Genomics of biotrophic, plant-infecting plasmodiophorids using in vitro dual cultures

The plasmodiophorids are a phylogenetically distinct group of parasitic protists that infect plants and stramenopiles, causing several important agricultural diseases. Because of the obligate intracellular part of their lifecycle, none of the plasmodiophorids has been axenically cultured. Further, the molecular biology of the plasmodiophorids is poorly understood because pure cultures are not available from any species. We report on an in-vitro dual culture system of the plasmodiophorids Plasmodiophora brassicae and Spongospora subterranea with their respective plant hosts, Brassica rapa and Solanum tuberosum. We show that these plasmodiophorids are capable of initiating and maintaining stable, long-term plant cell callus cultures in the absence of exogenous plant growth regulators. We show that callus cultures harbouring S. subterranea provide an excellent starting material for gene discovery from this organism by constructing a pilot-scale DNA library. Bioinformatic analysis of the sequences established that almost all of the DNA clones from this library were from S. subterranea rather than the plant host. The Spongospora genome was found to be rich in retrotransposable elements, and Spongospora protein-coding genes were shown to contain introns. The sequence of a near full-length non-LTR retrotransposon was obtained, the first transposable element reported from a cercozoan protist.     

Is naked barley an eastern or a western crop? The combined evidence of archaeobotany and genetics

Forms of Hordeum vulgare ssp. vulgare (barley) that possess a naked caryopsis are an important human staple and are mainly found today in eastern Asia. However, naked barley has not always been an eastern crop: archaeobotanical data show that it was prevalent in Europe and the Near East during various periods in prehistory. In this review we have collated data on the incidence of hulled and naked barley at archaeological sites in Europe and the Near East from two sources: archaeobotanical literature reviews and an archaeobotanical database, both assembled by Helmut Kroll. We have also examined the incidence of hulled and naked barleys in extant germplasm collections. Our compilation of this archaeobotanical data has enabled us to elucidate long-term changes in the ratio of hulled to naked barley under cultivation in these regions; specifically, these records show that naked barley begins to disappear from the archaeobotanical record from the Chalcolithic/Bronze Age onwards in the Near East, and from the Iron Age/Roman periods onwards in Europe. We discuss the possible causes of this decline in naked barley cultivation in these regions, along with the present-day prevalence of naked barley landraces in eastern Asia, particularly in relation to genetic evidence, which shows that naked barley has a single origin.     

HABITAT ACOUSTICS OF A NEOTROPICAL LOWLAND RAINFOREST

ABSTRACT

The acoustic characteristics of an Amazonian lowland rain forest study site in southern Venezuela was analysed to determine environmental constraints upon acoustic communication. Signal degradation was measured by conducting transmission experiments at different heights above ground level. Measurements of ambient noise served to determine possible communication distances for various times of day, heights above ground level and frequencies. “Sound windows” for acoustic long-range communication were found for low frequencies, calling heights in the midstorey and calling in the morning or during the night. Sound attenuation was affected by height and frequency but not by time of day. Background noise varied remarkably with time of day and frequency and had a greater impact on communication distance than signal attenuation.     

Phylogeny and evolution of corambid nudibranchs (Mollusca: Gastropoda)

Organismic diversity, as well as distributional and ecological patterns, can be fully understood in an evolutionary framework only. Reliable phylogenetic trees are required to ‘read history’, but are not yet available for most marine invertebrate groups. Molecular systematics offers an enormous potential, but still fails for ‘all‐species approaches’ on groups with species that are rare or occur in remote areas only, simply because there is no easily collectable material available for sequence analyses. Exploring morphologically aberrant corambid nudibranch gastropods as a case study, we assess whether or not morphology‐based phylogenetic analyses can fill this gap and produce a tree that allows a detailed view on evolutionary history. Morphology‐based parsimony analysis of corambids and potential relatives resulted in a well‐resolved and remarkably robust topology. As an offshoot of kelp‐associated onchidoridid ancestors, and obviously driven by the heterochronic shortening of life cycles and morphological juvenilization in an ephemeral habitat, the ancestor of corambids originated in cool northern Pacific coastal waters. A basal clade (the genus Loy) diverged there, adapting to live on soft bottoms under successive reversals of paedomorphic traits. The more speciose Corambe lineage radiated preying upon short‐lived encrusting bryozoa in a high‐energy kelp environment. Selection favoured transformation of the mantle into a cuticle‐covered shield, and successive paedomorphic translocations of dorid anal gills to the protected ventral side of the body, where compensatory, multiple gills evolved. Corambe species probably first colonized tropical American seas, and then radiated in worldwide temperate waters: this is explained by the excellent long‐distance dispersal abilities afforded by rafting on kelp, with the subsequent divergence of colonizers in allopatry. The competitive coexistence of Corambe pacifica MacFarland & O'Donoghue, 1929 and Corambe steinbergae (Lance, 1962) off California is the result of independent colonization events. The closing of the Isthmus of Panama separated the latter species from a flock that have radiated within warm Atlantic waters since then. Our case study shows that morphological structures, if investigated in depth, bear the potential for an efficient phylogenetic analysis of groups that are still elusive to molecular analyses. Tracing character evolution and integrating a wide range of geographic, biological, and ecological background information allowed us to reconstruct an evolutionary scenario for corambids that is detailed and plausible, and can be tested by future molecular approaches. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 585–604.     

