Metabolomics Unravel Contrasting Effects of Biodiversity on the Performance of Individual Plant Species

In spite of evidence for positive diversity-productivity relationships increasing plant diversity has highly variable effects on the performance of individual plant species, but the mechanisms behind these differential responses are far from being understood. To gain deeper insights into the physiological responses of individual plant species to increasing plant diversity we performed systematic untargeted metabolite profiling on a number of herbs derived from a grassland biodiversity experiment (Jena Experiment). The Jena Experiment comprises plots of varying species number (1, 2, 4, 8, 16 and 60) and number and composition of functional groups (1 to 4; grasses, legumes, tall herbs, small herbs). In this study the metabolomes of two tall-growing herbs (legume: Medicago x varia; non-legume: Knautia arvensis) and three small-growing herbs (legume: Lotus corniculatus; non-legumes: Bellis perennis, Leontodon autumnalis) in plant communities of increasing diversity were analyzed. For metabolite profiling we combined gas chromatography coupled to time-of-flight mass spectrometry (GC-TOF-MS) and UPLC coupled to FT-ICR-MS (LC-FT-MS) analyses from the same sample. This resulted in several thousands of detected m/z-features. ANOVA and multivariate statistical analysis revealed 139 significantly changed metabolites (30 by GC-TOF-MS and 109 by LC-FT-MS). The small-statured plants L. autumnalis, B. perennis and L. corniculatus showed metabolic response signatures to increasing plant diversity and species richness in contrast to tall-statured plants. Key-metabolites indicated C- and N-limitation for the non-leguminous small-statured species B. perennis and L. autumnalis, while the metabolic signature of the small-statured legume L. corniculatus indicated facilitation by other legumes. Thus, metabolomic analysis provided evidence for negative effects of resource competition on the investigated small-statured herbs that might mechanistically explain their decreasing performance with increasing plant diversity. In contrast, taller species often becoming dominant in mixed plant communities did not show modified metabolite profiles in response to altered resource availability with increasing plant diversity. Taken together, our study demonstrates that metabolite profiling is a strong diagnostic tool to assess individual metabolic phenotypes in response to plant diversity and ecophysiological adjustment

Earthworm and belowground competition effects on plant productivity in a plant diversity gradient

Diversity is one major factor driving plant productivity in temperate grasslands. Although decomposers like earthworms are known to affect plant productivity, interacting effects of plant diversity and earthworms on plant productivity have been neglected in field studies. We investigated in the field the effects of earthworms on plant productivity, their interaction with plant species and functional group richness, and their effects on belowground plant competition. In the framework of the Jena Experiment we determined plant community productivity (in 2004 and 2007) and performance of two phytometer plant species [Centaurea jacea (herb) and Lolium perenne (grass); in 2007 and 2008] in a plant species (from one to 16) and functional group richness gradient (from one to four). We sampled earthworm subplots and subplots with decreased earthworm density and reduced aboveground competition of phytometer plants by removing the shoot biomass of the resident plant community. Earthworms increased total plant community productivity (+11%), legume shoot biomass (+35%) and shoot biomass of the phytometer C. jacea (+21%). Further, phytometer performance decreased, i.e. belowground competition increased, with increasing plant species and functional group richness. Although single plant functional groups benefited from higher earthworm numbers, the effects did not vary with plant species and functional group richness. The present study indicates that earthworms indeed affect the productivity of semi-natural grasslands irrespective of the diversity of the plant community. Belowground competition increased with increasing plant species diversity. However, belowground competition was modified by earthworms as reflected by increased productivity of the phytometer C. jacea. Moreover, particularly legumes benefited from earthworm presence. Considering also previous studies, we suggest that earthworms and legumes form a loose mutualistic relationship affecting essential ecosystem functions in temperate grasslands, in particular decomposition and plant productivity. Further, earthworms likely alter competitive interactions among plants and the structure of plant communities by beneficially affecting certain plant functional groups

Plant Diversity Surpasses Plant Functional Groups and Plant Productivity as Driver of Soil Biota in the Long Term

One of the most significant consequences of contemporary global change is the rapid decline of biodiversity in many ecosystems. Knowledge of the consequences of biodiversity loss in terrestrial ecosystems is largely restricted to single ecosystem functions. Impacts of key plant functional groups on soil biota are considered to be more important than those of plant diversity; however, current knowledge mainly relies on short-term experiments.We studied changes in the impacts of plant diversity and presence of key functional groups on soil biota by investigating the performance of soil microorganisms and soil fauna two, four and six years after the establishment of model grasslands. The results indicate that temporal changes of plant community effects depend on the trophic affiliation of soil animals: plant diversity effects on decomposers only occurred after six years, changed little in herbivores, but occurred in predators after two years. The results suggest that plant diversity, in terms of species and functional group richness, is the most important plant community property affecting soil biota, exceeding the relevance of plant above- and belowground productivity and the presence of key plant functional groups, i.e. grasses and legumes, with the relevance of the latter decreasing in time.Plant diversity effects on biota are not only due to the presence of key plant functional groups or plant productivity highlighting the importance of diverse and high-quality plant derived resources, and supporting the validity of the singular hypothesis for soil biota. Our results demonstrate that in the long term plant diversity essentially drives the performance of soil biota questioning the paradigm that belowground communities are not affected by plant diversity and reinforcing the importance of biodiversity for ecosystem functioning

