Harnessing plant-bacteria-fungi interactions to improve plant growth and degradation of organic pollutants

Exploiting the potential of bacteria in phytoremediation for the removal of organic and inorganic pollutants from soils and (ground)water holds great promise. Besides bacteria, mycorrhizal fungi and free-living saprotrophs are well known for their strong degradative capacities and plant growth promotion effects, which makes them of high interest for use in different bioremediation strategies. To further increase the efficiency and successes of phytoremediation, interactions between plants and their associated microorganisms, both bacteria and fungi, should be further investigated, in addition to the close interactions between bacteria and fungi. Benefitting from an increased understanding of microbial community structure and assembly allows us to better understand how the holobiont can be modified to improve pollutant degradation and plant growth. In this review, we present an overview of insights in plant-bacteria-fungi interactions and the opportunities of exploiting these tripartite interactions to enhance the effectiveness of phytoremediation of organic pollutants.     

Understanding plant-microbe interactions for phytoremediation of petroleum-polluted soil

Plant-microbe interactions are considered to be important processes determining the efficiency of phytoremediation of petroleum pollution, however relatively little is known about how these interactions are influenced by petroleum pollution. In this experimental study using a microcosm approach, we examined how plant ecophysiological traits, soil nutrients and microbial activities were influenced by petroleum pollution in Phragmites australis, a phytoremediating species. Generally, petroleum pollution reduced plant performance, especially at early stages of plant growth. Petroleum had negative effects on the net accumulation of inorganic nitrogen from its organic forms (net nitrogen mineralization (NNM)) most likely by decreasing the inorganic nitrogen available to the plants in petroleum-polluted soils. However, abundant dissolved organic nitrogen (DON) was found in petroleum-polluted soil. In order to overcome initial deficiency of inorganic nitrogen, plants by dint of high colonization of arbuscular mycorrhizal fungi might absorb some DON for their growth in petroleum-polluted soils. In addition, through using a real-time polymerase chain reaction method, we quantified hydrocarbon-degrading bacterial traits based on their catabolic genes (i.e. alkB (alkane monooxygenase), nah (naphthalene dioxygenase) and tol (xylene monooxygenase) genes). This enumeration of target genes suggests that different hydrocarbon-degrading bacteria experienced different dynamic changes during phytoremediation and a greater abundance of alkB was detected during vegetative growth stages. Because phytoremediation of different components of petroleum is performed by different hydrocarbon-degrading bacteria, plants' ability of phytoremediating different components might therefore vary during the plant life cycle. Phytoremediation might be most effective during the vegetative growth stages as greater abundances of hydrocarbon-degrading bacteria containing alkB and tol genes were observed at these stages. The information provided by this study enhances our understanding of the effects of petroleum pollution on plant-microbe interactions and the roles of these interactions in the phytoremediation of petroleum-polluted soil.     

环境污染治理领域中的植物修复技术

植物修复是利用植物的吸收和代谢功能将环境介质中的污染物进行分解、富集和稳定的过程。由于污染物的理化特性和环境行为不同,加之植物新陈代谢的各异,污染物植物修复的作用机理也不尽相同。与其它修复方法相比,植物修复技术投入低、效果好和纯自然,并对土壤功能的维护和土壤生物恢复有积极的作用。本文综述了近年来国外有关植物修复技术在污染治理领域中的研究进展,详细论述了推广应用污染物植物修复过程中应注意的几个技术关键;并就植物修复技术中存在的问题进行了讨论。总之,污染物植物修复技术的发展目前还不完善,就其更为详细具体的作用机理和商业推广的研究还需要做大量的工作。     

Arsenic transformations in the soil-rhizosphere-plant system: fundamentals and potential application to phytoremediation

This paper reviews major processes that potentially affect the fate of arsenic in the rhizosphere of plants. Rhizosphere interactions are deemed to play a key role in controlling bioavailability to crop plants and for a better understanding and improvement of phytoremediation technologies. Substantial progress has been made towards an understanding of As transformation processes in soils. However, virtually no information is available that directly addresses the fate of As in the rhizosphere. We are proposing a conceptual model of the fate of As in the soil-rhizosphere-plant system by integrating the state-of-the art knowledge available in the contributing disciplines. Using this model and recent studies on hyperaccumulation of As, we discuss research needs and the potential application of rhizosphere processes to the development of phytoremediation technologies for As-polluted soils.     

