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Near infrared reflectance (NIR) spectroscopy has been used by the agricultural industry as a rapid and inexpensive technique to quantify nutritional chemistry in plants. The aim of this study was to evaluate the performance of NIR calibrations in predicting the nutritional composition of ten pasture species that underpin livestock industries in many countries. The species comprised a range of functional diversity (C3 legumes; C3/C4 grasses; annuals/perennials) and origins (tropical/temperate; introduced/native) that grew under varied environmental conditions (control and experimentally induced warming and drought) over a period of more than two years ( n = 2622). A maximal calibration set including 391 samples was used to develop and evaluate calibrations for all ten pasture species (global calibrations), as well as for subsets comprised of the plant functional groups. This study found that the global calibrations were appropriate to predict the six key nutritional quality parameters for the studied pasture species, with the highest estimation quality found for ash (ASH), crude protein (CP), amylase-treated neutral detergent fibre (aNDF) and acid detergent fibre (ADF), and the lowest for ether extract (EE) and acid detergent lignin (ADL) parameters. The plant functional group calibrations for C3 grasses performed better than the global calibrations for ASH, CP, ADF and EE parameters, whereas for C3 legumes and C4 grasses the functional group calibrations performed less well than the global calibrations for all nutritional parameters of these groups. Additionally, the calibrations were able to capture the range of variation in forage nutritional quality caused by future climate scenarios of warming and severe drought.

Research on use of foraging patches has focused on why herbivores visit or quit patches, yet little is known about visits to patches over time. Food quality, as reflected by higher nutritional quality and lower plant defenses, and physical patch characteristics, which offer protection from predators and weather, affect patch use and hence should influence their revisitation. Due to the potentially high costs of moving between patches, fragmented habitats are predicted to complicate foraging decisions of many animals. We aimed to determine how food quality, shelter availability and habitat fragmentation influence tree reuse by a specialist folivore, the koala, in a fragmented agricultural landscape. We GPS-tracked 23 koalas in northern New South Wales, Australia and collated number of revisits, average residence time, and average time-to-return to each tree. We measured tree characteristics including food quality (foliar nitrogen and toxic formylated phloroglucinol compounds, FPCs concentrations), tree size, and tree connectedness. We also modeled the costs of locomotion between trees. Koalas re-visited isolated trees with high leaf nitrogen disproportionately often. They spent longer time in trees with high leaf nitrogen, and in large trees used for shelter. They took longer to return to trees with low leaf nitrogen. Tree connectivity reduced travel costs between patches, being either individual or groups of trees. FPC levels had no detectable effect on patch revisitation. We conclude that food quality and shelter drive koala tree re-visits. Scattered, isolated trees with nutrient-rich leaves are valuable resource patches for koalas despite movement costs to reach them.

An animal’s diet is a crucial trait that defines their realised ecological niche, especially for dietary specialists such as the koala (Phascolarctos cinereus), a threatened arboreal marsupial folivore. Unfortunately, the current methods used to characterise koala diet are labour intensive, biased and/or unreliable. Further, in this study we show that four barcoding genes (ITS, ETS, CCRandmatK) are unable to resolve potential koala food trees to species. Therefore, we developed and tested a novel SNP-based method for the analysis of koala diet from faeces using the DArTseq platform. This method returned a large number of species-specific SNPs for candidate koala food tree species. Due to low within-species variation, few individuals of each tree species are needed to capture the majority of DArTseq SNP diversity. Nonetheless, we suggest sampling multiple trees to reduce the impact of high allele dropout rates in the DArTseq data. After identifying species-specific SNPs from candidate food tree species from two study sites with different assemblages of eucalypts we were able to detect those SNPs in koala faecal DNA using DArTag, a targeted genotyping assay. This enabled us to semi-quantitatively characterise the koalas’ diets. The food tree species identified were in broad agreement with previously known koala food tree species but also revealed additional species that may contribute to koala diet. This approach provides an important new tool for use in koala ecology and conservation and may prove useful in diet determination for other species where high taxonomic resolution is crucial and dietary DNA is scarce.

Koala retrovirus subtype A is the youngest endogenized retrovirus, providing a unique system to elucidate retroviral-host co-evolution. We characterised KoRV geography using faecal DNA from 192 samples across 20 populations throughout the koala’s range. We reveal an abrupt change in KoRV genetics and incidence at the Victoria/NSW state border. In northern koalas, pol gene copies were ubiquitously present at greater than 5 per-cell, consistent with endogenous KoRV. In southern koalas, pol copies were detected in only 25.8% of koalas and always at copy numbers less than one, while the env gene was detected in all animals and in a majority at copy numbers of greater than one per-cell. These results suggest that southern koalas carry partial endogenous KoRV-like sequences. Deep sequencing of the env hypervariable region revealed three putatively endogenous KoRV-A sequences in northern koalas and a single, distinct sequence present in all southern koalas. Among northern populations, env sequence diversity decreased with distance from the equator, suggesting infectious KoRV-A invaded the koala genome in northern Australia and then spread south. The previously described exogenous KoRV subtypes (B-K), two novel subtypes (L and M), and intermediate or hybrid subtypes were detected in all northern koala populations but strikingly absent from all southern animals tested. Apart from KoRV-D, these exogenous subtypes were generally locally prevalent but geographically restricted, producing KoRV genetic differentiation among northern populations. This suggests that sporadic evolution and local transmission of the exogenous subtypes has occurred within northern Australia, but this has not extended into animals within southern Australia.Author SummaryRetrovirus infection is generally synonymous with disease; however, retroviruses can also become endogenous (incorporated into the germline) and thereby directly contribute to the genetic makeup of a species. This has occurred in all vertebrates, yet little is known about the endogenization process. As the youngest virus known to be endogenized, koala retrovirus (KoRV) offers a unique opportunity to study these early stages of co-evolution. This study reveals a comprehensive picture of KoRV biogeography that informs our understanding of how host population history, host suppression and transmission dynamics can influence retroviral evolution. KoRV is also associated with chlamydiosis and neoplasia in the vulnerable koala. Our improved understanding of how KoRV variants are distributed should guide conservation management to help limit disease.

