Microbiological interactions with cold plasma

There is a diverse range of microbiological challenges facing the food, healthcare and clinical sectors. The increasing and pervasive resistance to broad‐spectrum antibiotics and health‐related concerns with many biocidal agents drives research for novel and complementary antimicrobial approaches. Biofilms display increased mechanical and antimicrobial stability and are the subject of extensive research. Cold plasmas (CP) have rapidly evolved as a technology for microbial decontamination, wound healing and cancer treatment, owing to the chemical and bio‐active radicals generated known collectively as reactive oxygen and nitrogen species. This review outlines the basics of CP technology and discusses the interactions with a range of microbiological targets. Advances in mechanistic insights are presented and applications to food and clinical issues are discussed. The possibility of tailoring CP to control specific microbiological challenges is apparent. This review focuses on microbiological issues in relation to food‐ and healthcare‐associated human infections, the role of CP in their elimination and the current status of plasma mechanisms of action.     

Investigating a flower-insect forager network in a mountain grassland community using pollen DNA barcoding

Faced with the decline of pollinators, it is relevant to strengthen our understanding of the whole plant-pollinator web in semi-natural grasslands that serve as refuges for pollinator populations. The aim of this study was to explore the diversity of flower-foraging insects involved in pollen transfer in mountain semi-natural grasslands. Insects actively collecting pollen and/or nectar were caught in spring in six mountain semi-natural grasslands displaying a floristic richness gradient. Individual determinations of insects were made at the finest possible taxonomic scale and pollen loads were removed from the insect body. Using next-generation DNA sequencing, pollens were identified through the ribosomal DNA cistron using the ITS2 database and the ITS plant rDNA cistron sequences from Genbank. A total of 236 flower-foraging insects were collected. Diptera represented 82% of the total catches distantly followed by Hymenoptera (15%) and Apoidea (bees) (11%). Visual observations revealed that Diptera foraged on 16 of the 21 flower species visited by insects. DNA metabarcoding showed that 82% (191) of all of the collected insects were carrying pollen and 44% (104) were carrying two genera of plants or more. Our results demonstrate that Diptera are potential key-pollinators in mountain semi-natural grasslands that cannot be overlooked by the scientific community. However difficulties of taxonomic determination due to severe shortage of experts for Diptera have to be urgently overcome. Further studies on the link between pollen transfer and actual pollination in a global change context are also required. Moreover, our results support the idea that DNA metabarcoding provides accurate information about the plants-insects networks but it also pointed out sensitive issues, especially the necessity to build reliable national barcode databases.     

Molluscan shell colour

The phylum Mollusca is highly speciose, and is the largest phylum in the marine realm. The great majority of molluscs are shelled, including nearly all bivalves, most gastropods and some cephalopods. The fabulous and diverse colours and patterns of molluscan shells are widely recognised and have been appreciated for hundreds of years by collectors and scientists alike. They serve taxonomists as characters that can be used to recognise and distinguish species, however their function for the animal is sometimes less clear and has been the focus of many ecological and evolutionary studies. Despite these studies, almost nothing is known about the evolution of colour in molluscan shells. This review summarises for the first time major findings of disparate studies relevant to the evolution of shell colour in Mollusca and discusses the importance of colour, including the effects of visual and non‐visual selection, diet and abiotic factors. I also summarise the evidence for the heritability of shell colour in some taxa and recent efforts to understand the molecular mechanisms underpinning synthesis of shell colours. I describe some of the main shell pigments found in Mollusca (carotenoids, melanin and tetrapyrroles, including porphyrins and bile pigments), and their durability in the fossil record. Finally I suggest that pigments appear to be distributed in a phylogenetically relevant manner and that the synthesis of colour is likely to be energetically costly.     

Herbivore regulation of plant abundance in aquatic ecosystems

Herbivory is a fundamental process that controls primary producer abundance and regulates energy and nutrient flows to higher trophic levels. Despite the recent proliferation of small‐scale studies on herbivore effects on aquatic plants, there remains limited understanding of the factors that control consumer regulation of vascular plants in aquatic ecosystems. Our current knowledge of the regulation of primary producers has hindered efforts to understand the structure and functioning of aquatic ecosystems, and to manage such ecosystems effectively. We conducted a global meta‐analysis of the outcomes of plant–herbivore interactions using a data set comprised of 326 values from 163 studies, in order to test two mechanistic hypotheses: first, that greater negative changes in plant abundance would be associated with higher herbivore biomass densities; second, that the magnitude of changes in plant abundance would vary with herbivore taxonomic identity. We found evidence that plant abundance declined with increased herbivore density, with plants eliminated at high densities. Significant between‐taxa differences in impact were detected, with insects associated with smaller reductions in plant abundance than all other taxa. Similarly, birds caused smaller reductions in plant abundance than echinoderms, fish, or molluscs. Furthermore, larger reductions in plant abundance were detected for fish relative to crustaceans. We found a positive relationship between herbivore species richness and change in plant abundance, with the strongest reductions in plant abundance reported for low herbivore species richness, suggesting that greater herbivore diversity may protect against large reductions in plant abundance. Finally, we found that herbivore–plant nativeness was a key factor affecting the magnitude of herbivore impacts on plant abundance across a wide range of species assemblages. Assemblages comprised of invasive herbivores and native plant assemblages were associated with greater reductions in plant abundance compared with invasive herbivores and invasive plants, native herbivores and invasive plants, native herbivores and mixed‐nativeness plants, and native herbivores and native plants. By contrast, assemblages comprised of native herbivores and invasive plants were associated with lower reductions in plant abundance compared with both mixed‐nativeness herbivores and native plants, and native herbivores and native plants. However, the effects of herbivore–plant nativeness on changes in plant abundance were reduced at high herbivore densities. Our mean reductions in aquatic plant abundance are greater than those reported in the literature for terrestrial plants, but lower than aquatic algae. Our findings highlight the need for a substantial shift in how biologists incorporate plant–herbivore interactions into theories of aquatic ecosystem structure and functioning. Currently, the failure to incorporate top‐down effects continues to hinder our capacity to understand and manage the ecological dynamics of habitats that contain aquatic plants.     

