Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts

Phytoplasmas ("Candidatus Phytoplasma," class Mollicutes) cause disease in hundreds of economically important plants and are obligately transmitted by sap-feeding insects of the order Hemiptera, mainly leafhoppers and psyllids. The 706,569-bp chromosome and four plasmids of aster yellows phytoplasma strain witches' broom (AY-WB) were sequenced and compared to the onion yellows phytoplasma strain M (OY-M) genome. The phytoplasmas have small repeat-rich genomes. This comparative analysis revealed that the repeated DNAs are organized into large clusters of potential mobile units (PMUs), which contain tra5 insertion sequences (ISs) and genes for specialized sigma factors and membrane proteins. So far, these PMUs appear to be unique to phytoplasmas. Compared to mycoplasmas, phytoplasmas lack several recombination and DNA modification functions, and therefore, phytoplasmas may use different mechanisms of recombination, likely involving PMUs, for the creation of variability, allowing phytoplasmas to adjust to the diverse environments of plants and insects. The irregular GC skews and the presence of ISs and large repeated sequences in the AY-WB and OY-M genomes are indicative of high genomic plasticity. Nevertheless, segments of approximately 250 kb located between the lplA and glnQ genes are syntenic between the two phytoplasmas and contain the majority of the metabolic genes and no ISs. AY-WB appears to be further along in the reductive evolution process than OY-M. The AY-WB genome is approximately 154 kb smaller than the OY-M genome, primarily as a result of fewer multicopy sequences, including PMUs. Furthermore, AY-WB lacks genes that are truncated and are part of incomplete pathways in OY-M.     

A standardized method for the sampling of rhizosphere and rhizoplan soil bacteria associated to a herbaceous root system

Plants-microorganisms interactions play a fundamental role in terrestrial ecosystems and various methods have been reported for plant-associated bacteria extraction. However, these methods exhibit notable variations and lack of some procedural details that may impact the interpretations of results. We propose here a standardized and detailed protocol for the independent extraction of bulk, rhizosphere and rhizoplan soil fractions. This protocol was applied to the sampling of different polluted soil fractions collected in the vicinity of Arabidopsis halleri dense root system. It allowed us to determine the cultivable bacterial densities in each fraction and to confirm the existence of a bacterial gradient linked to roots distance, with a higher amount of bacteria in the rhizospheric area. We suggest to use this unified procedure as a common basis for soil sampling and bacterial communities analysis from other roots systems.     

When insects help to resolve plant phylogeny: evidence for a paraphyletic genus Acacia from the systematics and host-plant range of their seed-predators

In this study we use an indirect method to address the issue of the systematics of the large and economically important genus Acacia (Leguminosae, Mimosoideae, Acacieae). We propose the use of host-preference data in closely related insect species as a potentially useful tool to investigate host systematic issues, especially when other approaches yield inconsistent results. We have examined the evolution of host-plant use of a highly specialized group of seed-feeders who predate Acacia — the seed-beetles (Coleoptera, Chrysomelidae, Bruchinae). First, the evolution of host-plant preferences in a large clade of Bruchidius species was investigated using molecular phylogenetics and character optimization methods. Second, the scope of our study was enlarged by critically reviewing the host-plant records of all bruchine genera associated with Acacia . Both morphological and molecular data were used to define relevant insect clades, for which comparisons of host-plant range were performed. Interestingly, the analyses of host-plant preferences from 163 seed-beetle species recovered similar patterns of host-plant associations in the distinct clades which develop within Acacia seeds. Our results clearly support the hypothesis of Acacia being a paraphyletic genus and provide useful insights with reference to the systematics of the whole subfamily as well. This study should also be of interest to those involved in the numerous biological control programs which either already use or aim to use seed-beetles as auxiliary species to limit the propagation of several invasive legume tree species.     

