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Publikation

Trogisch, S.; Liu, X.; Rutten, G.; Xue, K.; Bauhus, J.; Brose, U.; Bu, W.; Cesarz, S.; Chesters, D.; Connolly, J.; Cui, X.; Eisenhauer, N.; Guo, L.; Haider, S.; Härdtle, W.; Kunz, M.; Liu, L.; Ma, Z.; Neumann, S.; Sang, W.; Schuldt, A.; Tang, Z.; van Dam, N. M.; von Oheimb, G.; Wang, M.-Q.; Wang, S.; Weinhold, A.; Wirth, C.; Wubet, T.; Xu, X.; Yang, B.; Zhang, N.; Zhu, C.-D.; Ma, K.; Wang, Y.; Bruelheide, H.; The significance of tree-tree interactions for forest ecosystem functioning Basic and Applied Ecology 55, 33-52, (2021) DOI: 10.1016/j.baae.2021.02.003

Global change exposes forest ecosystems to many risks including novel climatic conditions, increased frequency of climatic extremes and sudden emergence and spread of pests and pathogens. At the same time, forest landscape restoration has regained global attention as an integral strategy for climate change mitigation. Owing to unpredictable future risks and the need for new forests that provide multiple ecosystem services, mixed-species forests have been advocated for this purpose. However, the successful establishment of mixed forests requires intrinsic knowledge of biodiversity\'s role for forest ecosystem functioning. In this respect, a better understanding of tree-tree interactions and how they contribute to observed positive tree species richness effects on key ecosystem functions is critical. Here, we review the current knowledge of the underlying mechanisms of tree-tree interactions and argue that positive net biodiversity effects at the community scale may emerge from the dominance of positive over negative interactions at the local neighbourhood scale. In a second step, we demonstrate how tree-tree interactions and the immediate tree neighbourhood\'s role can be systematically assessed in a tree diversity experiment. The expected results will improve predictions about the effects of tree interactions on ecosystem functioning based on general principles. We argue that this knowledge is urgently required to guide the design of tree species mixtures for the successful establishment of newly planted forests.
Publikation

Marr, S.; Hageman, J. A.; Wehrens, R.; van Dam, N. M.; Bruelheide, H.; Neumann, S.; LC-MS based plant metabolic profiles of thirteen grassland species grown in diverse neighbourhoods Sci. Data 8, 52, (2021) DOI: 10.1038/s41597-021-00836-8

In plants, secondary metabolite profiles provide a unique opportunity to explore seasonal variation and responses to the environment. These include both abiotic and biotic factors. In field experiments, such stress factors occur in combination. This variation alters the plant metabolic profiles in yet uninvestigated ways. This data set contains trait and mass spectrometry data of thirteen grassland species collected at four time points in the growing season in 2017. We collected above-ground vegetative material of seven grass and six herb species that were grown in plant communities with different levels of diversity in the Jena Experiment. For each sample, we recorded visible traits and acquired shoot metabolic profiles on a UPLC-ESI-Qq-TOF-MS. We performed the raw data pre-processing in Galaxy-W4M and prepared the data for statistical analysis in R by applying missing data imputation, batch correction, and validity checks on the features. This comprehensive data set provides the opportunity to investigate environmental dynamics across diverse neighbourhoods that are reflected in the metabolomic profile.
Publikation

Vieira, S.; Sikorski, J.; Dietz, S.; Herz, K.; Schrumpf, M.; Bruelheide, H.; Scheel, D.; Friedrich, M. W.; Overmann, J.; Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands ISME J. 14, 463-475, (2020) DOI: 10.1038/s41396-019-0543-4

The active bacterial rhizobiomes and root exudate profiles of phytometers of six plant species growing in central European temperate grassland communities were investigated in three regions located up to 700 km apart, across diverse edaphic conditions and along a strong land use gradient. The recruitment process from bulk soil communities was identified as the major direct driver of the composition of active rhizosphere bacterial communities. Unexpectedly, the effect of soil properties, particularly soil texture, water content, and soil type, strongly dominated over plant properties and the composition of polar root exudates of the primary metabolism. While plant species-specific selection of bacteria was minor, the RNA-based composition of active rhizosphere bacteria substantially differed between rhizosphere and bulk soil. Although other variables could additionally be responsible for the consistent enrichment of particular bacteria in the rhizosphere, distinct bacterial OTUs were linked to the presence of specific polar root exudates independent of individual plant species. Our study also identified numerous previously unknown taxa that are correlated with rhizosphere dynamics and hence represent suitable targets for future manipulations of the plant rhizobiome.
Publikation

