Biology subjects

Schmid, B.

Publications and source records attributed to Schmid, B..

51 records · Page 3Linked to original sources

bioRxiv2020

Plant diversity and community age shape soil microbial communities

Plant and soil microbial diversity are linked through a range of interactions, including the exchange of carbon and nutrients but also herbivory and pathogenic effects. Over time, associations between plant communities and their soil microbiota may strengthen and become more specific, resulting in stronger associations between plant and soil microbial diversity. We tested this hypothesis in a 4-year long field experiment in which we factorially combined plant community history and soil legacy with plant diversity (1, 2, 4, 8, 60 species). Plant community history and soil legacy refer to the presence ("old") or absence ("new") of a common history of plants and soils in 52 different plant species compositions during 8 years in a long-term biodiversity experiment in Jena, Germany. After 4 years of growth, we took soil samples in the new field experiment and determined soil bacterial and fungal composition in terms of operational taxonomic units (OTUs) using 16S rRNA gene and ITS DNA sequencing. Plant community history did not affect overall soil community composition but differentially affected bacterial richness and abundances of specific bacteria taxa in association with particular plant species compositions. Soil legacy markedly increased soil bacterial richness and evenness and decreased fungal evenness. Soil fungal richness increased with plant species richness, regardless of plant community history or soil legacy, with the strongest difference between plant monocultures and mixtures. Particular plant species compositions and functional groups were associated with particular bacterial and fungal community compositions. Grasses increased and legumes decreased fungal richness and evenness. Our findings indicate that as experimental ecosystems varying in plant diversity develop over 8 years, plant species associate with specific soil microbial taxa. This can have long-lasting effects on belowground community composition in re-assembled plant communities, as reflected in strong soil legacy signals still visible after 4 years of growing new plant communities. Effects of plant community history on soil communities are subtle and may take longer to fully develop.

ecology↗

bioRxiv2020

Diversity increases yield but reduces reproductive effort in crop mixtures

Resource allocation to reproduction is a critical trait for plant fitness1,2. This trait, called harvest index in the agricultural context3-5, determines how plant biomass is converted to seed yield and consequently financial revenue of numerous major staple crops. While plant diversity has been demonstrated to increase plant biomass6-8, plant diversity effects on seed yield of crops are ambiguous9. This discrepancy could be explained through changes in the proportion of resources invested into reproduction in response to changes in plant diversity, namely through changes of species interactions and microenvironmental conditions10-13. Here we show that increasing crop plant diversity from monoculture over 2- to 4-species mixtures increased annual primary productivity, resulting in overall higher plant biomass and, to a lesser extent, higher seed yield in mixtures compared with monocultures. The difference between the two responses to diversity was due to a reduced reproductive effort of the eight tested crop species in mixtures, possibly because their common cultivars have been bred for maximum performance in monoculture. While crop diversification provides a sustainable measure of agricultural intensification14, the use of currently available cultivars may compromise larger gains in seed yield. We therefore advocate regional breeding programs for crop varieties to be used in mixtures that should exploit facilitative interactions15 among crop species.

ecology↗

bioRxiv2020

Recombinant protein production and purification of SiiD, SiiE and SiiF - components of the SPI4-encoded type I secretion system from Salmonella Typhimurium

In humans, Salmonella enterica infections are responsible for a pleiotropy of medical conditions. These include intestinal inflammation and typhoid fever. The initial contact between Salmonella and polarized epithelial cells is established by the SPI4-encoded type I secretion system (T1SS), which secrets SiiE, a giant non-fimbrial adhesin. We have recombinantly produced various domains of this T1SS from Salmonella enterica serovar Typhimurium in Escherichia coli for further experimental characterization. We purified three variants of SiiD, the periplasmic adapter protein spanning the space between the inner and outer membrane, two variants of the SiiE N-terminal region and the N-terminal domain of the SiiF ATP-binding cassette (ABC) transporter. In all three proteins, at least one variant yielded high amounts of pure soluble protein. Proper folding and cooperative unfolding were investigated by circular dichroism (CD) spectroscopy. Secondary structure content estimations from CD spectra were in good agreement with the values derived from SiiD and SiiF homology models or, in case of the SiiE N-terminal region, a secondary structure prediction. For one SiiD variant, protein crystals could be obtained that diffracted X-rays to approximately 4 [A] resolution.

