Daniel van der Lelie

DNA-guided crystallization of colloidal nanoparticles

Many nanometre-sized building blocks will readily assemble into macroscopic structures. If the process is accompanied by effective control over the interactions between the blocks and all entropic effects, then the resultant structures will be ordered with a precision hard to achieve with other fabrication methods. But it remains challenging to use self-assembly to design systems comprised of different types of building blocks—to realize novel magnetic, plasmonic and photonic metamaterials, for example. A conceptually simple idea for overcoming this problem is the use of ‘encodable’ interactions between building blocks; this can in principle be straightforwardly implemented using biomolecules. Strategies that use DNA programmability to control the placement of nanoparticles in one and two dimensions have indeed been demonstrated. However, our theoretical understanding of how to extend this approach to three dimensions is limited, and most experiments have yielded amorphous aggregates and only occasionally crystallites of close-packed micrometre-sized particles. Here, we report the formation of three-dimensional crystalline assemblies of gold nanoparticles mediated by interactions between complementary DNA molecules attached to the nanoparticles’ surface. We find that the nanoparticle crystals form reversibly during heating and cooling cycles. Moreover, the body-centred-cubic lattice structure is temperature-tuneable and structurally open, with particles occupying only ∼4% of the unit cell volume. We expect that our DNA-mediated crystallization approach, and the insight into DNA design requirements it has provided, will facilitate both the creation of new classes of ordered multicomponent metamaterials and the exploration of the phase behaviour of hybrid systems with addressable interactions.

Phytoremediation of contaminated soils and groundwater: lessons from the field.

Background, aim, and scopeThe use of plants and associated microorganisms to remove, contain, inactivate, or degrade harmful environmental contaminants (generally termed phytoremediation) and to revitalize contaminated sites is gaining more and more attention. In this review, prerequisites for a successful remediation will be discussed. The performance of phytoremediation as an environmental remediation technology indeed depends on several factors including the extent of soil contamination, the availability and accessibility of contaminants for rhizosphere microorganisms and uptake into roots (bioavailability), and the ability of the plant and its associated microorganisms to intercept, absorb, accumulate, and/or degrade the contaminants. The main aim is to provide an overview of existing field experience in Europe concerning the use of plants and their associated microorganisms whether or not combined with amendments for the revitalization or remediation of contaminated soils and undeep groundwater. Contaminations with trace elements (except radionuclides) and organics will be considered. Because remediation with transgenic organisms is largely untested in the field, this topic is not covered in this review. Brief attention will be paid to the economical aspects, use, and processing of the biomass.Conclusions and perspectivesIt is clear that in spite of a growing public and commercial interest and the success of several pilot studies and field scale applications more fundamental research still is needed to better exploit the metabolic diversity of the plants themselves, but also to better understand the complex interactions between contaminants, soil, plant roots, and microorganisms (bacteria and mycorrhiza) in the rhizosphere. Further, more data are still needed to quantify the underlying economics, as a support for public acceptance and last but not least to convince policy makers and stakeholders (who are not very familiar with such techniques).

Endophytic Bacteria and Their Potential Applications

The authors wish to acknowledge the European Commission for their support to the ENDEGRADE project (EU PROJECT: QLK3- CT2000-00164). DvdL and ST are presently being supported by Laboratory Directed Research and Development funds at the Brookhaven National Laboratory under contract with the U.S. Department of Energy.

Engineered endophytic bacteria improve phytoremediation of water-soluble, volatile, organic pollutants.

Phytoremediation of highly water soluble and volatile organic xenobiotics is often inefficient because plants do not completely degrade these compounds through their rhizospheres. This results in phytotoxicity and/or volatilization of chemicals through the leaves, which can cause additional environmental problems. We demonstrate that endophytic bacteria equipped with the appropriate degradation pathway improve the in planta degradation of toluene. We introduced the pTOM toluene-degradation plasmid of Burkholderia cepacia G4 into B. cepacia L.S.2.4, a natural endophyte of yellow lupine. After surface-sterilized lupine seeds were successfully inoculated with the recombinant strain, the engineered endophytic bacteria strongly degraded toluene, resulting in a marked decrease in its phytotoxicity, and a 50–70% reduction of its evapotranspiration through the leaves. This strategy promises to improve the efficiency of phytoremediating volatile organic contaminants.

Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes

Ralstonia metallidurans, formerly known as Alcaligenes eutrophus and thereafter as Ralstonia eutropha, is a beta-Proteobacterium colonizing industrial sediments, soils or wastes with a high content of heavy metals. The type strain CH34 carries two large plasmids (pMOL28 and pMOL30) bearing a variety of genes for metal resistance. A chronological overview describes the progress made in the knowledge of the plasmid-borne metal resistance mechanisms, the genetics of R. metallidurans CH34 and its taxonomy, and the applications of this strain in the fields of environmental remediation and microbial ecology. Recently, the sequence draft of the genome of R. metallidurans has become available. This allowed a comparison of these preliminary data with the published genome data of the plant pathogen Ralstonia solanacearum, which harbors a megaplasmid (of 2.1 Mb) carrying some metal resistance genes that are similar to those found in R. metallidurans CH34. In addition, a first inventory of metal resistance genes and operons across these two organisms could be made. This inventory, which partly relied on the use of proteomic approaches, revealed the presence of numerous loci not only on the large plasmids pMOL28 and pMOL30 but also on the chromosome. It suggests that metal-resistant Ralstonia, through evolution, are particularly well adapted to the harsh environments typically created by extreme anthropogenic situations or biotopes.