Silicon (Si) accumulation in plants is widely recognised as an effective physical defence against chewing herbivores. However, its effects on some feeding guilds such as cell-content feeders are understudied despite being severe economic pests (e.g. Tetranychus urticae). Moreover, most studies focus on direct impacts of Si, but there is growing evidence that Si also impacts indirect defence. We examined the effects of Si on French bean, Phaseolus vulgaris, defences against the two-spotted spider mite, T. urticae. We grew plants hydroponically with (+ Si) or without (–Si) silicon, assessed T. urticae performance and tested the preference of the predatory mite, Phytoseiulus persimilis, for volatiles from T. urticae-infested (+ M) or uninfested (–M) plants. The provision of Si to plants suppressed T. urticae egg-laying, population growth and leaflet damage, and partially ameliorated T. urticae-induced reductions in stomatal conductance and net photosynthesis. Furthermore, T. urticae infestation increased foliar Si accumulation. Predatory mites were more attracted (64%) to volatiles from + Si plants experiencing herbivory than to –Si plants. The relative emissions (%) of volatile compounds, viz. E-2-hexanyl benzoate, hexanal, E-trans-β-ocimene, D-limonene, β-caryophyllene and methyl salicylate were elevated from + Si + M plants, while the relative emissions of 3-hexanol, trans-calamenene, o-xylene and o-cymene were lowered compared to –Si + M plants. Our results show, for the first time, that Si defences are inducible and effective even in low Si-accumulating plants against T. urticae and suggest that Si could play a role in pest biocontrol.

For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings., Host defense genotype has previously been shown to affect associations with ectomycorrhizal (EM) fungi, but the extent to which secondary metabolites such as terpenes affect these associations is unknown. We conducted a reciprocal transplant field experiment to test the effect of varying terpene genotype on the EM community composition of individual seedlings and found that the only the location of a seedling affects community composition. Other processes affecting EM community composition at small scales, such as environmental preference and interspecific interactions, may thus preclude the expression of any effect of genotype in wild conditions.

Near infrared spectroscopy is widely used to rapidly and cost-effectively collect chemical information from plant samples. Large datasets with hundreds to thousands of spectra and reference values are increasingly becoming more common as researchers accumulate data over many years or across research groups. These datasets potentially contain great spectral and chemical variation and could produce a broadly-applicable calibration model. In this study, partial least squares regression was used to model relationships between near infrared spectra and the foliar concentration of two ecologically-important chemical traits, available nitrogen and total formylated phloroglucinol compounds in Eucalyptus leaves. The nested spatial structure within the extensive dataset of spectra and reference values from 80 species of Eucalyptus was taken into account during calibration development and model validation. Geographic variation amongst samples influenced how well available nitrogen could be predicted. Predictive error of the model was greatest when tested against samples from different Australian states and local government areas to the calibration set. In addition, the results showed that simply relying on spectral variation (assessed by Mahalanobis distance) may mislead researchers into how many reference values are needed. The prediction accuracy of the model of available nitrogen differed little whether 300 or up to 987 calibration samples were included, which indicated that an excessive number of reference values were obtained. Lastly, a suitable multi-species calibration for formylated phloroglucinol compounds was produced and the difficulties associated with predicting complex chemical traits were discussed. Directing effort towards broadly applicable models will encourage sharing of calibration models across projects and research groups and facilitate the integration of near infrared spectroscopy in many research fields.

Shifts in the timing, intensity and/or frequency of climate extremes, such as severe drought and heatwaves, can generate sustained shifts in ecosystem function with important ecological and economic impacts for rangelands and managed pastures. The Pastures and Climate Extremes experiment (PACE) in Southeast Australia was designed to investigate the impacts of a severe winter/spring drought (60% rainfall reduction) and, for a subset of species, a factorial combination of drought and elevated temperature (ambient +3°C) on pasture productivity. The experiment included nine common pasture and Australian rangeland species from three plant functional groups (C3 grasses, C4 grasses and legumes) planted in monoculture. Winter/spring drought resulted in productivity declines of 45% on average and up to 74% for the most affected species (Digitaria eriantha) during the 6-month treatment period, with eight of the nine species exhibiting significant yield reductions. Despite considerable variation in species’ sensitivity to drought, C4 grasses were more strongly affected by this treatment than C3 grasses or legumes. Warming also had negative effects on cool-season productivity, associated at least partially with exceedance of optimum growth temperatures in spring and indirect effects on soil water content. The combination of winter/spring drought and year-round warming resulted in the greatest yield reductions. We identified responses that were either additive (Festuca), or less-than-additive (Medicago), where warming reduced the magnitude of drought effects. Results from this study highlight the sensitivity of diverse pasture species to increases in winter and spring drought severity similar to those predicted for this region, and that anticipated benefits of cool-season warming are unlikely to be realized. Overall, the substantial negative impacts on productivity suggest that future, warmer, drier climates will result in shortfalls in cool-season forage availability, with profound implications for the livestock industry and natural grazer communities.

