Land‐use effects on terrestrial consumers through changed size structure of aquatic insects

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Strong land‐use effects on the dispersal patterns of adult stream insects: implications for transfers of aquatic subsidies to terrestrial consumers

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Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

Deforestation continues to jeopardize Malagasy primates as viable habitats become smaller, more fragmented, and more disturbed. This deforestation can lead to changes in diet, microhabitat, and gene flow between populations of endangered species, and it remains unclear how these changes may affect gut microbiome (GM) characteristics. The black‐and‐white ruffed lemur (Varecia variegata), which is among Madagascar's most threatened lemur species, provides a critical model for understanding the relationships between historical and on‐going deforestation (habitat disturbance), feeding ecology, and GM composition and diversity. We studied four populations inhabiting two rainforests (relatively pristine vs. highly disturbed) in southeastern Madagascar. We conducted full‐day focal animal behavioral follows and collected fecal samples opportunistically across a three‐month period. Our results indicate that lemurs inhabiting sites characterized by habitat disturbance and low dietary diversity exhibited reduced gut microbial alpha diversity. We also show that these same factors were associated with high community dissimilarity using weighted and unweighted UniFrac metrics. Finally, an indicator species analysis showed that the most pristine site was characterized by an abundance of methanogenic archaea. While it is impossible to disentangle the relative contributions of each confounding variable presented by our sampling design, these results provide crucial information about GM variability, thereby underscoring the importance of monitoring endangered species at the population‐level.     

The effects of drought and herbivory on plant–herbivore interactions across 16 soybean genotypes in a field experiment

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Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe

Wide‐scale application of biochar to soil has been suggested as a mechanism to offset increases in CO₂ emissions through the long‐term sequestration of a carbon rich and inert substance to the soil, but the implications of this for soil diversity and function remain to be determined. Biochar is capable of inducing changes in soil bacterial communities, but the exact impacts of its application are poorly understood. Using three European sites [UK SRC, short rotation coppice, French grassland (FR) and Italian SRF, short rotation forestry (IT)] treated with identical biochar applications, we undertook 16S and ITS amplicon DNA sequencing. In addition, we carried out assessments of community change over time and N and P mobilization in the UK. Significant changes in bacterial and community structure occurred due to treatment, although the nature of the changes varied by site. STAMP differential abundance analysis showed enrichment of Gemmatimonadete and Acidobacteria in UK biochar plots 1 year after application, whilst control plots exhibited enriched Gemmataceae, Isosphaeraceae and Koribacteraceae. Increased mobility of ammonium and phosphates was also detected after 1 year, coupled with a shift from acid to alkaline phosphomonoesterase activity, which may suggest an ecological and functional shift towards a more copiotrophic ecology. Italy also exhibited enrichments, in both the Proteobacteria (driven by an increase in the order Rhizobiales) and the Gemmatimonadetes. No significant change in the abundance of individual taxa was noted in FR, although a small significant change in unweighted UNIFRAC occurred, indicating variation in the identities of taxa present due to treatment. Fungal β diversity was affected by treatment in IT and FR, but was unaffected in UK samples. The effects of time and site were greater than that of biochar application in UK samples. Overall, this report gives a tantalizing view of the soil microbiome at several sites across Europe and suggests that although application of biochar has significant effects on microbial communities, these may be small compared with the highly variable soil microbiome that is found in different soils and changes with time.     

Smells from the desert: Microbial volatiles that affect plant growth and development of native and non‐native plant species

The plant microbiota can affect host fitness via the emission of microbial volatile organic compounds (mVOCs) that influence growth and development. However, evidence of these molecules and their effects in plants from arid ecosystems is limited. We screened the mVOCs produced by 40 core and representative members of the microbiome of agaves and cacti in their interaction with Arabidopsis thaliana and Nicotiana benthamiana. We used SPME‐GC‐MS to characterize the chemical diversity of mVOCs and tested the effects of selected compounds on growth and development of model and host plants. Our study revealed that approximately 90% of the bacterial strains promoted plant growth both in A. thaliana and N. benthamiana. Bacterial VOCs were mainly composed of esters, alcohols, and S‐containing compounds with 25% of them not previously characterized. Remarkably, ethyl isovalerate, isoamyl acetate, 3‐methyl‐1‐butanol, benzyl alcohol, 2‐phenylethyl alcohol, and 3‐(methylthio)‐1‐propanol, and some of their mixtures, displayed beneficial effects in A. thaliana and also improved growth and development of Agave tequilana and Agave salmiana in just 60 days. Volatiles produced by bacteria isolated from agaves and cacti are promising molecules for the sustainable production of crops in arid and semi‐arid regions.     

