Species Traits Predict Assemblage Dynamics at Ephemeral Resource Patches Created by Carrion

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.This research was supported by the Mulligans Flat – Goorooyarroo Woodland Experiment (Australian Research Council Linkage Grants LP0561817 and LP110100126). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Plant Strategies in Herbaceous Vegetation in Relation to Soil Disturbance, Fertilization and Sowing on the Northern Tablelands of NSW

This study examined whether the response of herbaceous vegetation to environmental disturbances such as mechanical soil disturbance and fertilization can be predicted from a knowledge of the component species' plant attributes. Some aspects of Grime's (1979) C-S-R model were also tested. The model proposed that the three permutations of low stress and low disturbance, low stress and high disturbance, and high stress and low disturbance are associated with competitive (C), ruderal (R) and stress-tolerant (S) plant strategies, respectively. A completely randomised block experiment with three factors, soil disturbance, fertilization and sowing, was established in an area of moderately grazed temperate grassland on the Northern Tablelands of New South Wales. The site was dominated by the tall, warm season perennial grasses, 'Aristida ramosa' and 'A. warburgii' and its yellow podzolic soil was deficient in phosphorus, nitrogen and sulphur. The study area experiences an annual average rainfall of 914 mm, an annual average maximum temperature of 20.3°C and an annual average minimum temperature of 7.3°C. There were three levels of soil disturbance (none, hand-hoed and rotary-hoed), two levels of fertilization (none and fertilized NPS) and two levels of sowing (none and sown). The sown treatment consisted of hand-sowing the propagules of seven exotic species into the plots. During the experimental period (August 1992 -February 1994), the sown treatment was applied once in August 1992, disturbance was applied annually in August, fertilizer was applied twice a year and the vegetation was sampled in spring (November) and summer (March/February) each year. ... In conclusion, the response of herbaceous vegetation to mechanical soil disturbance and fertilization could be predicted from a knowledge of the component species' plant attributes. Plant attributes relating to plant persistence, biomass partitioning (leaves vs reproduction vs storage), and use of resources (conservative versus liberal) were strongly related to fertilization and soil disturbance. Plant attributes can discriminate between habitats as well as, or better than, floristic data. On a community scale, the influence of historical factors on vegetation response was not removed by the plant attribute approach, although it was somewhat reduced. Thus, the relationships found using this approach were of intermediate generality and are applicable to sites with a similar fertilizer and disturbance history. The greatest support for the C-S-R model was found using the key (4 predictions upheld, 1 inconsistent and 2 rejected). Support for the model was also found by testing its underlying hypotheses (2 predictions upheld, 2 inconsistent and 2 rejected), while the ordination of vegetation samples by the mean Rmax and MI of its component species was unsuccessful (0 predictions upheld, 2 inconsistent and 3 rejected). The present study shows how vegetation models may be viewed as a starting point for research and refinement rather than something that must be either wholly accepted or rejected

Effects of digging by a native and introduced ecosystem engineer on soil physical and chemical properties in temperate grassy woodland

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.This work was supported by an Australian Research Council Linkage Grant (LP0561817, LP110100126, LP140100209). Catherine Ross was supported by an Australian Government Research Training Program (RTP) Scholarship, and an additional scholarship top-up from the ARC (LP140100209)

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

<p>Abstract</p> <p>Background</p> <p>Proteomic data is a potentially rich, but arguably unexploited, data source for genome annotation. Peptide identifications from tandem mass spectrometry provide <it>prima facie </it>evidence for gene predictions and can discriminate over a set of candidate gene models. Here we apply this to the recently sequenced <it>Aspergillus niger </it>fungal genome from the Joint Genome Institutes (JGI) and another predicted protein set from another <it>A.niger </it>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).</p> <p>Results</p> <p>405 identified peptide sequences were mapped to 214 different <it>A.niger </it>genomic <it>loci </it>to which 4093 predicted gene models clustered, 2872 of which contained the mapped peptides. Interestingly, 13 (6%) of these <it>loci </it>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.</p> <p>Conclusion</p> <p>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 <it>A.niger </it>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.</p

Herbivore management for biodiversity conservation: A case study of kangaroos in the Australian Capital Territory (ACT)

Populations of macropods are higher than estimated pre-European densities in many parts of Australia. To achieve appropriate densities of macropods in the Australian Capital Territory's nature reserves, multi-tenure kangaroo management units are used to tailor management of kangaroos and total grazing pressure to achieve conservation objectives. An adaptive management framework is recommended that monitors the state of the ground-layer vegetation and alters the cull accordingly. This case study may provide insights for kangaroo management in other temperate areas of Australia

Contrasting beetle assemblage responses to cultivated farmlands and native woodlands in a dynamic agricultural landscape

