Transplanting the leafy liverwort Herbertus hutchinsiae : A suitable conservation tool to maintain oceanic-montane liverwort-rich heath?

Thanks to the relevant landowners and managers for permission to carry out the experiments, Chris Preston for helping to obtain the liverwort distribution records and the distribution map, Gordon Rothero and Dave Horsfield for advice on choosing experimental sites and Alex Douglas for statistical advice. Juliane Geyer’s help with fieldwork was greatly appreciated. This study was made possible by a NERC PhD studentship and financial support from the Royal Botanic Garden Edinburgh and Scottish Natural Heritage.Peer reviewedPostprin

Restoration of upland hay meadows over an 11‐year chronosequence: an evaluation of the success of green hay transfer

Grassland restoration has become a key tool in addressing the drastic losses of seminatural grassland since the mid‐twentieth century. This study examined the restoration by green hay transfer of upland hay meadows, a particularly scarce and vulnerable habitat, over an 11‐year chronosequence. The community composition of 18 restoration meadows was compared with that of donor reference sites in two study areas in the Pennine region of northern England. The study investigated: differences in community composition between donor and restoration meadows; transfer of upland hay meadow target species; and the effect of time and isolation from neighboring meadows on the community composition of the restoration meadows. Results showed that restoration meadows differed from donor meadows in that some target species were easily transferred whilst others were not found in the restoration meadows, or were at low levels of cover. Time had a significant effect on the community composition of the restoration meadows, but the similarity between restoration sites and donor sites did not increase with time, and the effect of isolation was not significant. The study showed that the green hay transfer method increases botanical diversity and is an important first step in meadow restoration. However, further restoration activity, such as seed addition, is likely to be required if restoration sites are to resemble closely the reference donor sites

Quantifying soil hydrology to explain the development of vegetation at an ex-arable wetland restoration site

Wetland restoration frequently sets well-defined vegetation targets, but where restoration occurs on highly degraded land such targets are not practical and setting looser targets may be more appropriate. Where this more ‘open-ended’ approach to restoration is adopted, surveillance methods that can track developing wetland habitats need to be established. Water regime and soil structure are known to influence the distribution and composition of developing wetland vegetation, and may be quantified using Sum Exceedence Values (SEV), calculated using the position of the water table and knowledge of soil stress thresholds. Use of SEV to explain patterns in naturally colonizing vegetation on restored, ex-arable land was tested at Wicken Fen (UK). Analysis of values from ten locations showed that soil structure was highly heterogeneous. Five locations had shallow aeration stress thresholds and so had the potential to support diverse wetland assemblages. Deep aeration stress thresholds at other locations precluded the establishment of a diverse wetland flora, but identified areas where species-poor wetland assemblages may develop. SEV was found to be a useful tool for the surveillance of sites where restoration targets are not specified in detail at the outset and may help predict likely habitat outcomes at sites using an open-ended restoration approach

Exploring the predation of UK bumblebees (Apidae, Bombus spp.) by the invasive pitcher plant Sarracenia purpurea: examining the effects of annual variation, seasonal variation, plant density and bumblebee gender

Invasive carnivorous plant species can impact the native invertebrate communities on which they prey. This article explores the predation of native UK bumblebees (Bombus spp.) by the invasive pitcher plant species Sarracenia purpurea and discusses the potential effect of S. purpurea on native bumblebees. Specifically, it evaluates whether the extent to which bumblebees are captured varies (i) over successive years, (ii) across June and July, (iii) with density of distribution of pitchers or (iv) with bumblebee gender. Pitcher contents were examined from an established population of Sarracenia purpurea growing in Dorset, UK. Results show that the total extent to which bumblebees were captured differed over the years 2012–2014 inclusive. A 1-year study in 2013 showed that more bumblebees were caught in July than in June and more bumblebees were captured when pitchers grew at high density. Results from 2013 also showed that more pitchers caught more than one bumblebee than would be expected based on a normal probability distribution and that this phenomenon affects female and male bumblebees equally. We discuss possible reasons for these results including that the bumblebees may be using S. purpurea as a resource. Further work is required to establish the exact underpinning mechanisms and the relative roles of plant and bumblebee behaviour within the relationship. Such interaction complexity may have consequences for consideration in invasive carnivorous plant management

Osteoprotegerin in Exosome-Like Vesicles from Human Cultured Tubular Cells and Urine