Correlations of climate and plant ecology to leaf size and shape: potential proxies for the fossil record

The sizes and shapes (physiognomy) of fossil leaves are widely applied as proxies for paleoclimatic and paleoecological variables. However, significant improvements to leaf-margin analysis, used for nearly a century to reconstruct mean annual temperature (MAT), have been elusive; also, relationships between physiognomy and many leaf ecological variables have not been quantified. Using the recently developed technique of digital leaf physiognomy, correlations of leaf physiognomy to MAT, leaf mass per area, and nitrogen content are quantified for a set of test sites from North and Central America. Many physiognomic variables correlate significantly with MAT, indicating a coordinated, convergent evolutionary response of fewer teeth, smaller tooth area, and lower degree of blade dissection in warmer environments. In addition, tooth area correlates negatively with leaf mass per area and positively with nitrogen content. Multiple linear regressions based on a subset of variables produce more accurate MAT estimates than leaf-margin analysis (standard errors of ±2 vs. ±3°C); improvements are greatest at sites with shallow water tables that are analogous to many fossil sites. The multivariate regressions remain robust even when based on one leaf per species, and the model most applicable to fossils shows no more signal degradation from leaf fragmentation than leaf-margin analysis.     

Association of PCR and feeding bioassays as a large-scale method to screen tropical Bacillus thuringiensis isolates for a cry constitution with higher insecticidal effect against Spodoptera frugiperda (Lepidoptera: Noctuidae) larvae

AIMS: To verify whether the presence of any of the cry1C, 1D, 1E and 1F genes could be associated with high toxicity against fall armyworm. METHODS AND RESULTS: A sample of 60 strains from a large collection of tropical Bacillus thuringiensis (B.t.) isolates was subjected to feeding bioassays and gene-specific PCR. Positive amplification of cry-specific fragments, so confirmed by sequencing, revealed that cry1C was ubiquitous and distributed among high and low mortality classes, cry1D was underrepresented and showed no clear association to high toxicity, and cry1F was not detected. The presence of cry1E significantly correlated to high levels of insecticidal activity, as estimated by linear regression analysis. CONCLUSION: The PCR amplification of cry1E-specific fragments alone appears to be sufficient to identify B.t. strains with high mortality levels against tropical armyworm. SIGNIFICANCE AND IMPACT OF THE STUDY: The approach presented is promising as a simple and efficient method for first-tier, marker-assisted screening of environment-specific B.t. germplasm effective in controlling a single target pest.     

The long-distance abscisic acid signal in the droughted plant: the fate of the hormone on its way from root to shoot

Abscisic acid (ABA) is a potent molecule that certainly modifies stomatal behaviour and plant water loss and probably acts to modify the growth of leaves. The hormone is synthesized both in the leaves and the roots of the plant and in the soil and may move freely from plant to soil and soil to plant. It can also move rapidly through the plant in both the xylem and the phloem and will partition between different compartments in different tissues largely as a function of pH. It is described here how perturbations in soil conditions around the roots and the water status of the air can modify the fluxes of ABA around the plant and its accumulation in different compartments and different tissues. These fluxes can be interpreted as signals of different stresses imposed on the plant and consideration is given to how different perturbations can exert subtle changes which are manifest as modified shoot growth rates and functioning. Most emphasis in the discussion is placed upon the plant's responses to the imposition of soil and atmospheric drought.     

A small-scale five-hour procedure for isolating multiple samples of CsCl-purified DNA: application to isolations from mammalian, insect, higher plant, algal, yeast, and bacterial sources

A rapid and simple procedure is described for obtaining CsCl-purified DNA from multiple small samples of cells or tissue. The DNA is recovered in a high-molecular-weight form (greater than or equal to 50 kb) that is readily cleaved with restriction enzymes. Sufficient quantities of DNA (10-50 micrograms) are recovered to allow multiple analyses by Southern blotting and most cloning procedures. The isolation procedure involves addition of intact cells or powders of frozen tissues directly to a simple lysis buffer containing detergent (sodium dodecyl sulfate or sodium sarcosinate) and high concentrations of EDTA. Ultra-high-speed centrifugation of CsCl gradients allows the isolation of DNA from 10 different samples in as little as 5 h. Applications are described for mammalian cells (HeLa cells), insect tissues (Drosophila melanogaster adults and pupa, Manduca sexta pupa, and Musca domestica pupa), higher plant tissues (Vicia faba leaves and meristems), algal cells (walled and wall-less Chlamydomonas reinhardi), yeast cells (Saccharomyces cerevisiae), and bacterial cells (Escherichia coli spheroplasts for preparation of both chromosomal and plasmid DNA). The procedure can be scaled up with larger sample sizes and longer centrifugation times to provide bulk quantities of DNA.     