There is an urgent need to identify ways of managing agricultural landscapes for biodiversity conservation without reducing food production. Farming practices that consider spatiooral heterogeneity of farm fields may be a feasible alternative to large-scale revegetation of farmlands for maintaining arthropod biodiversity and their important ecological function. We examined seasonal differences in beetle assemblages in woodland remnants and four adjoining farmland uses in a highly modified agricultural landscape in southeastern Australia. The farmland uses were crops, fallows, and two restoration treatments (fine woody debris applied over harvested crop fields, and restoration plantings). Unexpectedly, overall species richness was significantly lower in remnants than in adjacent farmlands. Remnants and farmlands supported significantly different assemblages, with a third of species found in both habitats. Abundance responses were taxon-specific and influenced by interactions between land use and season. In particular, predator abundance was significantly higher in plantings and fallows during spring compared to summer. Detritivore abundance was significantly higher in the woody debris compared to the adjacent remnants. Herbivore abundance did not differ between remnants and farmlands over time. Complex responses provide strong support for a mosaic of land uses to effectively conserve different beetle groups. Species richness results suggest that further agricultural intensification, in farm fields and through the removal of remnant vegetation, risks reducing beetle diversity in this region. Maintaining farmland heterogeneity with a mix of low-intensity land uses, such as conservation tillage, crop-fallow rotation, restoration plantings, and the novel application of fine woody debris over cultivated fields, may provide seasonal refuge and resources for beetles

Disentangling the effects of farmland use, habitat edges, and vegetation structure on ground beetle morphological traits

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.This work was supported by Central Tablelands Local Land Services (through Australian Government funding), Lake Cowal Foundation and Mount Mulga Pastoral Company. KN was supported by an Australian Government Research Training Program (RTP) scholarship

Pneumococcal conjugate vaccines PREVenar13 and SynflorIX in sequence or alone in high-risk Indigenous infants (PREV-IX_COMBO): protocol of a randomised controlled trial.

INTRODUCTION: Otitis media (OM) starts within weeks of birth in almost all Indigenous infants living in remote areas of the Northern Territory (NT). OM and associated hearing loss persist from infancy throughout childhood and often into adulthood. Educational and social opportunities are greatly compromised. Pneumococcus and non-typeable Haemophilus influenzae (NTHi) are major OM pathogens that densely colonise the nasopharynx and infect the middle ear from very early in life. Our hypothesis is that compared to current single vaccine schedules, a combination of vaccines starting at 1 month of age, may provide earlier, broadened protection. METHODS AND ANALYSES: This randomised outcome assessor, blinded controlled trial will recruit 425 infants between 28 and 38 days of age and randomly allocate them (1:1:1) to one of three pneumococcal conjugate vaccine (PCV) schedules: Synflorix at 2, 4, 6 months of age, Prevenar13 at 2, 4 and 6 months of age, or an investigational schedule of Synflorix at 1, 2 and 4 months plus Prevenar13 at 6 months of age. The blinded primary outcomes at 7 months of age are immunogenicity of specific vaccine antigens (geometric mean concentration (GMC) and proportion of participants with above threshold GMC of 0.35 µg/L). Secondary outcomes at all timepoints are additional immunogenicity measures and proportion of participants with nasopharyngeal carriage of vaccine-type pneumococci and NTHi, and any OM, including any tympanic membrane perforation. Parental interviews will provide data on common risk factors for OM. ETHICS AND DISSEMINATION: Ethical approval has been obtained from NT Department of Health and Menzies HREC (EC00153), Central Australian HREC (EC00155) and West Australian Aboriginal Health Ethics Committee (WAAHEC- 377-12/2011). Final trial results, data analyses, interpretation and conclusions will be presented in appropriate written and oral formats to parents and guardians, participating communities, local, national and international conferences, and published in peer-reviewed open access journals. TRIAL REGISTRATION NUMBERS: ACTRN12610000544077 and NCT01174849

Biomass and floristic patterns in the ground layer vegetation of box-gum grassy eucalypt woodland in Goorooyarroo and Mulligans Flat Nature Reserves, Australian Capital Territory

We establish a methodology and present baseline data for a long-term grassy woodland restoration study that commenced in 2007 in two nature reserves (Mulligans Flat, Goorooyarroo (35° 9–13’ S; 149° 9–12’ E)) totalling 1386 ha on the northern boundary of Canberra, in the Australian Capital Territory in south eastern Australia. The experimental infrastructure comprises 96 × 1 ha sites established in Eucalyptus blakelyi / Eucalyptus melliodora dominated woodland. These are being subjected to varying kangaroo grazing pressure and augmentation with logs, while burning treatments are planned. One reserve (Mulligans Flat) has been fenced for feral predator control and contains half the sites, forming a companion experiment to Goorooyarroo. Our baseline floristic study comprised estimates, at the site level, of ground layer biomass, species biomass, ground cover types and soil (0–10 cm) properties. From these data we conclude that the groundlayer vegetation is dominated by Joycea pallida, Austrodanthonia spp., Themeda australis and Aristida ramosa. These grasses varied in abundance according to differences in soil pH, phosphorus and to a lesser extent nitrates. Forb frequencies were highly sensitive to nitrate levels with annual exotic forbs dominating at high nitrate sites. More generally, soil nutrient levels and exotic species in some sites indicated areas of previous pasture improvement activities. Biomass estimates indicated extremely high grazing pressure, sufficient to negatively affect the habitat quality for ground-dependent fauna and some soil processes. These data will provide an important basis for examining rates of ecosystem recovery under different restoration strategies

Returning a lost process by reintroducing a locally extinct digging marsupial

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