WARPP—web application for the research of parasitic plants

The lifestyle of parasitic plants is associated with peculiar morphological, genetic, and physiological adaptations that existing online plant-specific resources fail to adequately represent. Here, we introduce the Web Application for the Research of Parasitic Plants (WARPP) as an online resource dedicated to advancing research and development of parasitic plant biology. WARPP is a framework to facilitate international efforts by providing a central hub of curated evolutionary, ecological, and genetic data. The first version of WARPP provides a community hub for researchers to test this web application, for which curated data revolving around the economically important Broomrape family (Orobanchaceae) is readily accessible. The initial set of WARPP online tools includes a genome browser that centralizes genomic information for sequenced parasitic plant genomes, an orthogroup summary detailing the presence and absence of orthologous genes in parasites compared with nonparasitic plants, and an ancestral trait explorer showing the evolution of life-history preferences along phylogenies. WARPP represents a project under active development and relies on the scientific community to populate the web app’s database and further the development of new analysis tools. The first version of WARPP can be securely accessed at https://parasiticplants.app. The source code is licensed under GNU GPLv2 and is available at https://github.com/wickeLab/WARPP.

The WARPP online resource is a new, expandable, and interactive parasitic plant-specific data hub that provides online tools tailored to the peculiarities of parasitic angiosperms.     

Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures

Elevated dissolved iron concentrations in the methanic zone are typical geochemical signatures of rapidly accumulating marine sediments. These sediments are often characterized by co-burial of iron oxides with recalcitrant aromatic organic matter of terrigenous origin. Thus far, iron oxides are predicted to either impede organic matter degradation, aiding its preservation, or identified to enhance organic carbon oxidation via direct electron transfer. Here, we investigated the effect of various iron oxide phases with differing crystallinity (magnetite, hematite, and lepidocrocite) during microbial degradation of the aromatic model compound benzoate in methanic sediments. In slurry incubations with magnetite or hematite, concurrent iron reduction, and methanogenesis were stimulated during accelerated benzoate degradation with methanogenesis as the dominant electron sink. In contrast, with lepidocrocite, benzoate degradation, and methanogenesis were inhibited. These observations were reproducible in sediment-free enrichments, even after five successive transfers. Genes involved in the complete degradation of benzoate were identified in multiple metagenome assembled genomes. Four previously unknown benzoate degraders of the genera Thermincola (Peptococcaceae, Firmicutes), Dethiobacter (Syntrophomonadaceae, Firmicutes), Deltaproteobacteria bacteria SG8_13 (Desulfosarcinaceae, Deltaproteobacteria), and Melioribacter (Melioribacteraceae, Chlorobi) were identified from the marine sediment-derived enrichments. Scanning electron microscopy (SEM) and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) images showed the ability of microorganisms to colonize and concurrently reduce magnetite likely stimulated by the observed methanogenic benzoate degradation. These findings explain the possible contribution of organoclastic reduction of iron oxides to the elevated dissolved Fe²⁺ pool typically observed in methanic zones of rapidly accumulating coastal and continental margin sediments.Subject terms: Biogeochemistry, Microbial ecology     

Gradients in dry grassland and heath vegetation on rock outcrops in eastern Germany — An analysis of a large phytosociological data set

The following study presents a statistical analysis of 595 relevés gathered during a survey of isolated grasslands and dwarf shrub heaths in the region of Halle, eastern Germany. Relevés were classified with UPGMA clustering based on a Bray-Curtis distance matrix; the resulting classification was compared with a previously published phytosociological classification. Most of the 14 target communities were supported by both approaches, but in the case of communities on heavily disturbed sites cluster analysis corresponded to units on higher phytosociological levels (alliances). DCA ordinations clearly revealed that nutrient and moisture availability controlled the community differentiation. Both factors were, however, highly correlated with the distance to the outcrop edge. Thus the outcrop size also influenced differentiation of communities, making larger outcrops richer in xerophytic and endangered species. This appears to be largely due to edge effects since the relationships diminished sharply when we controlled for progressively increasing distances from the edge in partial ordinations. Thus, microtopography of outcrops was the most important factor for community differentiation. It is therefore suggested that future research and conservation management should concentrate on the consequences of nutrient influx and changing land use on larger outcrops.     

Vegetation state changes in the course of shrub encroachment in an African savanna since about 1850 CE and their potential drivers

1. Shrub encroachment has far‐reaching ecological and economic consequences in many ecosystems worldwide. Yet, compositional changes associated with shrub encroachment are often overlooked despite having important effects on ecosystem functioning.
2. We document the compositional change and potential drivers for a northern Namibian Combretum woodland transitioning into a Terminalia shrubland. We use a multiproxy record (pollen, sedimentary ancient DNA, biomarkers, compound‐specific carbon (δ¹³C) and deuterium (δD) isotopes, bulk carbon isotopes (δ¹³Corg), grain size, geochemical properties) from Lake Otjikoto at high taxonomical and temporal resolution.
3. We provide evidence that state changes in semiarid environments may occur on a scale of one century and that transitions between stable states can span around 80 years and are characterized by a unique vegetation composition. We demonstrate that the current grass/woody ratio is exceptional for the last 170 years, as supported by n‐alkane distributions and the δ¹³C and δ¹³Corg records. Comparing vegetation records to environmental proxy data and census data, we infer a complex network of global and local drivers of vegetation change. While our δD record suggests physiological adaptations of woody species to higher atmospheric pCO₂ concentration and drought, our vegetation records reflect the impact of broad‐scale logging for the mining industry, and the macrocharcoal record suggests a decrease in fire activity associated with the intensification of farming. Impact of selective grazing is reflected by changes in abundance and taxonomical composition of grasses and by an increase of nonpalatable and trampling‐resistant taxa. In addition, grain‐size and spore records suggest changes in the erodibility of soils because of reduced grass cover.
4. Synthesis. We conclude that transitions to an encroached savanna state are supported by gradual environmental changes induced by management strategies, which affected the resilience of savanna ecosystems. In addition, feedback mechanisms that reflect the interplay between management legacies and climate change maintain the encroached state.

     

Disarming and sequencing of Agrobacterium rhizogenes strain K599 (NCPPB2659) plasmid pRi2659

Agrobacterium rhizogenes strain K599 (pRi2659), a causative agent of hairy root disease, effectively induces hairy root formation in a variety of plant species, including numerous soybean (Glycine max) cultivars. Because Agrobacterium-mediated transformation of soybean remains challenging and labor intensive, K599 appeared a suitable progenitor for new agrobacteria strains for plant transformation. In this paper, we report the disarming and sequencing of pRi2659 and the usefulness of the resulting disarmed strain in plant transformation studies of Arabidopsis thaliana, maize (Zea mays), tomato (Lycopersicon esculentum), and soybean (G. max). Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.