microbiology↗

bioRxiv2019

Plant traits are poor predictors of long-term ecosystem functioning

Earth is home to over 350,000 vascular plant species1 that differ in their traits in innumerable ways. Yet, a handful of functional traits can help explaining major differences among species in photosynthetic rate, growth rate, reproductive output and other aspects of plant performance2-6. A key challenge, coined "the Holy Grail" in ecology, is to upscale this understanding in order to predict how natural or anthropogenically driven changes in the identity and diversity of co-occurring plant species drive the functioning of ecosystems7, 8. Here, we analyze the extent to which 42 different ecosystem functions can be predicted by 41 plant traits in 78 experimentally manipulated grassland plots over 10 years. Despite the unprecedented number of traits analyzed, the average percentage of variation in ecosystem functioning that they jointly explained was only moderate (32.6%) within individual years, and even much lower (12.7%) across years. Most other studies linking ecosystem functioning to plant traits analyzed no more than six traits, and when including either only six random or the six most frequently studied traits in our analysis, the average percentage of explained variation in across-year ecosystem functioning dropped to 4.8%. Furthermore, different ecosystem functions were driven by different traits, with on average only 12.2% overlap in significant predictors. Thus, we did not find evidence for the existence of a small set of key traits able to explain variation in multiple ecosystem functions across years. Our results therefore suggest that there are strong limits in the extent to which we can predict the long-term functional consequences of the ongoing, rapid changes in the composition and diversity of plant communities that humanity is currently facing.

ecology↗

bioRxiv2019

The results of biodiversity-ecosystem functioning experiments are realistic

A large body of research shows that biodiversity loss can reduce ecosystem functioning, thus providing support for the conservation of biological diversity1-4. Much of the evidence for this relationship is drawn from biodiversity-ecosystem functioning experiments (hereafter: biodiversity experiments), in which biodiversity loss is simulated by randomly assembling communities of varying species diversity, and ecosystem functions are measured5-9. This random assembly has led some ecologists to question the relevance of biodiversity experiments to real-world ecosystems, where community assembly may often be non-random and influenced by external drivers, such as climate or land-use intensification10-18. Despite these repeated criticisms, there has been no comprehensive, quantitative assessment of how experimental and real-world plant communities really differ, and whether these differences invalidate the experimental results. Here, we compare data from two of the largest and longest-running grassland biodiversity experiments globally (Jena Experiment, Germany; BioDIV, USA) to related real-world grassland plant communities in terms of their taxonomic, functional, and phylogenetic diversity and functional-trait composition. We found that plant communities of biodiversity experiments have greater variance in these compositional features than their real-world counterparts, covering almost all of the variation of the real-world communities (82-96%) while also containing community types that are not currently observed in the real world. We then re-analysed a subset of experimental data that included only ecologically-realistic communities, i.e. those comparable to real-world communities. For ten out of twelve biodiversity-ecosystem functioning relationships, biodiversity effects did not differ significantly between the full dataset of biodiversity experiments and the ecologically-realistic subset of experimental communities. This demonstrates that the results of biodiversity experiments are largely insensitive to the inclusion/exclusion of unrealistic communities. By bridging the gap between experimental and real-world studies, these results demonstrate the validity of inferences from biodiversity experiments, a key step in translating their results into specific recommendations for real-world biodiversity management.

ecology↗

bioRxiv2019

A geostatistical approach to estimate high resolution nocturnal bird migration densities from a weather radar network.