The Comparative Toxicogenomics Database (CTD): a resource for comparative toxicological studies

The etiology of most chronic diseases involves interactions between environmental factors and genes that modulate important biological processes (Olden and Wilson, 2000. Nat Rev Genet 1(2):149-153). We are developing the publicly available Comparative Toxicogenomics Database (CTD) to promote understanding about the effects of environmental chemicals on human health. CTD identifies interactions between chemicals and genes and facilitates cross-species comparative studies of these genes. The use of diverse animal models and cross-species comparative sequence studies has been critical for understanding basic physiological mechanisms and gene and protein functions. Similarly, these approaches will be valuable for exploring the molecular mechanisms of action of environmental chemicals and the genetic basis of differential susceptibility.     

Microbial metabolic exchange--the chemotype-to-phenotype link

The function of microbial interactions is to enable microorganisms to survive by establishing a homeostasis between microbial neighbors and local environments. A microorganism can respond to environmental stimuli using metabolic exchange-the transfer of molecular factors, including small molecules and proteins. Microbial interactions not only influence the survival of the microbes but also have roles in morphological and developmental processes of the organisms themselves and their neighbors. This, in turn, shapes the entire habitat of these organisms. Here we highlight our current understanding of metabolic exchange as well as the emergence of new technologies that are allowing us to eavesdrop on microbial conversations comprising dozens to hundreds of secreted metabolites that control the behavior, survival and differentiation of members of the community. The goal of the rapidly advancing field studying multifactorial metabolic exchange is to devise a microbial 'Rosetta stone' in order to understand the language by which microbial interactions are negotiated and, ultimately, to control the outcome of these conversations.     

Plant-microbe interactions: novel applications for exploitation in multipurpose remediation technologies

Soil remediation that revitalizes degraded or contaminated land while simultaneously contributing to biomass biofuel production and carbon sequestration is an attractive strategy to meet the food and energy requirements of the burgeoning world population. As a result, plant-based remediation approaches have been gaining in popularity. The drawbacks of phytoremediation, particularly those associated with low productivity and limitations to the use of contaminant-containing biomass, could be addressed through novel biotechnological approaches that harness recent advances in our understanding of chemical interactions between plants and microorganisms in the rhizosphere and within plant tissues. This opinion article highlights three promising approaches that provide environmental and economic benefits of bioremediation: transgenics, low-input 'designer' plants and nanotechnology.     

Biocatalytic conversion of lignocellulose to platform chemicals

Naturally occurring lignocellulose can be used as a renewable resource for the sustainable production of platform chemicals that can in turn be converted to valuable fine chemicals, polymers, and fuels. The biocatalytic conversion of lignocellulose is a very promising approach due to its high selectivity, mild conditions, and low exergy loss. However, such biocatalytic processes are still seldom applied at the industrial scale since the single conversion steps (pretreatment, hydrolysis, and fermentation) may exhibit low conversion rates, low efficiencies, or high costs. The biocatalytic conversion of lignocellulose to platform chemicals is reviewed in this work. Structures and production rates of lignocellulose are described, and platform chemicals that may be produced from lignocellulose are summarized. Biocatalytic conversion of lignocellulose is distinguished from conventional non-selective approaches. All essential conversion steps used in biocatalytic approaches (pretreatment, hydrolysis, and fermentation) are reviewed in detail. Finally, potential interactions between these conversion steps are highlighted and the advantages as well as disadvantages of integrated process configurations are elucidated. In conclusion, a comprehensive understanding of the biocatalytic conversion of lignocellulose is provided in this review.     

Ionization and charge-transfer: basic data for track structure calculations

It is widely accepted that an understanding of the detailed structure of charged particle tracks is essential for interpreting the mechanistic consequences of energy deposition by high linear energy transfer (LET) radiation. The spatial relationship of events along the path of a charged particle, including excitation, ionization, and charge-transfer, govern subsequent chemical, biochemical, and biological reactions that can lead to adverse biologic effects. The determination of spatial patterns of ionization and excitation relies on a broad range of cross-section data relating the interactions of charged particles to the molecular constituents of the absorbing medium. It is important that these data be absolute in magnitude, comprehensive in scope, and reliable if accurate assessment of track structure parameters is to be achieved. Great strides have been made in the development of this database, understanding the underlying theory, and developing analytic models, particularly for interactions involving electrons and protons with atoms and molecules. The database is less comprehensive for interactions involving heavier charged particles, especially those that carry bound electrons, and for interactions in condensed phase media. Although there has been considerable progress in understanding the physical mechanisms for interactions involving fast heavy ions and atomic targets during the past few years, we still lack sufficient understanding to confidently predict cross-sections for these ions with biologically relevant material. In addition, little is known of the interaction cross-sections for heavy charged particles as they near the end of their track, i.e., for low velocity ions where collision theory is less well developed and where the particle's net charge fluctuates owing to electron capture and loss processes. This presentation focuses on the current status of ionization and charge-transfer data. Compilations, reviews, Internet sources, theoretical models, and recent data applicable to track structure calculations are discussed.     