Characterization of the preprotein and amino acid transporter gene family in Arabidopsis

Seventeen loci encode proteins of the preprotein and amino acid transporter family in Arabidopsis (Arabidopsis thaliana). Some of these genes have arisen from recent duplications and are not in annotated duplicated regions of the Arabidopsis genome. In comparison to a number of other eukaryotic organisms, this family of proteins has greatly expanded in plants, with 24 loci in rice (Oryza sativa). Most of the Arabidopsis and rice genes are orthologous, indicating expansion of this family before monocot and dicot divergence. In vitro protein uptake assays, in vivo green fluorescent protein tagging, and immunological analyses of selected proteins determined either mitochondrial or plastidic localization for 10 and six proteins, respectively. The protein encoded by At5g24650 is targeted to both mitochondria and chloroplasts and, to our knowledge, is the first membrane protein reported to be targeted to mitochondria and chloroplasts. Three genes encoded translocase of the inner mitochondrial membrane (TIM)17-like proteins, three TIM23-like proteins, and three outer envelope protein16-like proteins in Arabidopsis. The identity of Arabidopsis TIM22-like proteins is most likely a protein encoded by At3g10110/At1g18320, based on phylogenetic analysis, subcellular localization, and complementation of a yeast (Saccharomyces cerevisiae) mutant and coexpression analysis. The lack of a preprotein and amino acid transporter domain in some proteins, localization in mitochondria, plastids, or both, variation in gene structure, and the differences in expression profiles indicate that the function of this family has diverged in plants beyond roles in protein translocation.     

Floral diversity, parasitoids and hyperparasitoids – A laboratory approach

Adding floral resources to agro-ecosystems to improve biological control can enhance the survival, egg load, and parasitism rate of insect parasitoids. However, this may not always be the case because the herbivore may benefit from the added resource as much as, or more than the third-trophic level. In addition, the natural enemies of those in the third-trophic level may also derive improved fitness from the added resources. Both these processes will dampen trophic cascades, leading to less-effective biological control. In this study, the effect of adding different flowering plants on the longevity, egg load, aphid parasitism rates and hyperparasitism of Aphidius ervi Haliday (Hymenoptera: Braconidae) by its hyperparasitoid Dendrocerus aphidum Rondani (Hymenoptera: Megaspilidae) were investigated, using the pea aphid Acyrthosiphon pisum Harris (Homoptera: Aphididae) as the herbivore. Parasitoids exposed to buckwheat survived, on average, between four to five times as long as those in the control (water) and those in phacelia, alyssum and coriander treatments survived three to four times as long. Hyperparasitoids exposed to buckwheat survived five to six times as long as those in the control and three to five times longer with the other plants compared with the control. Almost all flower species significantly increased parasitoid and hyperparasitoid egg loads and the number of parasitised aphids and parasitised mummies compared with control. Understanding the factors influencing the dynamics of multitrophic interactions involving flowering plants, herbivores, parasitoids and hyperparasitoids is a fertile area for future research. One of the most challenging areas in contemporary ecology concerns the relative importance of different types of biodiversity mediating trophic interactions and thereby influencing the structure of communities and food webs. This paper begins to explore this using an experimental, laboratory-based approach.