The acquisition and maturation of the gastrointestinal microbiome is a crucial aspect of mammalian development, particularly for specialist herbivores such as the koala (Phascolarctos cinereus). Joey koalas are thought to be inoculated with microorganisms by feeding on specialised maternal faeces (pap). We found that compared to faeces, pap has higher microbial density, higher microbial evenness and a higher proportion of rare taxa, which may facilitate the establishment of those taxa in joey koalas. We show that the microbiomes of captive joey koalas were on average more similar to those of their mothers than to other koalas, indicating strong maternal inheritance of the faecal microbiome, which can lead to intergenerational gut dysbiosis when the mother is ill. Directly after pap feeding, the joey koalas' microbiomes were enriched for milk-associated bacteria including Bacteroides fragilis, suggesting a conserved role for this species across mammalian taxa. The joeys' microbiomes then changed slowly over five months to resemble those of adults by one year of age. The relative abundance of fibrolytic bacteria and genes involved in the degradation of plant cell walls also increased in the infants over this time, likely in response to an increased proportion of Eucalyptus leaves in their diets. This article is protected by copyright. All rights reserved.

In the face of a changing climate, research indicates that more frequent and severe drought conditions are critical problems that will constrain production of high-quality forage and influence the performance of grazing animals in the future. In addition, the duration of drought and potential trade-offs between plant morphology and nutritional composition may influence plant drought adaptation strategies across pasture species, and the consequences for forage quality are not well understood. Here we present the results of a study investigating the effects of drought on biomass productivity, dead material, leaf:stem biomass allocation and nutritional composition (whole-plant and tissue-specific) across nine diverse pasture species. For this, we conducted a field experiment exposing species to a 6-month period of simulated severe drought (60% rainfall reduction during winter and spring) and samples were collected at multiple harvests. We found that drought had different, harvest-specific effects on plant biomass structure and nutritional composition among pasture species. The severity of drought impacts on productivity, but not on nutritional quality, increased with drought duration. In general, drought strongly reduced productivity, increased the percentage of dead material and had mixed effects (increases, decreases and no effect) on leaf:stem ratio and concentrations of crude protein, non-structural carbohydrates, neutral detergent fibre and lignin. Changes in plant-level nutritional quality were driven by simultaneous changes in both leaf and stem tissues for most, but not all, species. Our findings may be especially helpful for selection of adapted species/cultivars that could minimize potential drought risks on forage, thereby optimising pasture performance under future drought scenarios.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge., Measurement(s)plant traitTechnology Type(s)digital curationSample Characteristic - OrganismViridiplantaeSample Characteristic - LocationAustralia Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.14545755

In this study we compared the faecal microbiomes of wild joey koalas (Phascolarctos cinereus) to those of adults, including their mothers, to establish whether gut microbiome maturation and inheritance in the wild is comparable to that seen in captivity. Our findings suggest that joey koala microbiomes slowly shift towards an adult assemblage between 6 and 12 months of age, as the microbiomes of 9-month-old joeys were more similar to those of adults than those of 7-month-olds, but still distinct. At the phylum level, differences between joeys and adults were broadly consistent with those in captivity, with Firmicutes increasing in relative abundance over the joeys' development and Proteobacteria decreasing. Of the fibre-degrading genes that increased in abundance over the development of captive joeys, those involved in hemicellulose and cellulose degradation, but not pectin degradation, were also generally found in higher abundance in adult wild koalas compared to 7-month-olds. Greater maternal inheritance of the faecal microbiome was seen in wild than in captive koalas, presumably due to the more solitary nature of wild koalas. This strong maternal inheritance of the gut microbiome could contribute to the development of localized differences in microbiome composition, population health and diet through spatial clustering of relatives.

Insect herbivores employ various defences, including morphological, behavioural, and immune responses against their natural enemies (e.g., predators, parasitoids) which can make biocontrol of herbivorous pests challenging. Silicon (Si) accumulation in plants is a potent physical defence against herbivores. However, it remains uncertain how Si affects pest defences to their enemies and plant defences following herbivore attack. We grew the model grass, Brachypodium distachyon, hydroponically with (+Si) or without (–Si) Si and investigated the impacts of Si on morphological (integument resistance and thickness), behavioural (flee, headrear, thrash, and regurgitation), and immune defences of the cotton bollworm, Helicoverpa armigera. We further examined the effects of Si on plant compensatory growth and leaf trichome production. Larval growth, leaf consumption, and integument resistance were lower when feeding on +Si plants compared to when feeding on –Si plants. Larval integument thickness, defensive behaviours, hemocyte density and lysozyme-like activity in the hemolymph were unaffected by Si. Larvae fed on +Si plants had higher hemolymph phenoloxidase (PO) and total-PO activities than larvae fed on –Si plants, although this did not enhance larval melanisation response. Furthermore, Si supply increased plant compensatory growth and constitutive trichome production whereas herbivory induced trichome production only on –Si plants. We provide the first evidence that Si fertilisation affects insect defences in addition to reducing their growth and feeding. Lower integument resistance might enhance larval vulnerability to parasitoids and pathogens and higher PO activities could impose fitness costs (e.g., delayed development), potentially increasing overall insect susceptibility to enemies.

Near-infrared reflectance spectroscopy (NIRS) has been used by the agricultural industry as a high-precision technique to quantify nutritional chemistry in plants both rapidly and inexpensively. The aim of this study was to evaluate the performance of NIRS calibrations in predicting the nutritional composition of ten pasture species that underpin livestock industries in many countries. These species comprised a range of functional diversity (C3 legumes; C3/C4 grasses; annuals/perennials) and origins (tropical/temperate; introduced/native) that grew under varied environmental conditions (control and experimentally induced warming and drought) over a period of more than 2 years (n = 2,622). A maximal calibration set including 391 samples was used to develop and evaluate calibrations for all ten pasture species (global calibrations), as well as for subsets comprised of the plant functional groups. We found that the global calibrations were appropriate to predict the six key nutritional quality parameters studied for our pasture species, with the highest accuracy found for ash (ASH), crude protein (CP), neutral detergent fibre and acid detergent fibre (ADF), and the lowest for ether extract (EE) and acid detergent lignin parameters. The plant functional group calibrations for C3 grasses performed better than the global calibrations for ASH, CP, ADF and EE parameters, whereas for C3 legumes and C4 grasses the functional group calibrations performed less well than the global calibrations for all nutritional parameters of these groups. Additionally, our calibrations were able to capture the range of variation in forage quality caused by future climate scenarios of warming and severe drought.