Primordium initiation at the stem apex as the primary event controlling plant development: preliminary evidence from wheat for the regulation of leaf development

Abstract. The results from field studies of 12 crops of winter wheat (two seasons, four sites in the U.K., four cultivars), in which leaf appearance and events at the mainstem apex were fully documented, were used to investigate the inter-relationship between leaf initiation and appearance. It was shown that the progress of leaf appearance could be divided into two phases around collar initiation. During the first phase, which was common to all crops examined, leaf appearance was linearly related to leaf initiation, indicating that leaf appearance was not independently regulated by the environment but dependent on initiation. The slope of the second phase relationship varied between crops, indicating the intervention of an additional controlling factor. This shows that, for the first phase at least, the time course of leaf appearance was predetermined by the rate of leaf initiation at the stem apex.     

Tracing the trilobite tree from the root to the tips: A model marriage of fossils and phylogeny

Trilobites are a highly diverse group of extinct arthropods that persisted for nearly 300 million years. During that time, there was a profusion of morphological form, and they occupied a plethora of marine habitats. Their diversity, relative abundance, and complex morphology make them excellent candidates for phylogenetic analysis, and partly as a consequence they have been the subject of many cladistic studies. Although phylogenetic knowledge is certainly incomplete, our understanding of evolutionary patterns within the group has dramatically increased over the last 30 years. Moreover, trilobites have formed an important component of various studies of macroevolutionary processes. Here, we summarize the phylogenetic breadth of knowledge on the Trilobita, and present various hypotheses about phylogenetic patterns within the group, from the highest to the lowest taxonomic levels. Key topics we consider include the question of trilobite monophyly, the phylogenetic position of trilobites vis à vis extant arthropod groups, and inter- and intra-ordinal relationships.     

A density-based approach for the modelling of root architecture: application to Maritime pine (Pinus pinaster Ait.) root systems

Root morphology influences strongly plant/soil interactions. However, the complexity of root architecture is a major barrier when analysing many phenomena, e.g. anchorage, water or nutrient uptake. Therefore, we have developed a new approach for the representation and modelling of root architecture based on branching density. A general root branching density in a space of finite dimension was used and enabled us to consider various morphological properties. A root system model was then constructed which minimizes the difference between measured and simulated root systems, expressed with functions which map root density in the soil. The model was tested in 2D using data from Maritime pine Pinus pinaster Ait. structural roots as input. We showed that simulated and real root systems had similar root distributions in terms of radial distance, depth, branching angle and branching order. These results indicate that general density functions are not only a powerful basis for constructing models of architecture, but can also be used to represent such structures when considering root/soil interaction. These models are particularly useful in that they provide a local morphological characterization which is aggregated in a given unit of soil volume.     

A photometric technique for the measurement of plant surface area: the adsorption of Brilliant Blue dye on to plant surfaces

1. A new photometric method for determining the surface area of plants, which relies on the adsorption of Coomassie Brilliant Blue G-250 on the plant surface, is described and compared with other methods. 2. The method was applied to a variety of aquatic plants and found to provide a routine procedure to determine plant surface area.     

A history of plant biotechnology: from the Cell Theory of Schleiden and Schwann to biotech crops

Plant biotechnology is founded on the principles of cellular totipotency and genetic transformation, which can be traced back to the Cell Theory of Matthias Jakob Schleiden and Theodor Schwann, and the discovery of genetic transformation in bacteria by Frederick Griffith, respectively. On the 25th anniversary of the genetic transformation of plants, this review provides a historical account of the evolution of the theoretical concepts and experimental strategies that led to the production and commercialization of biotech (transformed or transgenic) plants expressing many useful genes, and emphasizes the beneficial effects of plant biotechnology on food security, human health, the environment, and conservation of biodiversity. In so doing, it celebrates and pays tribute to the contributions of scores of scientists who laid the foundation of modern plant biotechnology by their bold and unconventional thinking and experimentation. It highlights also the many important lessons to be learnt from the fascinating history of plant biotechnology, the significance of history in science teaching and research, and warns against the danger of the growing trends of ignoring history and historical illiteracy.     