有机污染环境的植物修复研究进展

分析了近年来国内外的文献资料,对有机污染物污染环境的植物修复研究进展作了综述。植物能通过根系从环境中吸收和积累PCBs、PAHs等有机污染物,并将吸收的TNT、TCE及有机农药降解为高极性产物、水和CO2;另一方面植物根际可促进有机污染物的根际生物吸收与,使植物对有机污染环境的修复效果更明显。文中探讨了有机污染环境的植物修复技术的优势、问题与未来的研究。     

Effects of air pollution on biogenic volatiles and ecological interactions

Chemical signals play important roles in ecological interactions but are vulnerable to perturbation by air pollution. In polluted air masses, signals may travel shorter distances before being destroyed by chemical reactions with pollutants, thus losing their specificity. To determine which scent-mediated interactions are likely to be affected, we review existing literature to build a picture of what chemicals are commonly found in such interactions and the spatial scales at which interactions occur. We find that pollination, attraction of natural enemies of plant pests, aggregation pheromones, and mate attraction are likely to be affected. We review the scant literature on this topic and extend the hypothesis to include heretofore unexplored interactions. New research should investigate whether air pollution deleteriously affects populations of organisms that rely on scent plumes. Additionally, we need to investigate whether or not breakdown products created by the reaction of signaling chemicals with pollutants can provide usable signals, and whether or not there has been adaptation on the part of scent emitters or receivers to use either breakdown products or more robust chemical signals. The proposed research will necessarily draw on tools from atmospheric science, evolutionary biology, and ecology in furthering our understanding of the ecological implications of how air pollution modifies the scentscape.     

Bioremediation of polynitrated aromatic compounds: plants and microbes put up a fight

Industrialization and the quest for a more comfortable lifestyle have led to increasing amounts of pollution in the environment. To address this problem, several biotechnological applications aimed at removing this pollution have been investigated. Among these pollutants are xenobiotic compounds such as polynitroaromatic compounds--recalcitrant chemicals that are degraded slowly. Whereas 2,4,6-trinitrophenol (TNP) can be mineralized and converted into carbon dioxide, nitrite and water, 2,4,6-trinitrotoluene (TNT) is more recalcitrant--although several microbes can use it as a nitrogen source. The most effective in situ biotreatments for TNT are the use of bioslurry (which can be preceded by an abiotic step) and phytoremediation. Phytoremediation can be enhanced by using transgenic plants alone or together with microbes.     

Chemosensory signaling in C. elegans

The nematode Caenorhabditis elegans can sense and respond to hundreds of different chemicals with a simple nervous system, making it an excellent model for studies of chemosensation. The chemosensory neurons that mediate responses to different chemicals have been identified through laser ablation studies, providing a cellular context for chemosensory signaling. Genetic and molecular analyses indicate that chemosensation in nematodes involves G protein signaling pathways, as it does in vertebrates, but the receptors and G proteins involved belong to nematode-specific gene families. It is likely that about 500 different chemosensory receptors are used to detect the large spectrum of chemicals to which C. elegans responds, and one of these receptors has been matched with its odorant ligand. C. elegans olfactory responses are also subject to regulation based on experience, allowing the nematode to respond to a complex and changing chemical environment.     

The emerging role of pharmacology in understanding consumer-prey interactions in marine and freshwater systems

Within our lakes, streams, estuaries, and oceans, there is an astounding chemodiversity of secondary metabolites produced by microbes, algae, and invertebrates. Nearly 30 years of study have yielded hundreds of examples in which secondary metabolites alter the foraging behavior or fitness of aquatic consumers, or both. However, our understanding of the mechanisms that mediate the fate and consequences of these metabolites in aquatic consumers remains in its infancy. Interactions between metabolites and consumers at the molecular and biochemical level are the purview of modern pharmacology, which is rooted in the long history of human-drug interactions and can be adopted for ecological studies. Here, we argue that a pharmacological approach to consumer-prey interactions will be as productive within aquatic systems as it has been for understanding terrestrial systems. We review the diversity of secondary metabolites in aquatic organisms, their known effects on the feeding behaviors and performance of aquatic consumers, and the few studies that have attempted to describe their biochemical manipulation within consumer tissues, i.e., their absorption, distribution, metabolism (including detoxification), and excretion. We then highlight vexing issues in the ecology and evolution of aquatic consumer-prey interactions that would benefit from a pharmacological approach, including specialist-versus-generalist feeding strategies, dietary mixing, nutrient-toxin interactions, and taste. Finally, we argue that a pharmacological approach could help to predict how consumer-prey interactions are altered by global changes in pH, water temperature and ultraviolet radiation, or by pollution. Arguably, the state of knowledge of aquatic consumer-prey interactions is equivalent to that faced by ecologists studying terrestrial herbivores in the 1970s; the literature documents profound variation among consumers in their feeding tolerances for secondary metabolites without a thorough understanding of the mechanisms that underlie that variation. The subsequent advancement in our understanding of terrestrial herbivores in the intervening decades provides confidence that applying a pharmacological approach to aquatic consumers will prove equally productive.     