The effects of increasing atmospheric carbon dioxide (CO2) concentrations on beneficial soil fauna, such as entomopathogenic nematodes (EPNs), are poorly understood. We hence aimed to characterize how elevated CO2 (eCO2) affects maize plant (Zea mays) growth, root morphology and the effectiveness of the EPN Heterorhabditis bacteriophora. We grew plants under ambient CO2 (aCO2; 400 μmol mol-1) and eCO2 (640 μmol mol-1) and quantified shoot growth and six root traits. We simultaneously quantified the effectiveness of EPNs (mortality of insect hosts (Galleria mellonella) and EPN density within hosts) when foraging in planted and plant-free environments. Structural equation modeling (SEM) was used to model direct and indirect relationships between atmospheric CO2, root morphology and EPN effectiveness. Root systems of plants grown under eCO2 grew faster, longer, denser, and larger than plants grown under aCO2. This in turn reduced EPN effectiveness as, despite no significant difference between aCO2 and eCO2 in host mortality, significantly more nematodes were recovered from hosts in the vicinity of plants grown in aCO2 environment. The SEM model revealed that this impact was indirect and mediated by the increased root morphological traits. We provide the first example of how changes in atmospheric CO2 indirectly reduce the effectiveness of an EPN used globally for crop protection. Other factors (e.g. plant volatile emissions) may moderate or exacerbate these patterns but our findings suggest that modifications in root traits at eCO2 negatively impact EPN effectiveness and therefore soil-dwelling insect pest management.

The diets of individual animals within populations can differ, but few studies determine whether this is due to fundamental differences in preferences or capacities to eat specific foods, or to external influences such as dominance hierarchies or spatial variation in food availability. The distinction is important because different drivers of dietary specialisation are likely to have different impacts on the way in which animal populations respond to, for example, habitat modification. We used a captive feeding study to investigate the mechanisms driving individual dietary specialisation in a population of wild koalas (Phascolarctos cinereus) in which individuals predominantly ate either Eucalyptus viminalis or Eucalyptus obliqua foliage. All six koalas that primarily ate E. viminalis in the wild avoided eating E. obliqua for more than 1 month in captivity. In contrast, all seven koalas that primarily ate E. obliqua could be maintained exclusively on this species in captivity, although they ate less from individual trees with higher foliar concentrations of unsubstituted B-ring flavanones (UBFs). Our results show that fundamental differences between individual animals allow some to exploit food resources that are less suitable for others. This could reduce competition for food, increase habitat carrying capacity, and is also likely to buffer the population against extinction in the face of habitat modification. The occurrence of fundamental individual specialisation within animal populations could also affect the perceived conservation value of different habitats, translocation or reintroduction success, and population dynamics. It should therefore be further investigated in other mammalian herbivore species.

In recent years, silicon (Si) has been increasingly linked to biotic stress management in plants including insect herbivory. The effectiveness of Si against chewing insects is now well recognized. Silicification of plant tissues makes them abrasive and tougher, reducing their masticability and digestibility to insect herbivores. This can cause mandibular wearing of chewers and affect their growth and feeding. Although there has been extensive research on the effects of Si on plant defences (i.e. antixenosis and antibiosis), it remains unclear how feeding on silicified plants affects insect defences to their natural enemies. Insect herbivores show morphological and behavioural defences when encountering predators and parasitoids. For example, lepidopteran larvae can regurgitate, twist the body, or even drop off the plants when attacked by natural enemies. Moreover, insects possess innate immunity (physiological defence) against the attackers, demonstrating cellular and humoral responses upon attack. Notably, there could be potential trade-offs between different defence and immunity traits. Given that feeding on Si-rich plants affects insect growth rates, this could impact their relative investment in different defences, thereby making insects more susceptible to their enemies. We are investigating the effects of Si on plant resistance and tolerance to herbivory and its cascading effects on insect defences to their enemies. We have been growing the model grass, Brachypodium distachyon, a high Si-accumulator, hydroponically with or without Si and examining the effects of Si against the global insect herbivore, Helicoverpa armigera. Our preliminary results suggest that Si supplementation enhances plant antixenotic and antibiotic traits and increases plant tolerance to herbivory. We are currently exploring insect defence and immunity traits when fed on silicified versus non-silicified plants. Our study would shed light on the impacts of Si on insects’ susceptibility to biocontrol agents and provide a better understanding of the effects of Si on insect-plant-natural enemy interactions.

Under warmer and drier future conditions, global livestock and dairy production are threatened by impacts on the productivity and nutritional quality of pastures. However, morphological and nutritional adjustments within plants in response to warming and drought vary among species and less is known how these relate to production and forage quality. To investigate this, we grew two common pasture species, tall fescue (Festuca arundinacea: grass) and lucerne (Medicago sativa: legume), in a climate-controlled facility, under different temperatures (ambient and elevated) and watering regimes (well-watered and droughted). We found that drought had a strong negative impact on biomass production, morphology and nutritional quality while warming only significantly affected both species when response metrics were considered in concert, although to a lesser degree than the drought. Furthermore, interactions between warming and drought were only seen for lucerne, with the greatest reduction in biomass and most dead material and dry matter content. In tall fescue, drought had bigger impacts on nutritional composition than morphological traits, while in lucerne, drought affected all morphological traits and most nutritional parameters. These findings suggest that in future climate scenarios, drought may be a stronger driver of changes in the morphology and nutritional composition of pasture grasses and legumes, compared to modest levels of warming.