Effects of landscape features on gene flow of valley oaks (<Emphasis Type="Italic">Quercus lobata</Emphasis>)

Landscape features affect habitat connectivity and patterns of gene flow and hence influence genetic structure among populations. We studied valley oak (Quercus lobata), a threatened species of California (USA) savannas and oak woodlands, with a distribution forming a ring around the Central Valley grasslands. Our main goal was to determine the role of topography and land cover on patterns of gene flow and to test whether elevation or land cover forms stronger barriers to gene flow among valley oak populations. We sampled valley oaks in 12 populations across the range of this species, genotyped each tree at eight nuclear microsatellite loci, and created a series of resistance surfaces by assigning different resistance values to land cover type and elevation. We also estimated recent migration rates and evaluated them with regard to landscape features. There was a significant but weak relationship between Euclidian distance and genetic distance. There was no relationship between genetic distances and land cover, but a significant relationship between genetic distances and elevation resistance. We conclude that gene flow is restricted by high elevations in the northern part of the valley oak range and by high elevations and the Central Valley further south. Migration rate analysis indicated some gene flow occurring east–west but we suggest that the high connectivity in the northern Central Valley is facilitating the formation of these links. We predict that southern populations may become more differentiated in the future through genetic isolation and local adaptation taking place in the face of climate change.     

Intrinsic and extrinsic drivers of recruitment across the distribution range of a seed-dimorphic herb

Recruitment of new individuals, through germination and seedling survival, is a key process for short-lived plants. Here, we analyzed intraspecific variation in recruitment across the latitudinal range of Plantago coronopus, a widespread herb that produces both large basal seeds with a mucilaginous coat and small apical seeds without coat. We experimentally tested the effects of seed traits and water availability on recruitment, by using seeds from a wide environmental stress gradient from N Africa to N Europe. Our experiments were carried out in controlled environmental conditions and in dunes where the species naturally occurs. Water shortage decreased seed germination and seedling survival for all populations, showing the importance of water supply for P. coronopus. Basal seeds showed higher and faster germination rates than apical seeds. Since among-population variation in seed mass was not related to potential germination rate, it is the mucilaginous coat rather than size difference that likely drives the differential success between seed morphs. Seed mass positively affected seedling survival instead, but only in controlled conditions with regular water supply. An experiment in a dune showed indeed that the highest survival corresponded to the local population and not the one with the largest seeds. Our results demonstrate that both intrinsic and extrinsic factors drive inter-population variation in the early life stages of this short-lived plant, allowing it to adapt across the environmentally heterogeneous distribution range. Gathering information on intraspecific variation in recruitment-related traits will help us to understand and predict plant responses in a context of climatic change.     

A Method for Identification and Analysis of Non-Overlapping Myeloid Immunophenotypes in Humans

The development of flow cytometric biomarkers in human studies and clinical trials has been slowed by inconsistent sample processing, use of cell surface markers, and reporting of immunophenotypes. Additionally, the function(s) of distinct cell types as biomarkers cannot be accurately defined without the proper identification of homogeneous populations. As such, we developed a method for the identification and analysis of human leukocyte populations by the use of eight 10-color flow cytometric protocols in combination with novel software analyses. This method utilizes un-manipulated biological sample preparation that allows for the direct quantitation of leukocytes and non-overlapping immunophenotypes. We specifically designed myeloid protocols that enable us to define distinct phenotypes that include mature monocytes, granulocytes, circulating dendritic cells, immature myeloid cells, and myeloid derived suppressor cells (MDSCs). We also identified CD123 as an additional distinguishing marker for the phenotypic characterization of immature LIN^-CD33⁺HLA-DR^- MDSCs. Our approach permits the comprehensive analysis of all peripheral blood leukocytes and yields data that is highly amenable for standardization across inter-laboratory comparisons for human studies.