Insights into phytoremediation solutions for environmental recovery

Our environment is contaminated with organic and inorganic compounds released by anthropogenic activities that cause negative impacts on biological productivity and ecosystem sustainability and place human health at risk. Within the available remediation technologies, phytoremediation has emerged with high potential due to its reduced environmental impacts and economic costs. The research into phytoremediation has developed through a wide array of approaches, which also pertains to its inherent interdisciplinary characteristics, towards enhancing the potential of the technology for application in the field. Numerous patents present molecular solutions through which plants can be engineered to display improvements in key characteristics, such as the tolerance, uptake and accumulation of contaminants. The manipulation of plant growth and of the physico-chemical characteristics of the contaminated environments in order to enhance the remediation potential has also been the focus of several issued patents. This review attempts to highlight the most relevant patented advances in phytoremediation and to emphasise recent research efforts through which this green technology might be expected to develop into a commercially competitive alternative to other remediation methods.     

Phytoremediation of toxic aromatic pollutants from soil

The enormous growth of industrialization, and the use of numerous aromatic compounds in dyestuffs, explosives, pesticides and pharmaceuticals has resulted in serious environmental pollution and has attracted considerable attention continuously over the last two decades. Many aromatic hydrocarbons, nitroaromatic compounds, polycyclic aromatic hydrocarbons, polychlorinated biphenyls, diauxins and their derivatives are highly toxic, mutagenic and/or carcinogenic to natural microflora as well as to higher systems including humans. The increasing costs and limited efficiency of traditional physicochemical treatments of soil have spurred the development of new remediation technologies. Phytoremediation is emerging as an efficient treatment technology that uses plants to bioremediate pollutants from soil environments. Various modern tools and analytical devices have provided insight into the selection and optimization of remediation processes by various plant species. Sites heavily polluted with organic contaminants require hyperaccumulators, which could be developed by genetic engineering approaches. However, efficient hyperaccumulation by naturally occurring plants is also feasible and can be made practical by improving their nutritional and environmental requirements. Thus, phytoremediation of organics appears a very promising technology for the removal of contaminants from polluted soil. In this review, certain aspects of plant metabolism associated with phytoremediation of organic contaminants and their relevant phytoremediation efforts are discussed.IMTECH Communication No. 013/2002     

Towards expanding relevance vector machines to large scale datasets

In this paper we develop and analyze methods for expanding automated learning of Relevance Vector Machines (RVM) to large scale text sets. RVM rely on Bayesian inference learning and while maintaining state-of-the-art performance, offer sparse and probabilistic solutions. However, efforts towards applying RVM to large scale sets have met with limited success in the past, due to computational constraints. We propose a diversified set of divide-and-conquer approaches where decomposition techniques promote the definition of smaller working sets that permit the use of all training examples. The rationale is that by exploring incremental, ensemble and boosting strategies, it is possible to improve classification performance, taking advantage of the large training set available. Results on Reuters-21578 and RCV1 are presented, showing performance gains and maintaining sparse solutions that can be deployed in distributed environments.     

Monitoring and modeling horizontal gene transfer

Monitoring efforts have failed to identify horizontal gene transfer (HGT) events occurring from transgenic plants into bacterial communities in soil or intestinal environments. The lack of such observations is frequently cited in biosafety literature and by regulatory risk assessment. Our analysis of the sensitivity of current monitoring efforts shows that studies to date have examined potential HGT events occurring in less than 2 g of sample material, when combined. Moreover, a population genetic model predicts that rare bacterial transformants acquiring transgenes require years of growth to out-compete wild-type bacteria. Time of sampling is there-fore crucial to the useful implementation of monitoring. A population genetic approach is advocated for elucidating the necessary sample sizes and times of sampling for monitoring HGT into large bacterial populations. Major changes in current monitoring approaches are needed, including explicit consideration of the population size of exposed bacteria, the bacterial generation time, the strength of selection acting on the transgene-carrying bacteria, and the sample size necessary to verify or falsify the HGT hypotheses tested.     

