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Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography–mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography–MS (GC-MS) and ultraperformance liquid chromatography–MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control–based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.

Land-use change due to agriculture has a major influence on arthropod biodiversity, and may influence species differently depending on their traits. It is unclear how species traits vary across different land uses and their edges, with most studies focussing on single habitat types and overlooking edge effects. We examined variation in morphological traits of carabid beetles (Coleoptera:Carabidae) on both sides of edges between woodlands and four adjoining, but contrasting farmland uses in an agricultural landscape. We asked: (1) how do traits differ between woodlands and different adjoining farmland uses (crop, fallow, restoration planting, and woody debris applied over crop), and do effects depend on increasing distances from the farmland–woodland edge? (2) Does vegetation structure explain observed effects of adjoining farmland use and edge effects on these traits? We found that carabid communities varied in body size and shape, including traits associated with diet, robustness, and visual ability. Smaller sized species were associated with woodlands and larger sized species with farmlands. Farmland use further influenced these associations, where woodlands adjoining plantings supported smaller species, while fallows and crops supported larger species. Vegetation structure significantly influenced body size, flying ability, and body shape, and helped explain the effects of farmland use and distance from edges on body size. We highlight the important role of vegetation structure, farmland use, and edge effects in filtering the morphological traits of carabid assemblages across a highly modified agricultural landscape. Our findings suggest that farmland management can influence body size and dispersal-related traits in farmland and adjacent native vegetation.

Phenotyping of 1,200 ‘healthy’ adults from the UK has been performed through the investigation of diverse classes of hydrophilic and lipophilic metabolites present in serum by applying a series of chromatography–mass spectrometry platforms. These data were made robust to instrumental drift by numerical correction; this was prerequisite to allow detection of subtle metabolic differences. The variation in observed metabolite relative concentrations between the 1,200 subjects ranged from less than 5 % to more than 200 %. Variations in metabolites could be related to differences in gender, age, BMI, blood pressure, and smoking. Investigations suggest that a sample size of 600 subjects is both necessary and sufficient for robust analysis of these data. Overall, this is a large scale and non-targeted chromatographic MS-based metabolomics study, using samples from over 1,000 individuals, to provide a comprehensive measurement of their serum metabolomes. This work provides an important baseline or reference dataset for understanding the ‘normal’ relative concentrations and variation in the human serum metabolome. These may be related to our increasing knowledge of the human metabolic network map. Information on the Husermet study is available at http://www.husermet.org/ . Importantly, all of the data are made freely available at MetaboLights ( http://www.ebi.ac.uk/metabolights/ ).

Carrion is an ephemeral and spatially patchy resource that supports a diverse subset of species linked to nutrient cycling and the decomposition process. A number of studies have separately documented changes in the diversity of plants, arthropods and vertebrates at individual carcasses, but there are few studies that have examined how functional traits of different groups of organisms underpin their responses to carrion patches. We used a carrion addition experiment to compare changes in composition and functional traits of insect and plant assemblages at carcasses compared with control sites. We found that significant changes in insect assemblage evenness and heterogeneity was associated with species' dispersal traits, and that plant assemblage responses to subsequent soil nitrogen changes was most apparent among graminoids and exotic species. Beetles at carcasses were twice as large as their counterparts at control sites during the first week of carrion decomposition, and also had higher wing loadings. Plants with high specific leaf area responded faster to the carcass addition, and twice as many species recolonised the centre of carcasses in exotic-dominated grassland compared with carcasses in native-dominated grassland. These results provide an example of how traits of opportunist species enable them to exploit patchy and dynamic resources. This increases our understanding of how carcasses can drive biodiversity dynamics, and has implications for the way carrion might be managed in ecosystems, such as appropriate consideration of spatial and temporal continuity in carrion resources to promote heterogeneity in nutrient cycling and species diversity within landscapes.

The eastern bettong ( Bettongia gaimardi ), a medium-sized digging marsupial, was reintroduced to a predator-free reserve after 100 years of absence from the Australian mainland. The bettong may have the potential to restore temperate woodlands degraded by a history of livestock grazing, by creating numerous small disturbances by digging. We investigated the digging capacity of the bettong and compared this to extant fauna, to answer the first key question of whether this species could be considered an ecosystem engineer, and ultimately if it has the capacity to restore lost ecological processes. We found that eastern bettongs were frequent diggers and, at a density of 0.3–0.4 animals ha −1 , accounted for over half the total foraging pits observed (55%), with echidnas ( Tachyglossus aculeatus ), birds and feral rabbits ( Oryctolagus cuniculus ) accounting for the rest. We estimated that the population of bettongs present dug 985 kg of soil per ha per year in our study area. Bettongs dug more where available phosphorus was higher, where there was greater basal area of Acacia spp. and where kangaroo grazing was less. There was no effect on digging of eucalypt stem density or volume of logs on the ground. While bettong digging activity was more frequent under trees, digging also occurred in open grassland, and bettongs were the only species observed to dig in scalds (areas where topsoil has eroded to the B Horizon). These results highlight the potential for bettongs to enhance soil processes in a way not demonstrated by the existing fauna (native birds and echidna), and introduced rabbit.