Genome Survey and Characterization of Endophytic Bacteria Exhibiting a Beneficial Effect on Growth and Development of Poplar Trees

ABSTRACT The association of endophytic bacteria with their plant hosts has a beneficial effect for many different plant species. Our goal is to identify endophytic bacteria that improve the biomass production and the carbon sequestration potential of poplar trees (Populus spp.) when grown in marginal soil and to gain an insight in the mechanisms underlying plant growth promotion. Members of the Gammaproteobacteria dominated a collection of 78 bacterial endophytes isolated from poplar and willow trees. As representatives for the dominant genera of endophytic gammaproteobacteria, we selected Enterobacter sp. strain 638, Stenotrophomonas maltophilia R551-3, Pseudomonas putida W619, and Serratia proteamaculans 568 for genome sequencing and analysis of their plant growth-promoting effects, including root development. Derivatives of these endophytes, labeled with gfp, were also used to study the colonization of their poplar hosts. In greenhouse studies, poplar cuttings (Populus deltoides × Populus nigra DN-34) inoculated with Enterobacter sp. strain 638 repeatedly showed the highest increase in biomass production compared to cuttings of noninoculated control plants. Sequence data combined with the analysis of their metabolic properties resulted in the identification of many putative mechanisms, including carbon source utilization, that help these endophytes to thrive within a plant environment and to potentially affect the growth and development of their plant hosts. Understanding the interactions between endophytic bacteria and their host plants should ultimately result in the design of strategies for improved poplar biomass production on marginal soils as a feedstock for biofuels.

Phytoremediation: plant-endophyte partnerships take the challenge.

A promising field to exploit plant-endophyte partnerships is the remediation of contaminated soils and (ground) water. Many plant growth promoting endophytes can assist their host plant to overcome contaminant-induced stress responses, thus providing improved plant growth. During phytoremediation of organic contaminants, plants can further benefit from endophytes possessing appropriate degradation pathways and metabolic capabilities, leading to more efficient contaminant degradation and reduction of both phytotoxicity and evapotranspiration of volatile contaminants. For phytoremediation of toxic metals, endophytes possessing a metal-resistance/sequestration system can lower metal phytotoxicity and affect metal translocation to the above-ground plant parts. Furthermore, endophytes that can degrade organic contaminants and deal with or, even better, improve extraction of the metals offer promising ways to improve phytoremediation of mixed pollution.

The versatility and adaptation of bacteria from the genus Stenotrophomonas

The genus Stenotrophomonas comprises at least eight species. These bacteria are found throughout the environment, particularly in close association with plants. Strains of the most predominant species, Stenotrophomonas maltophilia, have an extraordinary range of activities that include beneficial effects for plant growth and health, the breakdown of natural and man-made pollutants that are central to bioremediation and phytoremediation strategies and the production of biomolecules of economic value, as well as detrimental effects, such as multidrug resistance, in human pathogenic strains. Here, we discuss the versatility of the bacteria in the genus Stenotrophomonas and the insight that comparative genomic analysis of clinical and endophytic isolates of S. maltophilia has brought to our understanding of the adaptation of this genus to various niches.

Exploiting plant–microbe partnerships to improve biomass production and remediation

Although many plant-associated bacteria have beneficial effects on their host, their importance during plant growth and development is still underestimated. A better understanding of their plant growth-promoting mechanisms could be exploited for sustainable growth of food and feed crops, biomass for biofuel production and feedstocks for industrial processes. Such plant growth-promoting mechanisms might facilitate higher production of energy crops in a more sustainable manner, even on marginal land, and thus contribute to avoiding conflicts between food and energy production. Furthermore, because many bacteria show a natural capacity to cope with contaminants, they could be exploited to improve the efficiency of phytoremediation or to protect the food chain by reducing levels of agrochemicals in food crops.

Rhizosphere chemical dialogues: plant–microbe interactions

Every organism on earth relies on associations with its neighbors to sustain life. For example, plants form associations with neighboring plants, microflora, and microfauna, while humans maintain symbiotic associations with intestinal microbial flora, which is indispensable for nutrient assimilation and development of the innate immune system. Most of these associations are facilitated by chemical cues exchanged between the host and the symbionts. In the rhizosphere, which includes plant roots and the surrounding area of soil influenced by the roots, plants exude chemicals to effectively communicate with their neighboring soil organisms. Here we review the current literature pertaining to the chemical communication that exists between plants and microorganisms and the biological processes they sustain.