Plant Community Diversity Influences Allocation to Direct Chemical Defence in Plantago lanceolata

Background: Forecasting the consequences of accelerating rates of changes in biodiversity for ecosystem functioning requires a mechanistic understanding of the relationships between the structure of biological communities and variation in plant functional characteristics. So far, experimental data of how plant species diversity influences the investment of individual plants in direct chemical defences against herbivores and pathogens is lacking. Methodology/Principal Findings: We used Plantago lanceolata as a model species in experimental grasslands differing in species richness and composition (Jena Experiment) to investigate foliar concentrations of the iridoid glycosides (IG), catalpol and its biosynthetic precursor aucubin. Total IG and aucubin concentrations decreased, while catalpol concentrations increased with increasing plant diversity in terms of species or functional group richness. Negative plant diversity effects on total IG and aucubin concentrations correlated with increasing specific leaf area of P. lanceolata, suggesting that greater allocation to light acquisition reduced the investment into these carbon-based defence components. In contrast, increasing leaf nitrogen concentrations best explained increasing concentrations of the biosynthetically more advanced IG, catalpol. Observed levels of leaf damage explained a significant proportion of variation in total IG and aucubin concentrations, but did not account for variance in catalpol concentrations. Conclusions/Significance: Our results clearly show that plants growing in communities of varying species richness an

Emission of Volatile Organic Compounds After Herbivory from Trifolium pratense (L.) Under Laboratory and Field Conditions

Plants emit a wide range of volatile organic compounds in response to damage by herbivores, and many of the compounds have been shown to attract the natural enemies of insect herbivores or serve for inter- and intra-plant communication. Most studies have focused on volatile emission in the laboratory while little is known about emission patterns in the field. We studied the emission of volatiles by Trifolium pratense (red clover) under both laboratory and field conditions. The emission of 24 compounds was quantified in the laboratory, of which eight showed increased emission rates after herbivory by Spodoptera littoralis caterpillars, including (E)-β-ocimene, the most abundant compound, (Z)-β-ocimene, linalool, (E)-β-caryophyllene, (E,E)-α-farnesene, 4,8-dimethyl-1,3,7-nonatriene (DMNT), 1-octen-3-ol, and methyl salicylate (MeSA). While most of these compounds have been reported as herbivore-induced volatiles from a wide range of plant taxa, 1-octen-3-ol seems to be a characteristic volatile of legumes. In the field, T. pratense plants with varying herbivore damage growing in established grassland communities emitted only 13 detectable compounds, and the correlation between herbivore damage and volatile release was more variable than in the laboratory. For example, the emission of (E)-β-ocimene, (Z)-β-ocimene, and DMNT actually declined with damage, while decanal exhibited increased emission with increasing herbivory. Elevated light and temperature increased the emission of many compounds, but the differences in light and temperature conditions between the laboratory and the field could not account for the differences in emission profiles. Our results indicate that the release of volatiles from T. pratense plants in the field is likely to be influenced by additional biotic and abiotic factors not measured in this study. The elucidation of these factors may be important in understanding the physiological and ecological functions of volatiles in plants

Plant Species Loss Affects Life-History Traits of Aphids and Their Parasitoids

The consequences of plant species loss are rarely assessed in a multi-trophic context and especially effects on life-history traits of organisms at higher trophic levels have remained largely unstudied. We used a grassland biodiversity experiment and measured the effects of two components of plant diversity, plant species richness and the presence of nitrogen-fixing legumes, on several life-history traits of naturally colonizing aphids and their primary and secondary parasitoids in the field. We found that, irrespective of aphid species identity, the proportion of winged aphid morphs decreased with increasing plant species richness, which was correlated with decreasing host plant biomass. Similarly, emergence proportions of parasitoids decreased with increasing plant species richness. Both, emergence proportions and proportions of female parasitoids were lower in plots with legumes, where host plants had increased nitrogen concentrations. This effect of legume presence could indicate that aphids were better defended against parasitoids in high-nitrogen environments. Body mass of emerged individuals of the two most abundant primary parasitoid species was, however, higher in plots with legumes, suggesting that once parasitoids could overcome aphid defenses, they could profit from larger or more nutritious hosts. Our study demonstrates that cascading effects of plant species loss on higher trophic levels such as aphids, parasitoids and secondary parasitoids begin with changed life-history traits of these insects. Thus, life-history traits of organisms at higher trophic levels may be useful indicators of bottom-up effects of plant diversity on the biodiversity of consumers