Silicon accumulation is a key defence against herbivorous pests, but may have wider detrimental impacts if plants become unpalatable for livestock. We argue that some herbivores are better adapted to silicon-rich diets than others; herbivore anatomy and physiology, and the nature of silicon deposition, are crucial to understanding these differences.

The diets of individual animals within populations can differ, but few studies determine whether this is due to fundamental differences in preferences or capacities to eat specific foods, or to external influences such as dominance hierarchies or spatial variation in food availability. The distinction is important because different drivers of dietary specialisation are likely to have different impacts on the way in which animal populations respond to, for example, habitat modification. We used a captive feeding study to investigate the mechanisms driving individual dietary specialisation in a population of wild koalas (Phascolarctos cinereus) in which individuals predominantly ate either Eucalyptus viminalis or Eucalyptus obliqua foliage. All six koalas that primarily ate E. viminalis in the wild avoided eating E. obliqua for more than 1 month in captivity. In contrast, all seven koalas that primarily ate E. obliqua could be maintained exclusively on this species in captivity, although they ate less from individual trees with higher foliar concentrations of unsubstituted B-ring flavanones (UBFs). Our results show that fundamental differences between individual animals allow some to exploit food resources that are less suitable for others. This could reduce competition for food, increase habitat carrying capacity, and is also likely to buffer the population against extinction in the face of habitat modification. The occurrence of fundamental individual specialisation within animal populations could also affect the perceived conservation value of different habitats, translocation or reintroduction success, and population dynamics. It should therefore be further investigated in other mammalian herbivore species.

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1–5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2 concentration6. Although evidence gathered from young aggrading forests has generally indicated a strong CO2 fertilization effect on biomass growth3–5, it is unclear whether mature forests respond to eCO2 in a similar way. In mature trees and forest stands7–10, photosynthetic uptake has been found to increase under eCO2 without any apparent accompanying growth response, leaving the fate of additional carbon fixed under eCO2 unclear4,5,7–11. Here using data from the first ecosystem-scale Free-Air CO2 Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responded to four years of eCO2 exposure. We show that, although the eCO2 treatment of +150 parts per million (+38 per cent) above ambient levels induced a 12 per cent (+247 grams of carbon per square metre per year) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone accounting for half of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on ubiquitous CO2 fertilization as a driver of increased carbon sinks in global forests. Carbon dioxide enrichment of a mature forest resulted in the emission of the excess carbon back into the atmosphere via enhanced ecosystem respiration, suggesting that mature forests may be limited in their capacity to mitigate climate change.

Background Grasses are hyper-accumulators of silicon (Si) and often up-regulate Si following herbivory. Positive correlations exist between Si and plant water content, yet the extent to which Si uptake responses can be mediated by changes in soil water availability has rarely been studied and never, to our knowledge, under field conditions. We used field-based rain-exclusion shelters to investigate how simulated grazing (shoot clipping) and altered rainfall patterns (drought and elevated precipitation, representing 50% and 150% of ambient precipitation levels, respectively) affected initial patterns of root- and shoot-Si uptake in a native Australian grass (Microlaena stipoides) in Si-supplemented and untreated soils. Results Si supplementation increased soil water retention under ambient and elevated precipitation but not under drought, although this had little effect on Si uptake and growth (tiller numbers or root biomass) of M. stipoides. Changes in rainfall patterns and clipping had strong individual effects on plant growth and Si uptake and storage, whereby clipping increased Si uptake by M. stipoides under all rainfall treatments but to the greatest extent under elevated precipitation. Moreover, above-ground–below-ground Si distribution only changed following elevated precipitation by decreasing the ratio of root:shoot Si concentrations. Conclusions Results highlight the importance of soil water availability for Si uptake and suggest a role for both active and passive Si transport mechanisms. Such manipulative field studies may provide a more realistic insight into how grasses initially respond to herbivory in terms of Si-based defence under different environmental conditions. Electronic supplementary material The online version of this article (10.1186/s12898-018-0208-6) contains supplementary material, which is available to authorized users.

1. Plants defend themselves from insect herbivore attack using a range of physical and chemical defences which are in many cases regulated by phytohormones such as jasmonates. While much more is known about how jasmonates regulate defence against above‐ground herbivores (e.g. herbivores of leaves), there is increasing interest in how they influence below‐ground defences. 2. For the Poaceae, most below‐ground studies focus on highly domesticated cereals. Here it is demonstrated how exogenous application of methyl jasmonate (MeJA) to the leaf blades of a non‐domesticated pasture grass (Microlaena stipoides) caused a more than two‐fold decrease in relative growth rate (RGR) of a root‐feeding chafer (Dermolepida albohirtum). MeJA treatment did not affect root consumption rates, but substantially reduced the efficiency of conversion of ingested food to body mass. 3. Non‐targeted metabolomics identified significant changes in the metabolome of MeJA‐induced plants, with three compounds (a galactolipid, a trihydroxy fatty acid and a lysophospholipid) found to be correlated with herbivore RGR, although their roles in herbivore defence remain uncertain. 4. This study suggests that an important Australian pasture grass can become better defended against root herbivores via enhanced jasmonate activity.