Temperate grasslands and woodlands are the focus of extensive restoration efforts worldwide. Reintroduction of locally extinct soil-foraging and burrowing animals has been suggested as a means to restore soil function in these ecosystems. Yet little is known about the physical and chemical effects of digging on soil over time and how these effects differ between species of digging animal, vegetation types or ecosystems. We compared foraging pits of a native reintroduced marsupial, the eastern bettong ( Bettongia gaimardi ) and that of the exotic European rabbit ( Oryctolagus cuniculus ). We simulated pits of these animals and measured pit dimensions and soil chemical properties over a period of 2 years. We showed that bettong and rabbit pits differed in their morphology and longevity, and that pits had a strong moderating effect on soil surface temperatures. Over 75% of the simulated pits were still visible after 2 years, and bettong pits infilled faster than rabbit pits. Bettong pits reduced diurnal temperature range by up to 25 °C compared to the soil surface. We did not find any effects of digging on soil chemistry that were consistent across vegetation types, between bettong and rabbit pits, and with time since digging, which is contrary to studies conducted in arid biomes. Our findings show that animal foraging pits in temperate ecosystems cause physical alteration of the soil surface and microclimatic conditions rather than nutrient changes often observed in arid areas.

Background Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide prima facie evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced Aspergillus niger fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another A.niger sequence. Tandem mass spectra (MS/MS) were acquired from 1d gel electrophoresis bands and searched against all available gene models using Average Peptide Scoring (APS) and reverse database searching to produce confident identifications at an acceptable false discovery rate (FDR). Results 405 identified peptide sequences were mapped to 214 different A.niger genomic loci to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these loci either had no preferred predicted gene model or the genome annotators' chosen \"best\" model for that genomic locus was not found to be the most parsimonious match to the identified peptides. The peptides identified also boosted confidence in predicted gene structures spanning 54 introns from different gene models. Conclusion This work highlights the potential of integrating experimental proteomics data into genomic annotation pipelines much as expressed sequence tag (EST) data has been. A comparison of the published genome from another strain of A.niger sequenced by DSM showed that a number of the gene models or proteins with proteomics evidence did not occur in both genomes, further highlighting the utility of the method.

1. Examining the consequences of environmental change for the provision of ecosystem services can be facilitated through trait-based frameworks that consider linkages between traits that influence a species' response to change and traits that determine its effect on ecosystem services. 2. Developing these frameworks requires a systematic approach to trait selection and addressing the interrelationships among the scale of the environmental change, area of ecosystem service provision and the most appropriate traits for analysis. 3. We examine key issues in the application of trait approaches to vertebrates, drawing specifically on the substantial progress made in this area for plants. We argue that vertebrate ecologists need to develop more coherent and systematic trait-based approaches that are broadly applicable. 4. We present a new framework for selecting response and effect traits to link environmental change with ecosystem services. An empirical example of each step in the framework is provided using birds as a case study, linking the environmental change of loss of tree cover with the ecosystem service of invertebrate pest regulation in apple orchards. We found that as tree cover around orchards increased so did the abundance and foraging rate of bird species that pursue invertebrates in flight, and this may help reduce the abundance of certain pests of apples (e.g. adult stages of Cydia pomonella and Helicoverpa armigera). 5. Implementing a systematic and transparent approach to trait selection should further refine the development of trait-based approaches for vertebrates.

Grasslands and grassy woodlands worldwide have experienced declines in extent and condition, with substantial changes to their ground-layer biodiversity. In Australia, this decline has coincided with the extinction of many digging mammals that may have once created regeneration niches for native ground layer plants. These digging mammals are widely recognised as ‘ecosystem engineers’, due to their influence on biopedturbation and resultant soil functions. Yet there is uncertainty as to the benefits of digging in restoring grassland diversity with current levels of modification and the presence of exotic plants. We investigated the effect of digging by the reintroduced eastern bettong (Bettongia gaimardi) on seedling germination in a temperate grassy woodland in south-eastern Australia. We marked fresh bettong foraging pits and undisturbed control plots in dense and open grassland. We added seeds of seven native forb species and monitored germination and establishment over 2 years. We found significantly more seedlings in bettong pits than controls, particularly in dense grassland. This effect persisted beyond 1 year, suggesting that pits may have increased seedling survival in dry conditions. Surprisingly, native species displayed a stronger positive response to pits than exotic species, particularly in a wet year. There was an initial reduction in exotic species, but this was followed by their increase in 1-year-old pits, suggesting that the disturbance created by digging could eventually lead to an increase in weed abundance. Our results demonstrate that while bettong pits provide a germination niche for native forbs, reintroducing digging animals will not necessarily result in the desired restoration outcomes. Ongoing persistence of exotic species is to be expected, and seed addition may be required for species that are seed-limited.

Vegetation effects on arthropods are well recognized, but it is unclear how different vegetation attributes might influence arthropod assemblages across mixed-agricultural landscapes. Understanding how plant communities influence arthropods under different habitat and seasonal contexts can identify vegetation management options for arthropod biodiversity. We examined relationships between vegetation structure, plant species richness and plant species composition, and the diversity and composition of beetles in different habitats and time periods. We asked: (1) What is the relative importance of plant species richness, vegetation structure and plant composition in explaining beetle species richness, activity-density and composition? (2) How do plant-beetle relationships vary between different habitats over time? We sampled beetles using pitfall traps and surveyed vegetation in three habitats (woodland, farmland, their edges) during peak crop growth in spring and post-harvest in summer. Plant composition better predicted beetle composition than vegetation structure. Both plant richness and vegetation structure significantly and positively affected beetle activity-density. The influence of all vegetation attributes often varied in strength and direction between habitats and seasons for all trophic groups. The variable nature of plant-beetle relationships suggests that vegetation management could be targeted at specific habitats and time periods to maximize positive outcomes for beetle diversity. In particular, management that promotes plant richness at edges, and promotes herbaceous cover during summer, can support beetle diversity. Conserving ground cover in all habitats may improve activity-density of all beetle trophic groups. The impacts of existing weed control strategies in Australian crop margins on arthropod biodiversity require further study.