Species trait shifts in vegetation and soil seed bank during fen degradation

Fens in Central Europe are characterised by waterlogged organic substrate and low productivity. Human-induced changes due to drainage and mowing lead to changes in plant species composition from natural fen communities to fen meadows and later to over-drained, degraded meadows. Moderate drainage leads to increased vegetation productivity, and severe drainage results in frequent soil disturbances and less plant growth. In the present article, we analyse changes in plant trait combinations in the vegetation and the soil seed bank as well as changes in the seed bank types along gradient of drainage intensity. We hypothesize that an increase in productivity enhances traits related to persistence and that frequent disturbance selects for regeneration traits. We use multivariate statistics to analyse data from three disturbance levels: undisturbed fen, slightly drained fen meadow and severely drained degraded meadow. We found that the abundance of plants regenerating from seeds and accumulating persistent seed banks was increasing with degradation level, while plants reproducing vegetatively were gradually eliminated along the same trajectory. Plants with strong resprouting abilities increased during degradation. We also found that shifts in trait combinations were similar in the aboveground vegetation and in soil seed banks. We found that the density of short-term persistent seeds in the soil is highest in fen meadows and the density of long-term persistent seeds is highest in degraded meadows. The increase in abundance of species with strong regeneration traits at the cost of species with persistence-related traits has negative consequences for the restoration prospects of severely degraded sites

Herbage nutritive value of binary- and multi-species swards relative to single-species swards in intensive silage systems

peer-reviewedThe nutritive value of sown binary- and multi-species grassland mixtures may differ from the values expected based on single-species swards of their constituent species. Field plots were established in a split-plot design to assess the nutritive value of binary- and multi-species mixtures compared to single-species swards of three grass species and red clover (RC) (Trifolium pratense L.) managed for intensive silage production. The nutritive value of grass–legume binary mixtures reflected the values of the constituent species grown on their own, and thus may be predicted from monoculture values. The relatively low digestibility (dry matter digestibility [DMD]) and crude protein (CP) content of the Italian ryegrass (Lolium multiflorum L.) sward compared to perennial ryegrass (Lolium perenne L.) and timothy (Phleum pratense L.) suggests that it may have a limited role in binary- or multi-species swards. Herbage nutritive value in the multi-species swards (Mix 1: perennial ryegrass, timothy, RC and white clover [Trifolium repens L.]; Mix 2: perennial ryegrass, timothy, RC, ribwort plantain [Plantago lanceolata L.] and chicory [Cichorium intybus L.] ) appeared to be influenced more by the presence of legumes than herbs. Compared to perennial ryegrass, the multi-species swards had a slower rate of DMD decline prior to Cut 1, but subsequently had lower DMD values at the mid-season harvests. Both multi-species mixtures exhibited DMD, water-soluble carbohydrate (WSC) and CP values that would not have been predicted from their constituent species and thus need to be measured on herbage from field plots growing these mixtures

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.This work is supported by the UK Medical Research Council (MRC); Chinese Academy of Medical Sciences(CAMS) Innovation Fund for Medical Sciences (CIFMS), China; National Institute for Health Research (NIHR)Oxford Biomedical Research Centre, and UK Researchand Innovation (UKRI)/NIHR through the UK Coro-navirus Immunology Consortium (UK-CIC). Sequencing of SARS-CoV-2 samples and collation of data wasundertaken by the COG-UK CONSORTIUM. COG-UK is supported by funding from the Medical ResearchCouncil (MRC) part of UK Research & Innovation (UKRI),the National Institute of Health Research (NIHR),and Genome Research Limited, operating as the Wellcome Sanger Institute. T.I.d.S. is supported by a Well-come Trust Intermediate Clinical Fellowship (110058/Z/15/Z). L.T. is supported by the Wellcome Trust(grant number 205228/Z/16/Z) and by theUniversity of Liverpool Centre for Excellence in Infectious DiseaseResearch (CEIDR). S.D. is funded by an NIHR GlobalResearch Professorship (NIHR300791). L.T. and S.C.M.are also supported by the U.S. Food and Drug Administration Medical Countermeasures Initiative contract75F40120C00085 and the National Institute for Health Research Health Protection Research Unit (HPRU) inEmerging and Zoonotic Infections (NIHR200907) at University of Liverpool inpartnership with Public HealthEngland (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford.L.T. is based at the University of Liverpool. M.D.P. is funded by the NIHR Sheffield Biomedical ResearchCentre (BRC – IS-BRC-1215-20017). ISARIC4C is supported by the MRC (grant no MC_PC_19059). J.C.K.is a Wellcome Investigator (WT204969/Z/16/Z) and supported by NIHR Oxford Biomedical Research Centreand CIFMS. The views expressed are those of the authors and not necessarily those of the NIHR or MRC