Vavilov's Law of Homologous Series and de nove crop plant domestication

The law of homologous series, if valid, should provide us with useful guidelines in the domestication of new crop plants. The value of domesticants is likely to be in the production of materials which are in demand but otherwise unavailable in adequate amount or in the exploitation of agriculturally marginal environments where established crop plants are unreliable in performance. A model for such a system of new domestication can be developed in the Leguminosae and the tribe Phaseoleae in particular. The distribution of grain legumes in the family is not random. There are concentrations in the tribes Vicieae and Phaseoleae, with the greater number in the latter. Within the Phaseoleae the greatest concentration of domesticates is to be found in the sub-tribe Phaseolinae within the genera Vigna and Phaseolus . The sub-genus Ceralotropis of Vigna is remarkable in that the majority of species have been domesticated. This suggests that the two genera and perhaps Vigna in particular have a concentrated potential for domestication. It would certainly be sensible, if the need arose for new pulse crops in marginal agricultural environments, to consider candidate species with appropriate ecological adaptation from these genera. In product-led attempts at domestication it would be useful to consider the biosystematic background of candidate species and if there is a choice to concentrate efforts on those species with domesticated relatives. The application of the Law of Homologous Series could in these circumstances serve to direct and concentrate effort where it is likely to be most effective.     

Broadening the application of evolutionarily based genetic pest management

Insect- and tick-vectored diseases such as malaria, dengue fever, and Lyme disease cause human suffering, and current approaches for prevention are not adequate. Invasive plants and animals such as Scotch broom, zebra mussels, and gypsy moths continue to cause environmental damage and economic losses in agriculture and forestry. Rodents transmit diseases and cause major pre- and postharvest losses, especially in less affluent countries. Each of these problems might benefit from the developing field of Genetic Pest Management that is conceptually based on principles of evolutionary biology. This article briefly describes the history of this field, new molecular tools in this field, and potential applications of those tools. There will be a need for evolutionary biologists to interact with researchers and practitioners in a variety of other fields to determine the most appropriate targets for genetic pest management, the most appropriate methods for specific targets, and the potential of natural selection to diminish the effectiveness of genetic pest management. In addition to producing environmentally sustainable pest management solutions, research efforts in this area could lead to new insights about the evolution of selfish genetic elements in natural systems and will provide students with the opportunity to develop a more sophisticated understanding of the role of evolutionary biology in solving societal problems.     

Conservation of Aquatic Resources through the Use of Freshwater Protected Areas: Opportunities and Challenges

Freshwater environments are currently experiencing an alarming decline in biodiversity. As a result, scientists and managers must look for alternative management techniques to protect these aquatic systems. One such option that has potential to protect freshwater environments from numerous threats is the use of freshwater protected areas (FPAs). FPAs are portions of the freshwater environment partitioned to minimize disturbances and allow natural processes to govern populations and ecosystems. While similar conservation practices are well established in the terrestrial and marine environments, the use of FPAs for conservation of freshwater environments has been relatively slow. Despite this, numerous examples exist in which FPAs have been incorporated into successful management approaches for freshwater environments. In this paper, we outline some of the past success stories where FPAs have been used to protect freshwater environments, discuss some of the reasons that this technique has not proliferated to the same degree as marine protected areas, and present some of the challenges that managers and scientists must overcome if they wish to implement FPAs. We recommend that the term Freshwater Protected Area be adopted to such conservation efforts, thereby standardizing terminology and facilitating literature searches and dissemination of research findings. Furthermore, we encourage freshwater scientists, conservationists and managers to develop and implement FPAs in innovative and creative situations thereby permitting the growth of the research base for this valuable conservation technique.     

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

Environmental sequencing shows that plants harbor complex communities of microbes that vary across environments. However, many approaches for mapping plant genetic variation to microbe‐related traits were developed in the relatively simple context of binary host–microbe interactions under controlled conditions. Recent advances in sequencing and statistics make genome‐wide association studies (GWAS) an increasingly promising approach for identifying the plant genetic variation associated with microbes in a community context. This review discusses early efforts on GWAS of the plant phyllosphere microbiome and the outlook for future studies based on human microbiome GWAS. A workflow for GWAS of the phyllosphere microbiome is then presented, with particular attention to how perspectives on the mechanisms, evolution and environmental dependence of plant–microbe interactions will influence the choice of traits to be mapped.     