Plant breeding usually focuses on conspicuous above-ground plant traits, yet roots fundamentally underpin plant fitness. Roots show phenotypic plasticity in response to soil conditions but it is unclear whether domesticated plants respond like their ancestors. We aimed to determine how root traits differed between ancestral and domesticated types of a meadow grass (Microlaena stipoides) under altered regimes of precipitation and soil silicon availability. We subjected the two grass types to three simulated precipitation regimes (ambient, +50%/deluge and −50%/drought) in soil with (Si+) and without (Si−) silicon supplementation and then characterised root biomass, architectural complexity and toughness in addition to shoot traits. Domestication increased root tissue density, decreased specific root length (SRL) and decreased root architectural complexity. Domestication also increased root strength under Si− conditions but not Si+ conditions. Fine roots, SRL, architectural complexity and the force required to tear the roots all decreased under deluge. The ancestral and domesticated grasses responded similarly to precipitation, except that the latter had weaker roots (decreased fracture strain) under drought. Domestication and increased precipitation caused changes in M. stipoides root traits that could be beneficial against some stresses (e.g. soil compaction, herbivory) but not others (e.g. drought).

The Jarman-Bell principle seeks to explain why smaller herbivore species tend to select higher-quality forage (high protein and high fiber digestibility) than larger herbivore species. This principle may also provide insight into intraspecific differences in resource use in species with pronounced sexual size dimorphism. We examined the relationship between body mass and diet quality in a sexually dimorphic macropodid community comprising larger (17-55 kg) eastern and western gray kangaroos, Macropus giganteus and M. fuliginosus, and smaller (7-23 kg) red-necked and swamp wallabies, M. rufogriseus and Wallabia bicolor. We determined diet composition through microhistological analysis of fecal pellets, and then assessed diet quality by measuring available nitrogen and fiber (cellulose and hemicellulose) in the plants consumed. We predicted that the smaller species and smaller individuals within species would consume the highest-quality diets. The concentration of fiber consumed differed significantly among species; available nitrogen concentration did not. As predicted, the lowest-fiber diet was consumed by a wallaby (small species) and the highest-fiber diet was consumed by a kangaroo (large species). Contrary to predictions, we detected no sex-based differences in diet quality. However, large male red-necked wallabies consumed diets containing harder-to-digest fiber than small male red-necked wallabies. Body mass and diet type were related between and within species. However, body mass did not account for all differences in diet quality between species; swamp wallabies consumed less fiber than similarly sized red-necked wallabies. These differences are likely related to other adaptations that allow swamp wallabies to better tolerate tannin-rich browse-dominated diets.

Soil emissions of nitrous oxide (N2O), a potent greenhouse gas associated with agricultural systems, can be reduced by the activity of arbuscular mycorrhizal (AM) fungi. It is unclear, however, whether climate change may impact this ecosystem service provided by AM fungi. To assess the extent that warming may affect AM fungal mediation of N2O emissions from pastures, we grew lucerne (Medicago sativa, also called alfalfa) and tall fescue (Festuca arundinacea) under ambient (aT) and elevated (eT) temperature (+4 °C) regimes in the presence or absence of the AM fungus Rhizophagus irregularis. N2O emissions were measured from pots at five timepoints over a four-month period, while total plant biomass, nitrogen, phosphorus and mycorrhizal parameters (root length colonised and extraradical hyphal biomass in soil) were measured following a final destructive harvest. For both species, AM fungi significantly reduced N2O fluxes to a similar extent under both temperatures. The N2O reduction due to AM fungal inoculation was not influenced by warming. Overall, AM fungi were shown to reduce N2O emissions under current and predicted future warming scenarios for these two common pasture species, highlighting the role of microbial symbionts in mediating terrestrial feedbacks to future climate change.

Mammals maintain specific body temperatures (Tb ) across a broad range of ambient temperatures. The energy required for thermoregulation ultimately comes from the diet, and so what animals eat is inextricably linked to thermoregulation. Endothermic herbivores must balance energy requirements and expenditure with complicated thermoregulatory challenges from changing thermal, nutritional and toxicological environments. In this review we provide evidence that plant-based diets can influence thermoregulation beyond the control of herbivores, and that this can render them susceptible to heat stress. Notably, herbivorous diets often require specialised digestive systems, are imbalanced, and contain plant secondary metabolites (PSMs). PSMs in particular are able to interfere with the physiological processes responsible for thermoregulation, for example by uncoupling mitochondrial oxidative phosphorylation, binding to thermoreceptors, or because the pathways required to detoxify PSMs are thermogenic. It is likely, therefore, that increased ambient temperatures due to climate change may have greater and more-specific impacts on herbivores than on other mammals, and that managing internal and external heat loads under these conditions could drive changes in feeding ecology.

Apex predator extirpation has been identified as a key driver of biodiversity losses. The mesopredator release hypothesis (MRH) predicts that reduced abundance of apex predators results in an increase in the abundance and predatory impact of mesopredators. Here we test predictions made according to the MRH that an apex predator, the dingo (Canis dingo), benefits a small ground-nesting bird, the little button-quail (Turnix velox), by reducing the abundance of introduced mesopredators, the red fox (Vulpes vulpes) and feral cat (Felis catus). We also examined an alternative hypothesis that herbivore grazing negatively affects little button-quail abundance by reducing ground cover. To test our predictions we compared dingo, mesopredator, quail, herbivore and ground cover abundances and predator diets over a 25 month period and across a 10,000 km2 region encompassing areas where dingoes were common and rare, pastoral properties, and conservation reserves. Little button-quails were primarily observed where dingoes were common and foxes rare. Cats were detected at low numbers throughout the sample area irrespective of the index abundance of little button-quails, dingoes or foxes. Birds occurred less frequently in dingo than fox or cat scats. Ground cover and herbivore grazing activity were poor correlates of little button-quail abundance. Our results are consistent with the hypothesis that apex predators’ mesopredator-suppressive effects translate to population-level benefits for a ground-nesting bird. Positive associations between the abundances of dingoes and small-prey species suggests that positive management of dingoes could be incorporated into broad-scale biodiversity conservation programs as a strategy to alleviate the predatory impacts of foxes.