Non‐adaptive phenotypic plasticity: the effects of terrestrial and aquatic herbicides on larval salamander morphology and swim speed

Phenotypic plasticity, although ubiquitous, may not always be advantageous. Non‐adaptive plasticity is likely to occur in response to novel environmental stress. Anthropogenic contaminants, such as herbicides, are novel stressors that are not present in the evolutionary history of most species. We investigated the pattern and consequences of phenotypic plasticity induced by four glyphosate‐based herbicides (two terrestrial and two aquatic) in larvae of the spotted salamander, Ambystoma maculatum, by determining (1) whether the herbicides induced different morphologies; (2) if different morphologies translated to differences in burst swim performance; and (3) how induced individuals performed relative to non‐induced controls. Different herbicide formulations led to the production of significantly different head and tail morphologies, and tail morphology correlated with fastest escape speed. However, escape speed did not vary among treatments. In addition, three out of four herbicide treatments experienced accelerated growth rates, in terms of the lateral size of tails, although the tail shapes were either similar to preliminary controls or intermediate between preliminary and final controls. These observations suggest that herbicide‐induced morphology is a case of non‐adaptive phenotypic plasticity, and that there is potentially a trade‐off between growth and development for larvae exposed to different formulations. Understanding the functional significance of induced phenotypes is important for determining their importance in shaping an organism's ecological interactions and evolutionary trajectories. Furthermore, under different conditions, the morphological changes that we observed in response to exposure to herbicides might affect salamander fitness and influence population dynamics.     

The structure of the littoral: effects of waterlily density and perch predation on sediment and plant‐associated macroinvertebrate communities

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The gut microbiome and metabolome of saddleback tamarins (Leontocebus weddelli): Insights into the foraging ecology of a small‐bodied primate

Body mass is a strong predictor of diet and nutritional requirements across a wide range of mammalian taxa. In the case of small‐bodied primates, because of their limited gut volume, rapid food passage rate, and high metabolic rate, they are hypothesized to maintain high digestive efficiency by exploiting foods rich in protein, fats, and readily available energy. However, our understanding of the dietary requirements of wild primates is limited because little is known concerning the contributions of their gut microbiome to the breakdown and assimilation of macronutrients and energy. To study how the gut microbiome contributes to the feeding ecology of a small‐bodied primate, we analyzed the fecal microbiome composition and metabolome of 22 wild saddleback tamarins (adult body mass 360–390 g) in Northern Bolivia. Samples were analyzed using high‐throughput Illumina sequencing of the 16 S rRNA gene V3‐V5 regions, coupled with GC‐MS metabolomic profiling. Our analysis revealed that the distal microbiome of Leontocebus weddelli is largely dominated by two main bacterial genera: Xylanibacter and Hallella (34.7 ± 14.7 and 22.6 ± 12.4%, respectively). A predictive analysis of functions likely carried out by bacteria in the tamarin gut demonstrated the dominance of membrane transport systems and carbohydrate metabolism as the predominant metabolic pathways. Moreover, given a fecal metabolome composed mainly of glucose, fructose, and lactic acid (21.7 ± 15.9%, 16.5 ± 10.7%, and 6.8 ± 5.5%, respectively), the processing of highly fermentable carbohydrates appears to play a central role in the nutritional ecology of these small‐bodied primates. Finally, the results also show a potential influence of environmentally‐derived bacteria in colonizing the tamarin gut. These results indicate high energetic turnover in the distal gut of Weddell's saddleback tamarin, likely influenced by dominant bacterial taxa that facilitate dietary dependence on highly digestible carbohydrates present in nectar, plant exudates, and ripe fruits.     