Engineering production of antihypertensive peptides in plants

To date, a number of antihypertensive peptides (AHPs) have been identified. Most of these are derived from proteins present in common edible consumables, including milk, egg, and plant foods. Consumption of these foods serves as means of AHP delivery and thus contributing favorable health benefits. It is hypothesized that food crops, either over-expressing AHP precursor proteins or producing particular peptides as heterologous components, may serve as viable vehicles for production and delivery of functional foods as alternative hypertension therapies. In recent years, genetic engineering efforts have been undertaken to add value to functional foods. Pioneering approaches have been pursued in several crop plants, such as rice and soybean. In this review, a summary of current tools used for discovery of new AHPs, as well as strategies and perspectives of capitalizing on these AHPs in genetic engineering efforts will be presented and discussed. The implications of these efforts on the development of functional foods for preventing and treating hypertension are also presented.     

No allocation trade-offs between flowering and sproutingin the lignotuberous,Mediterranean shrub Erica australis

Trade-offs between allocation to sexual or vegetative regeneration capacity are well established as a driving force in the life history patterns of plants in fire-prone environments. However, it is not known whether such trade-offs exist in plants which after aboveground removing disturbances, such as fire, may regenerate by sexual (seeding) or asexual (sprouting) mechanisms. We evaluated whether in the fire-recruiting resprouter Erica australis, which after fire can regenerate by seedling establishment or resprouting, a larger investment in flowers and seeds prior to being disturbed by clipping its aboveground parts would decrease subsequent sprouting, that is, its vegetative regeneration capacity. We analysed the relationships between flower and seed production and the ensuing production and growth of sprouts of six plants from thirteen different sites in central-western Spain. We found no significant relationships between measures of sexual reproductive effort and resprout production and growth 6 months after clipping the aboveground parts of the plants. No evidence of trade-offs between sexual and asexual efforts was found. Furthermore, no significant relationship was found between lignotuber total non-structural carbohydrates and sexual reproductive effort. In addition, 2 years after the disturbance, resprout biomass was positively and significantly correlated with sexual reproductive effort prior to the disturbance. This indicates that growth of resprouts was higher at the sites where plants made a greater reproductive effort. The sites that were more favourable to producing flowers and seeds could also be more favourable to resprouting.     

Breeding cereals for Mediterranean conditions: ecophysiological clues for biotechnology application

Water stress is the main environmental factor limiting cereal yield in Mediterranean environments. For particular regions, such as the Mediterranean basin, the agroecological conditions are expected to get worse. In response to this challenge attempts are being made to improve crop yield through farm‐ management practices and plant breeding efforts. Here we examine traits that may be used as selection criteria for breeding C3 cereal crops with improved yield and stability in Mediterranean conditions. Emphasis is made on the potential implications of defining proper selection traits and target environments when adopting biotechnology approaches in breeding programmes.     

Pod shatter-resistant Brassica fruit produced by ectopic expression of the FRUITFULL gene

Arabidopsis has proven to be extremely useful as a reference organism for studies in plant biology, and huge efforts have been employed to unravel various mechanisms of Arabidopsis growth. A major challenge now is to demonstrate that this wealth of knowledge can be used for global agricultural and environmental improvement. Brassica species are closely related to Arabidopsis and represent ideal candidates for model-to-crop approaches as they include important crop plants, such as canola. Brassica plants normally disperse their seeds by a pod-shattering mechanism. Although this mechanism is an advantage in nature, unsynchronized pod shatter constitutes one of the biggest problems for canola farmers. Here, we show that ectopic expression of the Arabidopsis FRUITFULL gene in Brassica juncea is sufficient to produce pod shatter-resistant Brassica fruit and that the genetic pathway leading to valve margin specification is conserved between Arabidopsis and Brassica . These studies demonstrate a genetic strategy for the control of seed dispersal that should be generally applicable to diverse Brassica crop species to reduce seed loss.     