Quantifying the potential of restored natural capital to alleviate poverty and help conserve nature: A case study from South Africa

Poverty and environmental degradation seem to be endemic in many of the former homeland territories of South Africa. The political legacy of Apartheid might have ceased, but the economic and environmental consequences thereof still have to be dealt with. In one interesting case such a poverty-stricken and environmentally degraded area (Bushbuckridge) lies adjacent to a world conservation icon, the Kruger National Park. Currently, however, the community of Bushbuckridge does not enjoy much benefit from this unique geographic location. On the contrary there seems to be increasing tension between the community in their quest for survival and the national park as a conservation enclave. This tension will not disappear automatically. The situation needs to be managed. It is proposed here that by broadening the conservation corridor through land restoration and by incorporating the Bushbuckridge communal land as an IUCN Category VI protected area (a protected area within which sustainable resource harvesting by communities is permitted) into the Kruger National Park and under the provision that the community remains the land owner, the conservation initiative could benefit the community as much as by a factor of four. For this to be successful a proper managerial and institutional system will have to be in place, including a system that will allow the trade in ecosystem goods and services.     

Yeast factories for the production of aromatic compounds: from building blocks to plant secondary metabolites

The aromatic amino acid biosynthesis pathway is a source to a plethora of commercially relevant chemicals with very diverse industrial applications. Tremendous efforts in microbial engineering have led to the production of compounds ranging from small aromatic molecular building blocks all the way to intricate plant secondary metabolites. Particularly, the yeast Saccharomyces cerevisiae has been a great model organism given its superior capability to heterologously express long metabolic pathways, especially the ones containing cytochrome P450 enzymes. This review contains a collection of state-of-the-art metabolic engineering work devoted towards unraveling the mechanisms for enhancing the flux of carbon into the aromatic pathway. Some of the molecules discussed include the polymer precursor muconic acid, as well as important nutraceuticals (flavonoids and stilbenoids), and opium-derived drugs (benzylisoquinoline alkaloids).     

Chemotactic responses of the ladybeetle Harmonia axyridis (Coleoptera: Coccinellidae) to volatile compounds from the scale insect Drosicha corpulenta (Hemiptera: Coccoidea: Monophlebidae) and its host plant

The ladybeetle Harmonia axyridis Pallas (Coleoptera: Coccinellidae), is a key predator of the scale insect Drosicha corpulenta (Kuwana), (Hemiptera: Coccoidea: Monophlebidae) in persimmon tree orchards. We used a Y-tube olfactometer and gas chromatograph/mass spectrometry to assess the possible role of volatiles from persimmon trees in attracting H. axyridis. The results showed more ladybeetles aggregated at odour sources from heavily damaged trees than from slightly damaged or undamaged trees. The relative amounts and types of terpenoid and alcohol compounds changed, usually increased, in the volatiles from damaged persimmon trees: α-pinene increased from 26 to 43%. The ladybeetle was attracted to α-pinene in a Y-tube assay at most tested concentrations.     

Analytical study of the effects of some soil and plant parameters on root growth due to absorption of one mobile ion: A free-boundary model

The object of our study is: a model for root growth through a free-boundary problem and the effects resulting from differences in nutrient availability and transport of only one mobile nutrient between the root surface and the rhizosphere produced by an absorption Michaelis-Menten for low and high concentrations. The model equations are solved by two methods: the quasi-stationary method and the balance integral method. The numerical solutions are used to compute radial root growth. Curves of nutrient concentration at the root-soil interface, curve as a function of root radius as well as curves representing root radius as a function of time are plotted. The parameters which are varied are the root absorption power, flux velocity at the root surface, efflux, rhizosphere radius, diffusion coefficient, buffer power, and maximum influx. The two methods show the theoretical results for radial root growth in the range of low and high concentrations. The balance integral method provides more detailed information.     

Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series

Background  

Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants.