。在众多生物监测体系中,转基因植物监测系统脱颖而出。综述了几种成功应用于污染物质遗传毒性监测的转基因植物系统,并对今后生产高效率转基因植物监测体系的关键问题进行了探讨。     

盐胁迫环境下植物促生菌的作用机制研究进展

盐胁迫是限制干旱和半干旱地区作物生产的主要非生物胁迫之一,严重影响作物的生长发育,植物促生菌(Plant growth-promoting bacteria,PGPB)可有效减轻植物的盐胁迫损伤,合理施用PGPB是盐胁迫下促进作物生长的重要途径。本文从盐胁迫环境下PGPB在调节植物激素内稳态、促进养分吸收和诱导植物产生系统耐受性等方面的作用阐述了PGPB提高植物耐盐性、减轻植物胁迫损伤的作用机制。讨论了能够在植物根际稳定定殖并在盐生环境下稳定保持PGP活性的功能菌株对未来农业的可持续发展的重要意义,同时,对该研究方向的重难点和未来的发展趋势作出展望。     

Revegetation of a lakeside barren area by the application of plant growth-promoting rhizobacteria

The growth stimulation of wild plants by several bacterial species showing plant growth-promoting capabilities was examined in a barren lakeside area at Lake Paro, Korea. Microbial numbers and activities in the field soil were monitored for 73 days after inoculation of the bacteria. The acridine orange direct counts for the total soil bacterial populations ranged between 2.0-2.3x10(9) cells/g soil and 1.4-1.8x10(9) cells/g soil in the inoculated and uninoculated soils, respectively. The numbers of Pseudomonas spp., which is known as a typical plant growth-promoting rhizobacteria, and the total microbial activity were higher in the inoculated soil compared to those in the uninoculated soil. The average shoot and root lengths of the wild plants grown in the inoculated soil were 17.3 cm and 12.4 cm, respectively, and longer than those of 11.4 cm and 8.5 cm in the uninoculated soil. The total dry weight of the harvested wild plants was also higher in the inoculated soil (42.0 g) compared to the uninoculated soil (35.1 g). The plant growth-promoting capabilities of the inoculated bacteria may be used for the rapid revegetation of barren or disturbed land, and as biofertilizer in agriculture.     

Use of nitrogen-fixing bacteria as biofertiliser for non-legumes: prospects and challenges

The potential of nitrogen-fixing (NF) bacteria to form a symbiotic relationship with leguminous plants and fix atmospheric nitrogen has been exploited in the field to meet the nitrogen requirement of the latter. This phenomenon provides an alternative to the use of the nitrogenous fertiliser whose excessive and imbalanced use over the decades has contributed to green house emission (N(2)O) and underground water leaching. Recently, it was observed that non-leguminous plants like rice, sugarcane, wheat and maize form an extended niche for various species of NF bacteria. These bacteria thrive within the plant, successfully colonizing roots, stems and leaves. During the association, the invading bacteria benefit the acquired host with a marked increase in plant growth, vigor and yield. With increasing population, the demand of non-leguminous plant products is growing. In this regard, the richness of NF flora within non-leguminous plants and extent of their interaction with the host definitely shows a ray of hope in developing an ecofriendly alternative to the nitrogenous fertilisers. In this review, we have discussed the association of NF bacteria with various non-leguminous plants emphasizing on their potential to promote host plant growth and yield. In addition, plant growth-promoting traits observed in these NF bacteria and their mode of interaction with the host plant have been described briefly.     

Growth-promotion of strawberry plants inoculated with Azospirillum brasilense

Azospirillum brasilense (strains REC3, RLC1, PEC5) were root inoculated in strawberry plants of the cultivars ‘Milsei’, ‘Selva’ and ‘Camarosa’ to assess plant growth-promoting effects. The bacteria were able to promote plant growth (expressed as root length, root area, and dry weight of root and shoot), depending on the genotypes of plants and bacteria used, whereas the stolon production (3–4) depended only on the strawberry cultivar. To explain whether root exudates plays any role on the growth-promotion observed herein, total protein and sugar were determined, and chemotaxis properties were evaluated. The strains showed positive chemotaxis toward the root exudates, being influenced by the total sugars content, suggesting that the latter plays an important role in the chemotaxis effect and may contribute to enhance the root capacity to recruit azospirilla from rhizosphere, thus improving the growth-promoting effect exerted by these bacteria.     