Evolutionary bet-hedging in the real world: empirical evidence and challenges revealed by plants

Understanding the adaptations that allow species to live in temporally variable environments is essential for predicting how they may respond to future environmental change. Variation at the intergenerational scale can allow the evolution of bet-hedging strategies: a novel genotype may be favoured over an alternative with higher arithmetic mean fitness if the new genotype experiences a sufficiently large reduction in temporal fitness variation; the successful genotype is said to have traded off its mean and variance in fitness in order to ‘hedge its evolutionary bets’. We review the evidence for bet-hedging in a range of simple plant systems that have proved particularly tractable for studying bet-hedging under natural conditions. We begin by outlining the essential theory, reiterating the important distinction between conservative and diversified bet-hedging strategies. We then examine the theory and empirical evidence for the canonical example of bet-hedging: diversification via dormant seeds in annual plants. We discuss the complications that arise when moving beyond this simple case to consider more complex life-history traits, such as flowering size in semelparous perennial plants. Finally, we outline a framework for accommodating these complications, emphasizing the central role that model-based approaches can play.     

Some metabolic aspects of ecology

Summary

Due to the similarity of the major metabolic pathways in all living organisms it might be thought unlikely that the study of metabolic variation would add to an understanding of ecological differences. However, a quantitative study of the regulation of metabolism and its end-products indicates a link between cell biochemistry and the capability of certain species to succeed in particular environments. A study of anaerobic metabolism in animals and plants shows a number of similarities in those species able to survive in oxygen-poor environments. These include the production of nontoxic end-products and the avoidance of a large oxygen debt. As a large variety of organisms is examined, these comparisons suggest that the metabolic solutions to a given environmental stress, whether in plants or animals, can be strikingly similar. Therefore, although the main metabolic pathways in most living organism are the same, the regulation of metabolism varies with the ecology of the species. Examples are discussed in which a knowledge of metabolism in relation to ecology could have practical applications in forestry and agriculture.     

The polycyclic aromatic hydrocarbon phenanthrene causes oxidative stress and alters polyamine metabolism in the aquatic liverwort Riccia fluitans L

The polycyclic aromatic hydrocarbon (PAH) phenanthrene (PHEN) is a highly toxic pollutant, commonly found in aquatic environments, the effects of which on aquatic plants have not been studied in depth. As PAHs are known to induce oxidative stress and recent studies have shown that polyamines (PAs) participate in the defence reactions protecting plants against environmental stresses, PA metabolism and oxidative damage were investigated in the aquatic form of the liverwort Riccia fluitans L. exposed to PHEN. Exposure of Riccia fluitans plants to PHEN at concentrations of 0.5 microm or less induced oxidative stress, but at a level from which plants could recover. Despite increased levels of enzymatic and non-enzymatic antioxidants, recovery appeared, at least in part, due to increased synthesis of PAs, achieved via increased activities of the enzymes arginine decarboxylase (ADC) and S-adenosylmethionine decarboxylase (SAMDC). Chemical inhibition of these enzymes inhibited plant recovery, while treatment with PAs aided recovery. Finally, as chloroplasts and the plasma membrane appeared to be key targets for PHEN-induced damage, the potential roles of PAs in protecting these cellular components were considered. How PAs could protect plant cells from serious environmental pollutants such as PHEN and could prevent oxidative stress is discussed.     

Microbial communities in oil-contaminated seawater

Although diverse bacteria capable of degrading petroleum hydrocarbons have been isolated and characterized, the vast majority of hydrocarbon-degrading bacteria, including anaerobes, could remain undiscovered, as a large fraction of bacteria inhabiting marine environments are uncultivable. Using culture-independent rRNA approaches, changes in the structure of microbial communities have been analyzed in marine environments contaminated by a real oil spill and in micro- or mesocosms that mimic such environments. Alcanivorax and Cycloclasticus of the gamma-Proteobacteria were identified as two key organisms with major roles in the degradation of petroleum hydrocarbons. Alcanivorax is responsible for alkane biodegradation, whereas Cycloclasticus degrades various aromatic hydrocarbons. This information will be useful to develop in situ bioremediation strategies for the clean-up of marine oil spills.     