Urinary exosomes have been proposed as potential diagnostic tools. TNF superfamily cytokines and receptors may be present in exosomes and are expressed by proximal tubular cells. We have now studied the expression of selected TNF superfamily proteins in exosome-like vesicles from cultured human proximal tubular cells and human urine and have identified additional proteins in these vesicles by LC-MS/MS proteomics. Human proximal tubular cells constitutively released exosome-like vesicles that did not contain the TNF superfamily cytokines TRAIL or TWEAK. However, exosome-like vesicles contained osteoprotegerin (OPG), a TNF receptor superfamily protein, as assessed by Western blot, ELISA or selected reaction monitoring by nLC-(QQQ)MS/MS. Twenty-one additional proteins were identified in tubular cell exosomelike vesicles, including one (vitamin D binding protein) that had not been previously reported in exosome-like vesicles. Twelve were extracellular matrix proteins, including the basement membrane proteins type IV collagen, nidogen-1, agrin and fibulin-1. Urine from chronic kidney disease patients contained a higher amount of exosomal protein and exosomal OPG than urine from healthy volunteers. Specifically OPG was increased in autosomal dominant polycystic kidney disease urinary exosome-like vesicles and expressed by cystic epithelium in vivo. In conclusion, OPG is present in exosome-like vesicles secreted by proximal tubular epithelial cells and isolated from Chronic Kidney Disease urine.This work was supported by grants from the Instituto de Salud Carlos III (ISCIIIRETIC REDINREN RD06/0016, RD12/0021, PI11/01854, PI10/00072 PI09/ 00641 and PS09/00447); Comunidad de Madrid (Fibroteam S2010/BMD-2321, S2010/BMD-2378); Sociedad Española de NefrologÍa; European Network (HEALTH F2-2008-200647); DIALOK European project LSHB-CT-2007-036644; Fundacion Lilly and IRSIN/FRIAT to JE; Programa Intensificación Actividad Investigadora (ISCIII/ Agencia Laín-Entralgo/CM) to AO; Instituto de Salud Carlos III (FIS PI11/01401, CP09/00229); and Fundación Conchita Rábago de Jiménez DÍaz to GAL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189

With a genome size of ∼580 kb and approximately 480 protein coding regions, Mycoplasma genitalium is one of the smallest known self-replicating organisms and, additionally, has extremely fastidious nutrient requirements. The reduced genomic content of M. genitalium has led researchers to suggest that the molecular assembly contained in this organism may be a close approximation to the minimal set of genes required for bacterial growth. Here, we introduce a systematic approach for the construction and curation of a genome-scale in silico metabolic model for M. genitalium. Key challenges included estimation of biomass composition, handling of enzymes with broad specificities, and the lack of a defined medium. Computational tools were subsequently employed to identify and resolve connectivity gaps in the model as well as growth prediction inconsistencies with gene essentiality experimental data. The curated model, M. genitalium iPS189 (262 reactions, 274 metabolites), is 87% accurate in recapitulating in vivo gene essentiality results for M. genitalium. Approaches and tools described herein provide a roadmap for the automated construction of in silico metabolic models of other organisms

The natural exclusion of red deer from large boulder grazing refugia and the consequences for saxicolous bryophyte and lichen ecology

Large boulder grazing refugia permitted comparison of saxicolous bryophyte and lichen assemblages with those boulder tops accessible to red deer (Cervus elaphus) on a sporting estate in northwest Scotland. Plant succession was predicted to occur unchecked by grazing on the tops of these large boulders with cascading effects on bryophytes and lichens—assuming boulders had been in place over the same time period. Fifty pairs of boulders (one ≥2 m and the other accessible to red deer) were selected at random from various locations below north-facing crags. Percentage cover of each bryophyte and lichen species was estimated from three randomly placed quadrats on each boulder top. Due consideration was given to the influence of island biogeography theory in subsequent model simplification. Mean shrub cover and height, leaf-litter, bryophyte cover and bryophyte species richness were significantly higher within quadrats on large boulder tops that naturally excluded red deer. Lichen cover and lichen species richness were significantly higher on boulder tops accessible to red deer. Lichen cover was in a significant negative relationship with bryophyte cover, shrub cover and litter cover. Bryophyte cover showed a significant positive relationship with shrub height but there was an optimum shrub cover. Natural exclusion of red deer from the tops of large boulders has facilitated plant succession. The results suggest that grazing arrests the lithosere on boulder tops accessible to red deer at an early plagioclimax favouring saxicolous lichens. The results are relevant to situations where red deer might be excluded from boulder fields that hold lichen assemblages of conservation value