O_LIQuantifying nocturnal bird migration at high resolution is essential for (1) understanding the phenology of migration and its drivers, (2) identifying critical spatio-temporal protection zones for migratory birds, and (3) assessing the risk of collision with man-made structures.\nC_LIO_LIWe propose a tailored geostatistical model to interpolate migration intensity monitored by a network of weather radars. The model is applied to data collected in autumn 2016 from 69 European weather radars. To cross-validate the model, we compared our results with independent measurements of two bird radars.\nC_LIO_LIOur model estimated bird densities at high resolution (0.2{degrees}latitude-longitude, 15min) and assessed the associated uncertainty. Within the area covered by the radar network, we estimated that around 120 million birds were simultaneously in flight [10-90 quantiles: 107-134]. Local estimations can be easily visualized and retrieved from a dedicated interactive website: birdmigrationmap.vogelwarte.ch.\nC_LIO_LIThis proof-of-concept study demonstrates that a network of weather radar is able to quantify bird migration at high resolution and accuracy. The model presented has the ability to monitor population of migratory birds at scales ranging from regional to continental in space and daily to yearly in time. Near-real-time estimation should soon be possible with an update of the infrastructure and processing software.\nC_LI

ecology↗

bioRxiv2018

Rhizosphere bacterial community composition depends on plant diversity legacy in soil and plant species identity

Soil microbes are known to be involved in a number of essential ecosystem processes such as nutrient cycling, plant productivity and the maintenance of plant species diversity. However, how plant species diversity and identity affect soil microbial diversity and community composition is largely unknown. We tested whether, over the course of 11 years, distinct soil bacterial communities developed under plant monocultures and mixtures, and if over this timeframe plants with a monoculture or mixture history changed in the microbial communities they associated with. For eight species, we grew offspring of plants that had been grown for 11 years in the same monocultures or mixtures (monoculture- or mixture-type plants) in pots inoculated with microbes extracted from the monoculture and mixture soils. After five months of growth in the glasshouse, we collected rhizosphere soil from each plant and used 16S-rRNA gene sequencing to determine the community composition and diversity of the bacterial communities. Microbial community structure in the plant rhizosphere was primarily determined by soil legacy (monoculture vs. mixture soil) and by plant species identity, but not by plant legacy (monoculture- vs. mixture-type plants). In seven out of the eight plant species bacterial abundance was larger when inoculated with microbes from mixture soil. We conclude that plant diversity can strongly affect belowground community composition and diversity, feeding back to the assemblage of rhizosphere microbial communities in newly establishing plants. Thereby our work demonstrates that concerns for plant biodiversity loss are also concerns for soil biodiversity loss.

ecology↗

bioRxiv2018

Evidence for rapid evolution in a grassland biodiversity experiment

In long-term grassland biodiversity experiments positive effects of biodiversity on plant productivity commonly increase with time. It has been shown that such increased biodiversity effects persist even if plants are transferred into a common environment. Thus, we hypothesized that community diversity had acted as a selective agent, which resulted in the emergence of plant monoculture and mixture types. To test our hypothesis, we grew offspring from plants that were exposed for eleven years to a monoculture or mixture environment in a biodiversity experiment (Jena Experiment) under controlled greenhouse conditions in monocultures or two-species mixtures. We used epiGBS, a genotyping-by-sequencing approach combined with bisulfite conversion to provide integrative genetic and epigenetic data. We observed significant genetic and epigenetic divergence according to selection history in three out of five perennial grassland species, namely Galium mollugo, Prunella vulgaris and Veronica chamaedrys. For a fourth species, Lathyrus pratensis, we found mixed evidence and a fifth one, Plantago lanceolata, did not exhibit any divergence. In addition, current diversity levels in the greenhouse also had weak effects on epigenetic variation. Our results suggest that selection of genetic variants, and possibly epigenetic variants, caused the rapid emergence of monoculture and mixture types within plant species in the Jena Experiment. However, given the limited genome coverage, it remains unclear how much of the epigenetic divergence was independent of the genetic divergence.