Coping mechanisms for crop plants in drought-prone environments

Background: Drought is a major limitation to plant productivity. Variousoptions are available for increasing water availability andsustaining growth of crop plants in drought-prone environments. Scope: After a general introduction to the problems of water availability,this review focuses on a critical evaluation of recent progressin unravelling mechanisms for modifying plant growth responsesto drought. Conclusions: Investigations of key regulatory mechanisms integrating plantgrowth responses to water deficits at the whole-organism, cellularand genomic levels continue to provide novel and exiting researchfindings. For example, recent reports contradict the widespreadconception that root-derived abscisic acid is necessarily involvedin signalling for stomatal and shoot-growth responses to soilwater deficits. The findings bring into question the theoreticalbasis for alternate-side root-irrigation techniques. Similarly,recent reports indicate that increased ABA production or increasedaquaporin expression did not lead to improved drought resistance.Other reports have concerned key genes and proteins involvedin regulation of flowering (FT), vegetative growth (DELLA),leaf senescence (IPT) and desiccation tolerance (LEA). Introgressionof such genes, with suitable promoters, can greatly impact onwhole-plant responses to drought. Further developments couldfacilitate the introduction by breeders of new crop varietieswith growth physiologies tailored to improved field performanceunder drought. Parallel efforts to encourage the introductionof supplementary irrigation with water made available by improvedconservation measures and by sea- or brackish-water desalination,will probably provide comprehensive solutions to coping withdrought-prone environments.     

Developing stress tolerant plants through in vitro selection—An overview of the recent progress

Biotic and abiotic stresses impose a major threat to agriculture. Therefore, the efforts to develop stress-tolerant plants are of immense importance to increase crop productivity. In recent years, tissue culture based in vitro selection has emerged as a feasible and cost-effective tool for developing stress-tolerant plants. Plants tolerant to both the biotic and the abiotic stresses can be acquired by applying the selecting agents such as NaCl (for salt tolerance), PEG or mannitol (for drought tolerance) and pathogen culture filtrate, phytotoxin or pathogen itself (for disease resistance) in the culture media. Only the explants capable of sustaining such environments survive in the long run and are selected. In vitro selection is based on the induction of genetic variation among cells, tissues and/or organs in cultured and regenerated plants. The selection of somaclonal variations appearing in the regenerated plants may be genetically stable and useful in crop improvement. This review focuses on the progress made towards the development of stress-tolerant lines through tissue culture based in vitro selection. Plants have evolved many biochemical and molecular mechanisms to survive under stress conditions. The mechanisms of ROS (reaction oxygen species) generation and removal in plants under biotic and abiotic stress conditions have also been reviewed.     

Allometric covariation: a hallmark behavior of plants and leaves

Size is one of the most important axes of variation among plants. As such, plant biologists have long searched for unifying principles that can explain how matter and energy flux and organ partitioning scale with plant size. Several recent models have proposed a universal biophysical basis for numerous scaling phenomena in plants based on vascular network geometry. Here, we review statistical analyses of several large-scale plant datasets that demonstrate that a true hallmark of plant form variability is systematic covariation among traits. This covariation is constrained by allometries that combine and trade off with one another, rather than any single universal allometric scaling exponent for a trait or suite of traits. Further, we show that covariation can be successfully modeled using network approaches that allow for species-specific designs in plants and geometric approaches that constrain relationships among economic traits in leaves. Finally, we report large-scale efforts utilizing semi-automated software tools that quantify physical networks and can inform our attempts to link vascular network structure to plant form and function. Collectively, this work highlights how the linking of morphology, biomass partitioning and the structure of physical distribution networks can improve our empirical and theoretical understanding of important drivers of plant functional diversity.     

On the Function of Wall Sculpturing in Xylem Conduits

The water-conducting network of capillaries in vascular plants has evolved over hundreds of millions of years in order to beable to cope with bubble clogging,a problem which also affects modern microfluidic devices.Decades of anatomical studieshave revealed that plants growing in habitats in which the formation of bubbles,or emboli,is likely to be a frequent occurrenceoften have various forms of geometrical sculpturing on the internal surfaces of the xylem conduits.The possible function of suchwall sculpturing has long been the subject of speculation.We have investigated the hypothesis that wall sculpturing is a functionaladaptation designed to increase the wettability of the walls of xylem conduits,an effect which could be described as theinverse of the well-known lotus-effect.Our results show that wall sculpturing does enhance wettability.Importantly,theoreticalcalculations reveal that the geometric parameters of various types of wall sculpturing are such that the resulting surfaces aresufficiently rough to enhance wettability,but not significantly rougher.The results provide an appealing answer to thelong-standing debate on the function of wall sculpturing in xylem conduits,and may provide biomimetic clues for new approachesto the removal of bubbles in microfluidic channels.