Interactive direct and plant‐mediated effects of elevated atmospheric [CO2] and temperature on a eucalypt‐feeding insect herbivore

Understanding the direct and indirect effects of elevated [CO₂] and temperature on insect herbivores and how these factors interact are essential to predict ecosystem‐level responses to climate change scenarios. In three concurrent glasshouse experiments, we measured both the individual and interactive effects of elevated [CO₂] and temperature on foliar quality. We also assessed the interactions between their direct and plant‐mediated effects on the development of an insect herbivore of eucalypts. Eucalyptus tereticornis saplings were grown at ambient or elevated [CO₂] (400 and 650 μmol mol^?1 respectively) and ambient or elevated ( + 4 °C) temperature for 10 months. Doratifera quadriguttata (Lepidoptera: Limacodidae) larvae were feeding directly on these trees, on their excised leaves in a separate glasshouse, or on excised field‐grown leaves within the temperature and [CO₂] controlled glasshouse. To allow insect gender to be determined and to ensure that any sex‐specific developmental differences could be distinguished from treatment effects, insect development time and consumption were measured from egg hatch to pupation. No direct [CO₂] effects on insects were observed. Elevated temperature accelerated larval development, but did not affect leaf consumption. Elevated [CO₂] and temperature independently reduced foliar quality, slowing larval development and increasing consumption. Simultaneously increasing both [CO₂] and temperature reduced these shifts in foliar quality, and negative effects on larval performance were subsequently ameliorated. Negative nutritional effects of elevated [CO₂] and temperature were also independently outweighed by the direct positive effect of elevated temperature on larvae. Rising [CO₂] and temperature are thus predicted to have interactive effects on foliar quality that affect eucalypt‐feeding insects. However, the ecological consequences of these interactions will depend on the magnitude of concurrent temperature rise and its direct effects on insect physiology and feeding behaviour.     

A plant‐specific model approach to assess effects of repowering measures on existing biogas plants: The case of Baden‐Wuerttemberg

Up to the latest versions of the German renewable energy act (EEG), there had been a constant growth of new biogas plants (BGPs). After reaching a stagnation in the last years, today the focus has shifted to improving the existing BGPs. Assuming that most plants have not reached the technical end of life, the question arises on how an operation can be realized beyond the initial EEG support period of 20 years. In addition, new legal and economic conditions require the implementation of adjustments, that is, “repowering measures.” Based on a method review, a plant‐specific model approach is presented to assess repowering measures for a wide range of BGPs differing in capacity, substrate mixture and agricultural structures. The techno‐economic model includes different performance indicators like levelized cost of electricity (LCOE) and temporal aspects like technical progress. Using a data set for BGPs in the state of Baden‐Wuerttemberg (Germany), results are illustrated for the different model modules and three repowering scenarios of an extended operation period of ten years. The scenarios regard different options to meet the requirements of the current EEG, namely the flexibilization and restrictions on energy crops, in comparison with a reference case. While in repowering scenarios, the number of plants decreases between 54% and 69% and the overall power capacity changes between ?48% and 13% until 2035. The results further show a reduction potential in the specific area demand and GHG emission up to 12% and 24%, respectively. Technical progress, additional revenues and capacity premiums are shown to be an important factor for efficient substrate utilization, low LCOE and thereby the enabling of an extended operation period. The scenario results indicate that the agricultural areas for energy crop cultivation and the amount of manure used in BGPs will be reduced considerably, inducing new chances and challenges in the future.     

Early herbivore alert matters: plant‐mediated effects of egg deposition on higher trophic levels benefit plant fitness

Induction of plant defences, specifically in response to herbivore attack, can save costs that would otherwise be needed to maintain defences even in the absence of herbivores. However, plants may suffer considerable damage during the time required to mount these defences against an attacker. This could be resolved if plants could respond to early cues, such as egg deposition, that reliably indicate future herbivory. We tested this hypothesis in a field experiment and found that egg deposition by the butterfly Pieris brassicae on black mustard (Brassica nigra) induced a plant response that negatively affected feeding caterpillars. The effect cascaded up to the third and fourth trophic levels (larval parasitoids and hyperparasitoids) by affecting the parasitisation rate and parasitoid performance. Overall, the defences induced by egg deposition had a positive effect on plant seed production and may therefore play an important role in the evolution of plant resistance to herbivores.     