ecology↗

bioRxiv2018

Evolution increases ecosystem temporal stability and recovery from a flood in grassland communities

Understanding factors that increase ecosystem stability is critical in the face of environmental change. Experiments simulating species loss from grassland ecosystems have shown that losing biodiversity decreases the ability of ecosystems to buffer negative effects of disturbances. However, as the originally sown experimental communities with reduced biodiversity develop, plant evolutionary processes or the assembly of interacting soil organisms may allow them to develop stability and resilience over time. We explored such effects in a long-term grassland biodiversity experiment with plant communities with either a history of co-occurrence (selected communities) or no such history (naive communities) over a four-year period in which a major flood disturbance occurred. We found selected communities had temporally more stable biomass than the same communities of naive plants, especially at low species richness. Furthermore, selected communities showed greater short-term biomass recovery after flooding, resulting in more stable post-flood productivity. In contrast to a previous study, the positive diversity-stability relationship was maintained after the flooding. Our results were consistent across three soil treatments simulating the presence or absence of co-selected microbial communities. We suggest that prolonged exposure of plant populations to a particular community context and abiotic site conditions can increase ecosystem temporal stability and resistance to disturbance. We argue that selection during the course of a biodiversity experiment is the most parsimonious explanation for these effects. A history of co-occurrence can in part compensate for species loss, as can high plant diversity in part compensate for the missing opportunity of such adaptive adjustments.

ecology↗

bioRxiv2017

Testing for co-adaptation of plants and arbuscular mycorrhizal fungi in a biodiversity experiment

O_LIBiodiversity loss not only impairs ecosystem functioning but can also alter the selection for traits in plant communities. At high diversity selection favours traits that allow for greater niche partitioning, whereas at low diversity selection may favour greater defence against pathogens. However, it is unknown whether changes in plant diversity also select for altered interactions with soil organisms.\nC_LIO_LIWe assessed whether the responses in plant growth and functional traits to their local arbuscular mycorrhizal fungal (AMF) communities have been altered by the diversity of the plant communities from which both plants and AMF communities were obtained. We grew plants with AMF communities that originated from either plant monocultures or mixtures in a fully factorial design that included both negative and positive controls, by inoculating no AMF or a foreign AMF respectively.\nC_LIO_LIWe found that AMF from plant mixtures were more beneficial than monoculture AMF for two out of five plant species. Plants from mixtures generally grew better than those from monocultures, but suffered greater damage by leaf pathogens. Although plant growth and phenotypic responses were dependent on the AMF communities with which they associated, we found little evidence for plant growth responses specific to their local AMF communities and results differed between species and traits.\nC_LIO_LIOur results show that plants from mixtures were selected for increased growth at the expense of reduced defence and vice versa for plants from monocultures, providing evidence for plant diversity-dependent selection on competitive growth vs. defence. Furthermore, our study suggests that effects of a common history between plants and AMF do not follow a general pattern leading to increased or decreased mutualism.\nC_LIO_LISynthesis: Here we provide evidence that biodiversity loss can alter evolutionary trajectories of plant phenotypes and responses to their local AMF communities. However, the selection for altered plant-AMF interactions differ between plant species. To understand how plant communities respond and evolve under a changing environment requires further knowledge about life strategies of plant species and their above-belowground interactions.\nC_LI

ecology↗

bioRxiv2017

Pan-embryo cell dynamics of germlayer formation in zebrafish

Cell movements are coordinated across spatio-temporal scales to achieve precise positioning of organs during vertebrate gastrulation. In zebrafish, mechanisms governing such morphogenetic movements have so far only been studied within a local region or a single germlayer. Here, we present pan-embryo analyses of fate specification and dynamics of all three germlayers simultaneously within a gastrulating embryo, showing that cell movement characteristics are predominantly determined by its position within the embryo, independent of its germlayer identity. The spatially confined fate specification establishes a distinct distribution of cells in each germlayer during early gastrulation. The differences in the initial distribution are subsequently amplified by a unique global movement, which organizes the organ precursors along the embryonic body axis, giving rise to the blueprint of organ formation.