Predicting Human Genetic Interactions from Cancer Genome Evolution

Synthetic Lethal (SL) genetic interactions play a key role in various types of biological research, ranging from understanding genotype-phenotype relationships to identifying drug-targets against cancer. Despite recent advances in empirical measuring SL interactions in human cells, the human genetic interaction map is far from complete. Here, we present a novel approach to predict this map by exploiting patterns in cancer genome evolution. First, we show that empirically determined SL interactions are reflected in various gene presence, absence, and duplication patterns in hundreds of cancer genomes. The most evident pattern that we discovered is that when one member of an SL interaction gene pair is lost, the other gene tends not to be lost, i.e. the absence of co-loss. This observation is in line with expectation, because the loss of an SL interacting pair will be lethal to the cancer cell. SL interactions are also reflected in gene expression profiles, such as an under representation of cases where the genes in an SL pair are both under expressed, and an over representation of cases where one gene of an SL pair is under expressed, while the other one is over expressed. We integrated the various previously unknown cancer genome patterns and the gene expression patterns into a computational model to identify SL pairs. This simple, genome-wide model achieves a high prediction power (AUC = 0.75) for known genetic interactions. It allows us to present for the first time a comprehensive genome-wide list of SL interactions with a high estimated prediction precision, covering up to 591,000 gene pairs. This unique list can potentially be used in various application areas ranging from biotechnology to medical genetics.     

Volatile organic compound fate in phytoremediation applications: natural and engineered systems

Unique sampling techniques have generated a new understanding regarding the fate of volatile organic compounds (VOCs) in phytoremediation systems. Tissue sampling and diffusion traps were used to determine how VOCs are transported in and diffuse from vegetation, particularly woody species. These techniques were then utilized to observe how plants interact with different contaminated media, showing transport of contaminants occurs from the vadose zone (vapor phase) as well as the saturated zone (aqueous phase). Data was gathered in laboratory studies, in native vegetation, and in engineered phytoremediation systems. The findings reveal that diffusion from the xylem tissues to the atmosphere is a major fate for VOCs in phytoremediation applications. Linking VOCs' fate with groundwater hydraulics, mass removal rates from contaminant plumes can be estimated. These techniques were also utilized to observe the impact of engineered plant/microbe systems, which utilize recombinant, root-colonizing organisms to selectively degrade compounds and subsequently alter the fate of VOCs and other organic compounds. The genetically enhanced rhizoremediation methods pose a novel approach that may allow for biodegradation of compounds that formerly were considered recalcitrant.     

Quantifying Synergy: A Systematic Review of Mixture Toxicity Studies within Environmental Toxicology

Cocktail effects and synergistic interactions of chemicals in mixtures are an area of great concern to both the public and regulatory authorities. The main concern is whether some chemicals can enhance the effect of other chemicals, so that they jointly exert a larger effect than predicted. This phenomenon is called synergy. Here we present a review of the scientific literature on three main groups of environmentally relevant chemical toxicants: pesticides, metal ions and antifouling compounds. The aim of the review is to determine 1) the frequency of synergy, 2) the extent of synergy, 3) whether any particular groups or classes of chemicals tend to induce synergy, and 4) which physiological mechanisms might be responsible for this synergy. Synergy is here defined as mixtures with minimum two-fold difference between observed and predicted effect concentrations using Concentration Addition (CA) as a reference model and including both lethal and sub-lethal endpoints. The results showed that synergy occurred in 7%, 3% and 26% of the 194, 21 and 136 binary pesticide, metal and antifoulants mixtures included in the data compilation on frequency. The difference between observed and predicted effect concentrations was rarely more than 10-fold. For pesticides, synergistic mixtures included cholinesterase inhibitors or azole fungicides in 95% of 69 described cases. Both groups of pesticides are known to interfere with metabolic degradation of other xenobiotics. For the four synergistic metal and 47 synergistic antifoulant mixtures the pattern in terms of chemical groups inducing synergy was less clear. Hypotheses in terms of mechanisms governing these interactions are discussed. It was concluded that true synergistic interactions between chemicals are rare and often occur at high concentrations. Addressing the cumulative rather than synergistic effect of co-occurring chemicals, using standard models as CA, is therefore regarded as the most important step in the risk assessment of chemical cocktails.