Effects of macrolides on airway microbiome and cytokine of children with bronchiolitis: A systematic review and meta‐analysis of randomized controlled trials

Macrolides may attenuate airway inflammation of bronchiolitis with anti‐inflammatory and antiviral effects. However, the potential mechanisms of action underlying the efficiency of macrolides in treating bronchiolitis are limited. Therefore, we performed a meta‐analysis to assess the effects of macrolides on airway microbiome and cytokine of children with bronchiolitis. PubMed, Embase, and Cochrane Central Register of Controlled Trials were searched until May 2018. The reference lists of included studies and pertinent reviews were investigated for supplementing our search. Randomized controlled trials (RCTs) that compared macrolides with placebo assessing the change of microbiome in airway and cytokine were included. A total of four RCTs were included in this review. Data analysis showed no significant reduction of viruses at 48 hr after azithromycin treatment (p = 0.41). There were significant reductions in Streptococcus pneumoniae (risk ratio [RR] 0.28, 95% confidence interval (CI) 0.14 to 0.6, p < 0.01), Haemophilus influenza (RR 0.35, 95% CI 0.2 to 0.62, p < 0.01), and Moraxella catarrhalis (RR 0.29, 95% CI 0.17 to 0.5, p < 0.01), but no significant reduction of Staphylococcus aureus (p = 0.28) following treatment with macrolides. There was a significant decrease in the serum interleukin‐8(IL‐8), interleukin‐4(IL‐4), and eotaxin levels following 3 weeks of clarithromycin therapy. There was no significant difference in the serum IL‐8 level at Day 15 after the intervention between the azithromycin and control groups; however, a significant reduction of nasal lavage IL‐8 level was found. The macrolides may reduce the IL‐8 levels in the airway and plasma, but failed to demonstrate an antiviral effect in children with bronchiolitis.     

Geography,seasonality, and host‐associated population structure influence the fecal microbiome of a genetically depauparate Arctic mammal

The Canadian Arctic is an extreme environment with low floral and faunal diversity characterized by major seasonal shifts in temperature, moisture, and daylight. Muskoxen (Ovibos moschatus) are one of few large herbivores able to survive this harsh environment. Microbiome research of the gastrointestinal tract may hold clues as to how muskoxen exist in the Arctic, but also how this species may respond to rapid environmental changes. In this study, we investigated the effects of season (spring/summer/winter), year (2007–2016), and host genetic structure on population‐level microbiome variation in muskoxen from the Canadian Arctic. We utilized 16S rRNA gene sequencing to characterize the fecal microbial communities of 78 male muskoxen encompassing two population genetic clusters. These clusters are defined by Arctic Mainland and Island populations, including the following: (a) two mainland sampling locations of the Northwest Territories and Nunavut and (b) four locations of Victoria Island. Between these geographic populations, we found that differences in the microbiome reflected host‐associated genetic cluster with evidence of migration. Within populations, seasonality influenced bacterial diversity with no significant differences between years of sampling. We found evidence of pathogenic bacteria, with significantly higher presence in mainland samples. Our findings demonstrate the effects of seasonality and the role of host population‐level structure in driving fecal microbiome differences in a large Arctic mammal.     

Bottom‐up effects on a plant‐endophage‐parasitoid system: The role of flower‐head size and chemistry

The effects of water and nutrient addition on a trophic chain were studied in a plant‐endophage‐parasitoid system comprised of insects associated with flower heads of Chromolaena squalida (Asteraceae). Nine species of endophages associated with C. squalida flower heads were found, belonging to two families of Diptera – Tephritidae (Cecidochares sp1, Cecidochares sp2, Xanthaciura biocellata, X. chrysura, X. sp. and Neomyopites sp.) and Agromyzidae (Melanagromyza sp.), and two families of Coleoptera – Apionidae (Apion sp.) and Anthicidae (Anthicidae sp.). A factorial field experiment with water and nutrient addition showed that resource availability can affect the developmental process of flower heads. Fertilization increased flower‐head diameter and nitrogen and alkaloid concentrations. Although nutrient availability affected the size and chemistry of flower heads, endophage species did not respond consistently to the experimental treatments. This is contrary to other studies where endophages showed preference for larger flower heads. Thus, the plant vigour hypothesis was not corroborated for our study system. Our results also showed that coupled responses of plants to resource availability (i.e. tissue nutritional quality and investment in growth of the structure that serves as shelter for endophages) can represent distinct kinds of indirect interactions with opposing effects on the herbivore‐parasitoid interaction.     