Green hay application and diverse seeding approaches to restore grazed lowland meadows: progress after 4 years and effects of a flood risk gradient

The two most common approaches to target species introduction in European meadow restoration are green‐hay transfer from species‐rich donor sites and the use of diverse seed mixtures reflecting the chosen target community. The potential of both approaches to restore species‐rich grassland has been variously reviewed, but very few studies have experimentally compared them at one and the same site. Moreover, studies involving one or both approaches have rarely taken into account environmental gradients at a site, and measured the impacts of such gradients on restoration outcomes. Such gradients do e.g. exist during grassland restoration on former arable land in river floodplains, where gradients in the occurrence of flooding, and in associated edaphic characteristics such as nutrient availability, might affect restoration outcomes. Using a randomised complete block experimental design, based on five different indicators of restoration progress, we compared the usefulness of green‐hay application and diverse‐seeding to restore species‐rich grazed meadows of the MG5 grassland type according to the British National Vegetation Classification, and also investigated how restoration outcomes differed after four years between areas within experimental plots characterized by high flood risk, and areas characterized by low flood risk. Overall, both restoration approaches yielded similar results over the course of the experiment, whereas high flood risk levels and associated edaphic factors such as high availability of phosphorus negatively affected restoration progress particularly in terms of floristic similarity to restoration targets. These results highlight the need to take into account environmental gradients during meadow restoration

How robust are community-based plant bioindicators? Empirical testing of the relationship between Ellenberg values and direct environmental measures in woodland communities

There are several community-based bioindicator systems that use species presence or abundance data as proxies for environmental variables. One example is the Ellenberg system, whereby vegetation data are used to estimate environmental soil conditions. Despite widespread use of Ellenberg values in ecological research, the correlation between bioindicated values and actual values is often an implicit assumption rather than based on empirical evidence. Here, we correlate unadjusted and UK-adjusted Ellenberg values for soil moisture, pH, and nitrate in relation to direct environmental measures for 50 woodland sites in the UK, which were subject to repeat sampling. Our results show the accuracy of Ellenberg values is parameter specific; pH values were a good proxy for direct environmental measures but this was not true for soil moisture, when relationships were weak and non-significant. For nitrates, there were important seasonal differences, with a strong positive logarithmic relationship in the spring but a non-significant (and negative) correlation in summer. The UK-adjusted values were better than, or equivalent to, Ellenberg’s original ones, which had been quantified originally for Central Europe, in all cases. Somewhat surprisingly, unweighted values correlated with direct environmental measures better than did abundance-weighted ones. This suggests that the presence of rare plants can be highly important in accurate quantification of soil parameters and we recommend using an unweighted approach. However, site profiles created only using rare plants were inferior to profiles based on the whole plant community and thus cannot be used in isolation. We conclude that, for pH and nitrates, the Ellenberg system provides a useful estimate of actual conditions, but recalibration of moisture values should be considered along with the effect of seasonality on the efficacy of the system

Gendered Risk Perceptions Associated with Human-Wildlife Conflict: Implications for Participatory Conservation

This research aims to foster discourse about the extent to which gender is important to consider within the context of participatory approaches for biological conservation. Our objectives are to: (1) gender-disaggregate data about stakeholders' risk perceptions associated with human-wildlife conflict (HWC) in a participatory conservation context, and (2) highlight insights from characterizing gendered similarities and differences in the way people think about HWC-related risks. Two communal conservancies in Caprivi, Namibia served as case study sites. We analyzed data from focus groups (n = 2) to create gendered concept maps about risks to wildlife and livelihoods and any associations of those risks with HWC, and semi-structured interviews (n = 76; men = 38, women = 38) to measure explicit risk attitudes associated with HWC. Concept maps indicated some divergent perceptions in how groups characterized risks to wildlife and livelihoods; however, not only were identified risks to wildlife (e.g., pollution, hunting) dissimilar in some instances, descriptions of risks varied as well. Study groups reported similar risk perceptions associated with HWC with the exception of worry associated with HWC effects on local livelihoods. Gendered differences in risk perceptions may signal different priorities or incentives to participate in efforts to resolve HWC-related risks. Thus, although shared goals and interests may seem to be an obvious reason for cooperative wildlife management, it is not always obvious that management goals are shared. Opportunity exists to move beyond thinking about gender as an explanatory variable for understanding how different groups think about participating in conservation activities