Microbial hazards in plant tissue and cell cultures

Summary A wide range of microorganisms (filamentous fungi, yeasts, bacteria, viruses and viroids) and micro-arthropods (mites and thrips) have been identified as contaminants in plant tissue cultures. Contaminant may be introduced with the explant, during manipulations in the laboratory or by micro-arthropod vectors. Contaminants may express themselves immediately or can remain latent for long periods of time. This often makes it difficult to identify the source of contamination. Disinfection protocols have now been developed for a wide range of plant species including those infected with viruses/viroids or endophytic bacteria. They may include the selection of pathogen-free donor plants or donor plant treatments such as thermotherapy. Also microbiological quality assurance systems (e.g. Hazard Analysis Critical Control Point; HACCP procedures) have been adapted to the needs of commercial plant tissue culture laboratories. These are aimed at, preventing the introduction of pathogens, into tissue cultures at establishment and in the laboratory. In established in vitro cultures preventative strategies have proved to be essential, since it is extremely difficult to eliminate environmental bacterial and fungal contaminants using, antibiotics and fungicides. In many cases anti-microbial treatments only inhibit contaminants and low levels of contamination persist. In particular, the use of antibiotics against Gram-negative bacteria (including plant pathogenic bacteria and Agrobacterium tumefaciens vector systems used in genetic engineering) has been shown frequently to be extremely difficult or unsuccessful. Detection of latent contamination may involve the use of general and semi-selective microbial growth media or serological and PCR-based molecular techniques for specific pathogens. However, it is often difficult to detect low numbers of latent bacterial contaminants (e.g. levels present following antibiotic treatment or when acidified plant media are used). This poses a particular risk in the production of transgenic plants where the elimination or detection of Agrobacterium tumefaciens-based vector systems cannot be guaranteed with the currently available methodologies. Recent research has also shown that there is a risk of the transmission of human pathogens in plant tissue cultures.     

Allelopathic Bacteria and Their Impact on Higher Plants

The impact of allelopathic, nonpathogenic bacteria on plant growth in natural and agricultural ecosystems is discussed. In some natural ecosystems, evidence supports the view that in the vicinity of some allelopathically active perennials (e.g., Adenostoma fasciculatum, California), in addition to allelochemicals leached from the shrub's canopy, accumulation of phytotoxic bacteria or other allelopathic microorganisms amplify retardation of annuals. In agricultural ecosystems allelopathic bacteria may evolve in areas where a single crop is grown successively, and the resulting yield decline cannot be restored by application of minerals. Transfer of soils from areas where crop suppression had been recorded into an unaffected area induced crop retardation without readily apparent symptoms of plant disease. Susceptibility of higher plants to deleterious rhizobacteria is often manifested in sandy or so-called skeletal soils. Evaluation of phytotoxic activity under controlled conditions, as well as ways to apply allelopathic bacteria in the field, is approached. The allelopathic effect may occur directly through the release of allelochemicals by a bacterium that affects susceptible plant(s) or indirectly through the suppression of an essential symbiont. The process is affected by nutritional and other environmental conditions, some may control bacterial density and the rate of production of allelochemicals. Allelopathic nonpathogenic bacteria include a wide range of genera and secrete a diverse group of plant growth-mediating allelochemicals. Although a limited number of plant growth-promoting bacterial allelochemicals have been identified, a considerable number of highly diversified growth-inhibiting allelochemicals have been isolated and characterized. Some species may produce more than one allelochemical; for example, three different phyotoxins, geldanamycin, nigericin, and hydanthocidin, were isolated from Streptomyces hygroscopicus. Efforts to introduce naturally produced allelochemicals as plant growth-regulating agents in agriculture have yielded two commercial herbicides, phosphinothricin, a product of Streptomyces viridochromogenes, and bialaphos from S. hygroscopicus. Many species of allelopathic bacteria that affect growth of higher plants are not plant specific, but some do exhibit specificity; for example, dicotyledonous plants were more susceptible to Pseudomonas putida than were monocotyledons. Differential susceptibility of higher plants to allelopathic bacteria was noted also in much lower taxonomical categories, at the subspecies level, in different cultivars of wheat, or of lettuce. Therefore, when test plants are employed to evaluate bacterial allelopathy, final evaluation must include those species that are assumed to be suppressed in nature. The release of allelochemicals from plant residues in plots of ‘continuous crop cultivation’ or from allelopathic living plants may induce the development of specific allelopathic bacteria. Both the rate by which a bacterium gains from its allelopathic activity through utilizing plant excretions, and the reasons for the developing of allelopathic bacteria in such habitats, are important goals for further research.