developmental biology↗

bioRxiv2017

Facilitation between plants shapes pollination networks

SignificanceAlthough it is known that plant-plant and plant-pollinator interactions can strongly influence biodiversity and its effects on ecosystem functioning, the details of how competition and facili-tation among plants scale up to mutualistic interactions with pollinators and thus affect pollina-tion networks are poorly understood. We introduce a simple experimental system in which we control local plant interactions, measure pollinator responses and characterize plant-pollinator networks. We find that facilitation among plants produces synergistic and antagonistic effects on the pollinator community affecting the architecture and robustness of plant-pollinator net-works. Our results provide evidence for bottom-up non-additive effects of plant interactions on pollination networks and have implications for the way we study and manage ecosystems.

ecology↗

bioRxiv2017

Selection in response to community diversity alters plant performance in newly assembled test communities

In grassland biodiversity experiments the positive biodiversityn-ecosystem functioning relationship generally increases over time. However, we know little about the underlying short-term evolutionary processes. Using five plant species selected for twelve years in a biodiversity experiment in mixture or monoculture and plants without such a selection history, we assessed whether differential selection altered productivity, biodiversity effects, and functional trait differences within newly assembled monocultures and 2-species mixtures. Plants without past community selection history produced the lowest assemblage biomass and showed the weakest biodiversity effects. In newly assembled mixtures, plants with a selection history in mixtures produced more biomass than plants with a monoculture selection history. Biodiversity effects were generally positive and differed significantly between selection histories. However, contrary to our expectations, biodiversity effects were not stronger for mixture-type plants. Biodiversity effects were influenced by both trait differences between plants and community-weighted means, but these relationships were mostly independent of selection history. Our findings suggest that twelve years of selection history in monocultures or species mixtures differentiated plants of each species into monoculture- and mixture-types. Such rapid evolution of different community-types within grassland species and its effect on ecosystem services and functioning are likely to be important for species conservation practice.

ecology↗

bioRxiv2017

Positive interactions support the formation of complex spatial networks

Ecologists have recognised the effects of biotic interactions on the spatial distribution of living organisms. Yet, the spatial structure of plant interaction networks in real-world ecosystems has remained elusive so far. Using spatial pattern and network analyses, we found that alpine plant communities are organised in spatially variable and complex networks. Specifically, the cohesiveness of complex networks is promoted by short-distance positive plant interactions. At fine spatial scale, where positive mutual interactions prevailed, networks were characterised by a large connected component. With increasing scale, when negative interactions took over, network architecture became more hierarchical with many detached components that show a network collapse. This study highlights the crucial role of positive interactions for maintaining species diversity and the resistance of communities in the face of environmental perturbations.

ecology↗

bioRxiv2017

Community selection increases biodiversity effects

Species extinctions from local communities can negatively affect ecosystem functioning. Ecological mechanisms underlying these impacts are well studied but the role of evolutionary processes is rarely assessed. Using a long-term field experiment, we tested whether natural selection in plant communities increased the effects of biodiversity on productivity. We re-assembled communities with 8-year co-selection history adjacent to communities with identical species composition but no history of co-selection (\"naive communities\"). Monocultures and in particular mixtures of two to four co-selected species were more productive than their corresponding naive communities over four years in soils with or without co-selected microbial communities. At the highest diversity level of eight plant species, no such differences were observed. Our findings suggest that plant community evolution can lead to rapid increases in ecosystem functioning at low diversity but may take longer at high diversity. This effect was not modified by treatments that simulated additional co-evolutionary processes between plants and soil organisms.

ecology↗