Sound the alarm: A meta‐analysis on the effect of aquatic noise on fish behavior and physiology

The aquatic environment is increasingly bombarded by a wide variety of noise pollutants whose range and intensity are increasing with each passing decade. Yet, little is known about how aquatic noise affects marine communities. To determine the implications that changes to the soundscape may have on fishes, a meta‐analysis was conducted focusing on the ramifications of noise on fish behavior and physiology. Our meta‐analysis identified 42 studies that produced 2,354 data points, which in turn indicated that anthropogenic noise negatively affects fish behavior and physiology. The most predominate responses occurred within foraging ability, predation risk, and reproductive success. Additionally, anthropogenic noise was shown to increase the hearing thresholds and cortisol levels of numerous species while tones, biological, and environmental noise were most likely to affect complex movements and swimming abilities. These findings suggest that the majority of fish species are sensitive to changes in the aquatic soundscape, and depending on the noise source, species responses may have extreme and negative fitness consequences. As such, this global synthesis should serve as a warning of the potentially dire consequences facing marine ecosystems if alterations to aquatic soundscapes continue on their current trajectory.     

Long‐term dynamics of submerged macrophytes and algae in a small and shallow,eutrophic lake: implications for the stability of macrophyte‐dominance

1. Submerged macrophyte and phytoplankton components of eutrophic, shallow lakes have frequently undergone dynamic changes in composition and abundance with important consequences for lake functioning and stability. However, because of a paucity of long‐term survey data, we know little regarding the nature, direction and sequencing of such changes over decadal–centennial or longer timescales. 2. To circumvent this problem, we analysed multiple (n = 5) chronologically correlated sediment cores for plant macro‐remains and a single core for pollen and diatoms from one small, shallow, English lake (Felbrigg Hall Lake, Norfolk, U.K.), documenting 250 years of change to macrophyte and algal communities. 3. All five cores showed broadly similar stratigraphic changes in macrophyte remains with three distinct phases of macrophyte development: Myriophyllum–Chara–Potamogeton (c. pre‐1900), to Ceratophyllum–Chara–Potamogeton (c. 1900–1960) and finally to Zannichellia–Potamogeton (c. post‐1960). Macrophyte species richness declined from at least 10 species pre‐1900 to just four species at the present day. Additionally, in the final Zannichellia–Potamogeton phase, a directional shift between epi‐benthic and phytoplankton‐based primary production was indicated by the diatom data. 4. Based on macrophyte–seasonality relationships established for the region, concomitant with the final shift to Zannichellia–Potamogeton, we infer a reduction in the seasonal duration of plant dominance (plant‐covered period). Furthermore, we hypothesise that this change in species composition resulted in a situation whereby macrophyte populations were seasonally ‘sandwiched’ between two phytoplankton peaks in spring and late summer as observed in the contemporary lake. 5. We suggest that eutrophication‐induced reductions in macrophyte species richness, especially if the number of plant‐seasonal strategies is reduced, may constrict the plant growing season. In turn, this may render a shallow lake increasingly vulnerable to seasonal invasions of phytoplankton resulting in further species losses in the plant community. Thus, as part of a slow (over perhaps 10–100s of years) and self‐perpetuating process, macrophytes may be gradually pushed out by phytoplankton without the need for a perturbation as required in the alternative stable states model of plant loss.     

Autoimmunity and the microbiome: T‐cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts

I propose a T‐cell receptor (TcR)‐based mechanism by which immunity mediates both “genetic self” and “microbial self” thereby, connecting microbiome disease with autoimmunity. The hypothesis is based on simple principles. First, TcR are selected to avoid strong cross‐reactivity with “self,” resulting in selection for a TcR repertoire mimicking “genetic self.” Second, evolution has selected for a “microbial self” that mimics “genetic self” so as to share tolerance. In consequence, our TcR repertoire also mimics microbiome antigenicity, providing a novel mechanism for modulating tolerance to it. Also, the microbiome mimics the TcR repertoire, acting as a secondary immune system. I call this TcR‐microbiome mimicry “holoimmunity” to denote immune tolerance to the “holobiont self.” Logically, microbiome‐host mimicry means that autoimmunity directed at host antigens will also attack components of the microbiome, and conversely, an immunological attack on the microbiome may cross‐react with host antigens producing “holoautoimmunity.”