Background Differences between individuals in their gastrointestinal microbiomes can lead to variation in their ability to persist on particular diets. Koalas are dietary specialists, feeding almost exclusively on Eucalyptus foliage but many individuals will not feed on particular Eucalyptus species that are adequate food for other individuals, even when facing starvation. We undertook a faecal inoculation experiment to test whether a koala’s gastrointestinal (GI) microbiome influences their diet. Wild-caught koalas that initially fed on the preferred manna gum (Eucalyptus viminalis) were brought into captivity and orally inoculated with encapsulated material derived from faeces from koalas feeding on either the less preferred messmate (E. obliqua; treatment) or manna gum (control). Results The gastrointestinal microbiomes of wild koalas feeding primarily on manna gum were distinct from those feeding primarily on messmate. We found that the gastrointestinal microbiomes of koalas were unresponsive to dietary changes because the control koalas’ GI microbiomes did not change even when the nocturnal koalas were fed exclusively on messmate overnight. We showed that faecal inoculations can assist the GI microbiomes of koalas to change as the treatment koalas’ GI microbiomes became more similar to those of wild koalas feeding on messmate. There was no overall difference between the control and treatment koalas in the quantity of messmate they consumed. However, the greater the change in the koalas’ GI microbiomes, the more messmate they consumed after the inoculations had established. Conclusions The results suggest that dietary changes can only lead to changes in the GI microbiomes of koalas if the appropriate microbial species are present, and/or that the koala gastrointestinal microbiome influences diet selection. Electronic supplementary material The online version of this article (10.1186/s42523-019-0008-0) contains supplementary material, which is available to authorized users.

Plants have evolved numerous herbivore defences that are resistance- or tolerance-based. Resistance involves physical and chemical traits that deter and/or harm herbivores whereas tolerance minimizes fitness costs of herbivory, often via compensatory growth. The Poaceae frequently accumulate large amounts of silicon (Si), which can be used for herbivore resistance, including biomechanical and (indirectly) biochemical defences. To date, it is unclear whether Si improves tolerance of herbivory. Here we report how Si enabled a cereal ( Triticum aestivum ) to tolerate damage inflicted by above- and belowground herbivores. Leaf herbivory increased Si concentrations in the leaves by greater than 50% relative to herbivore-free plants, indicating it was an inducible defensive response. In plants without Si supplementation, leaf herbivory reduced shoot biomass by 52% and root herbivory reduced root biomass by 68%. Si supplementation, however, facilitated compensatory growth such that shoot losses were more than compensated for (+14% greater than herbivore-free plants) and root losses were minimized to −16%. Si supplementation did not improve plant resistance since Si did not enhance biomechanical resistance (i.e. force of fracture) or reduce leaf consumption and herbivore relative growth rates. We propose that Si-based defence operates in wheat via tolerance either in addition or as an alternative to resistance-based defence.

Atmospheric carbon dioxide enrichment (eCO2) can enhance plant carbon uptake and growth1,2,3,4,5, thereby providing an important negative feedback to climate change by slowing the rate of increase of the atmospheric CO2concentration6. While evidence gathered from young aggrading forests has generally indicated a strong CO2fertilization effect on biomass growth3,4,5, it is unclear whether mature forests respond to eCO2in a similar way. In mature trees and forest stands7,8,9,10, photosynthetic uptake has been found to increase under eCO2without any apparent accompanying growth response, leaving an open question about the fate of additional carbon fixed under eCO24, 5, 7,8,9,10,11. Here, using data from the first ecosystem-scale Free-Air CO2Enrichment (FACE) experiment in a mature forest, we constructed a comprehensive ecosystem carbon budget to track the fate of carbon as the forest responds to four years of eCO2exposure. We show that, although the eCO2treatment of ambient +150 ppm (+38%) induced a 12% (+247 gCm-2yr-1) increase in carbon uptake through gross primary production, this additional carbon uptake did not lead to increased carbon sequestration at the ecosystem level. Instead, the majority of the extra carbon was emitted back into the atmosphere via several respiratory fluxes, with increased soil respiration alone contributing ∼50% of the total uptake surplus. Our results call into question the predominant thinking that the capacity of forests to act as carbon sinks will be generally enhanced under eCO2, and challenge the efficacy of climate mitigation strategies that rely on CO2fertilization as a driver of increased carbon sinks in standing forests and afforestation projects.

The koala is a specialist feeder with a diet consisting almost exclusively of potentially toxic eucalypt leaves. Monoterpenes, an abundant class of plant secondary metabolites in eucalypts, are highly lipophilic. Chronic absorption and systemic exposure can be anticipated for the koala, causing health effects in various ways when consumed in high amounts, but particularly causing alterations in immune function in this species. Therefore, careful leaf selection, efficient detoxification pathways, and other specialist adaptations are required to protect animals from acute intoxication. This is the first paper providing insight into the systemic exposure of koalas to these compounds. Profiles of six selected major monoterpenes were investigated in the ingesta of deceased koalas from four different regions of NSW and South-East Queensland. Concentrations of the same compounds were measured in lymphoid tissues of deceased koalas and in the blood of live koalas from other regions of NSW. Analytical methods included liquid extraction and solid-phase micro-extraction, followed by gas-chromatography/ mass-spectrometry. Concentrations in the ingesta of individual animals vary remarkably, though the average proportions of individual monoterpenes in the ingesta of animals from the four different regions are highly comparable. Blood concentrations of the selected monoterpenes also varied considerably. The highest blood concentrations were found for 1,8-cineole, up to 971 ng/ml. There was similarity between circulating monoterpene profiles and ingesta profiles. Based on the observed lack of similarity between blood and lymph tissue concentrations, individual monoterpenes either exhibit different affinities for lymphatic tissue compared to blood or their accumulation in blood and lymph tissue differs temporally. In general, blood monoterpene concentrations found in koalas were low compared to those reported in other marsupial eucalypt feeders, but significant concentrations of monoterpenes were detected in all samples analysed. This data on blood and lymphatic tissue monoterpene concentrations builds the fundamental groundwork for future research into the effects of dietary monoterpenes on various biological processes of specialist herbivores and into the significance of these animals’ metabolic and behavioural strategies for coping with these compounds. We have shown that the systemic exposure of koalas to potentially anti-inflammatory eucalypt monoterpenes is continuous, and we provide data on physiological concentrations which will allow realistic future studies of the effects of monoterpenes on immune cell function.

BackgroundThe diet of the koala (Phascolarctos cinereus) is comprised almost exclusively of foliage from the genusEucalyptus(family Myrtaceae).Eucalyptusproduces a wide variety of potentially toxic plant secondary metabolites which have evolved as chemical defences against herbivory. The koala is classified as an obligate dietary specialist, and although dietary specialisation is rare in mammalian herbivores, it has been found elsewhere to promote a highly-conserved but low-diversity gut microbiome. The gut microbes of dietary specialists have been found sometimes to enhance tolerance of dietary PSMs, facilitating competition-free access to food. Although the koala and its gut microbes have evolved together to utilise a low nutrient, potentially toxic diet, their gut microbiome has not previously been assessed in conjunction with diet quality. Thus, linking the two may provide new insights in to the ability of the koala to extract nutrients and detoxify their potentially toxic diet.MethodThe 16S rRNA gene was used to characterise the composition and diversity of faecal bacterial communities from a wild koala population (n = 32) comprising individuals that predominately eat either one of two different food species, one the strongly preferred and relatively nutritious speciesEucalyptus viminalis, the other comprising the less preferred and less digestible speciesEucalyptus obliqua.ResultsAlpha diversity indices indicated consistently and significantly lower diversity and richness in koalas eatingE. viminalis. Assessment of beta diversity using both weighted and unweighted UniFrac matrices indicated that diet was a strong driver of both microbial community structure, and of microbial presence/absence across the combined koala population and when assessed independently. Further, principal coordinates analysis based on both the weighted and unweighted UniFrac matrices for the combined and separated populations, also revealed a separation linked to diet. During our analysis of the OTU tables we also detected a strong association between microbial community composition and host diet. We found that the phyla Bacteroidetes and Firmicutes were co-dominant in all faecal microbiomes, with Cyanobacteria also co-dominant in some individuals; however, theE. viminalisdiet produced communities dominated by the generaParabacteroidesand/orBacteroides, whereas theE. obliqua-associated diets were dominated by unidentified genera from the family Ruminococcaceae.DiscussionWe show that diet differences, even those caused by differential consumption of the foliage of two species from the same plant genus, can profoundly affect the gut microbiome of a specialist folivorous mammal, even amongst individuals in the same population. We identify key microbiota associated with each diet type and predict functions within the microbial community based on 80 previously identifiedParabacteroidesand Ruminococcaceae genomes.

Since the publication of the “The Ecology of Browsing and Grazing” (Gordon and Prins, The ecology of browsing and grazing. Springer, 2008), a number of researchers have taken the approach outlined in the book to assess the impacts of differences in food and nutrient supply on the ecology of other vertebrate taxa. In line with the slightly altered emphasis of the current book (The Ecology of Browsing and Grazing II), we also asked the authors of the Sections in this Chapter to provide insights into the impacts that these different vertebrate taxa have on the ecosystems in which they exist. As you will see, the depth of research on the ecology and impacts of the different herbivorous vertebrate taxa varies considerably and demonstrates the importance of further research endeavours, on herbivore/plant interactions, across the board.

Nutrient losses due to leaching from agricultural soils can be substantial but, in some cases, soil microbes such as arbuscular mycorrhizal (AM) fungi can buffer those losses. An important knowledge gap, however, is the extent to which climate change may affect AM fungal mediation of leaching via warming and drought. To investigate this, we grew lucerne (Medicago sativa) and tall fescue (Festuca arundinacea), in the presence and absence of AM fungal inoculation (Rhizophagus irregularis), under different temperature [ambient: 26 °C (aT); elevated: 30 °C (eT)] and water [well-watered: 100% soil water holding capacity (WHC); droughted: 40% WHC] treatments. After four months of plant growth, leached nutrients (PO4−, NH4+ and NO3−), plant biomass, nitrogen (N), phosphorus (P), and mycorrhizal parameters (colonization and extraradical hyphae biomass) were measured. The presence of AM fungi significantly reduced P leaching with lucerne by 46% for both temperature treatments, but P loss with tall fescue was only reduced under aT (by 48%). The negation of this benefit for tall fescue under eT was associated with a reduction in mycorrhizal root colonization, while temperature did not alter mycorrhizal root colonization of lucerne. Watering regime was not observed to influence P loss via leaching. We did not find a mycorrhizal effect on N leaching for either species; however, we found that N leaching increased under drought with lucerne and responded interactively to warming and drought with tall fescue. Overall, AM fungi significantly reduced P leaching for both species, but warming eliminated this effect for tall fescue, suggesting that warming may differentially affect P leaching depending upon plant species.