Dietz, S.; Herz, K.; Gorzolka, K.; Jandt, U.; Bruelheide, H.; Scheel, D.; Root exudate composition of grass and forb species in natural grasslands Sci. Rep. 10, 10691, (2020) DOI: 10.1038/s41598-019-54309-5

Plants exude a diverse cocktail of metabolites into the soil as response to exogenous and endogenous factors. So far, root exudates have mainly been studied under artificial conditions due to methodological difficulties. In this study, each five perennial grass and forb species were investigated for polar and semi-polar metabolites in exudates under field conditions. Metabolite collection and untargeted profiling approaches combined with a novel classification method allowed the designation of 182 metabolites. The composition of exuded polar metabolites depended mainly on the local environment, especially soil conditions, whereas the pattern of semi-polar metabolites was primarily affected by the species identity. The profiles of both polar and semi-polar metabolites differed between growth forms, with grass species being generally more similar to each other and more responsive to the abiotic environment than forb species. This study demonstrated the feasibility of investigating exudates under field conditions and to identify the driving factors of exudate composition.
Publikation

Herz, K.; Dietz, S.; Gorzolka, K.; Haider, S.; Jandt, U.; Scheel, D.; Bruelheide, H.; Correction: Linking root exudates to functional plant traits PLOS ONE 14, e0213965, (2019) DOI: 10.1371/journal.pone.0213965

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Publikation

Dietz, S.; Herz, K.; Döll, S.; Haider, S.; Jandt, U.; Bruelheide, H.; Scheel, D.; Semi‐polar root exudates in natural grassland communities Ecol. Evol. 9, 5526-5541, (2019) DOI: 10.1002/ece3.5043

In the rhizosphere, plants are exposed to a multitude of different biotic and abiotic factors, to which they respond by exuding a wide range of secondary root metabolites. So far, it has been unknown to which degree root exudate composition is species‐specific and is affected by land use, the local impact and local neighborhood under field conditions. In this study, root exudates of 10 common grassland species were analyzed, each five of forbs and grasses, in the German Biodiversity Exploratories using a combined phytometer and untargeted liquid chromatography‐mass spectrometry (LC‐MS) approach. Redundancy analysis and hierarchical clustering revealed a large set of semi‐polar metabolites common to all species in addition to species‐specific metabolites. Chemical richness and exudate composition revealed that forbs, such as Plantago lanceolata and Galium species, exuded more species‐specific metabolites than grasses. Grasses instead were primarily affected by environmental conditions. In both forbs and grasses, plant functional traits had only a minor impact on plant root exudation patterns. Overall, our results demonstrate the feasibility of obtaining and untargeted profiling of semi‐polar metabolites under field condition and allow a deeper view in the exudation of plants in a natural grassland community.
Publikation

Peters, K.; Gorzolka, K.; Bruelheide, H.; Neumann, S.; Seasonal variation of secondary metabolites in nine different bryophytes Ecol. Evol. 8, 9105-9117, (2018) DOI: 10.1002/ece3.4361

Bryophytes occur in almost all land ecosystems and contribute to global biogeochemical cycles, ecosystem functioning, and influence vegetation dynamics. As growth and biochemistry of bryophytes are strongly dependent on the season, we analyzed metabolic variation across seasons with regard to ecological characteristics and phylogeny. Using bioinformatics methods, we present an integrative and reproducible approach to connect ecology with biochemistry. Nine different bryophyte species were collected in three composite samples in four seasons. Untargeted liquid chromatography coupled with mass spectrometry (LC/MS) was performed to obtain metabolite profiles. Redundancy analysis, Pearson's correlation, Shannon diversity, and hierarchical clustering were used to determine relationships among species, seasons, ecological characteristics, and hierarchical clustering. Metabolite profiles of Marchantia polymorpha and Fissidens taxifolius which are species with ruderal life strategy (R‐selected) showed low seasonal variability, while the profiles of the pleurocarpous mosses and Grimmia pulvinata which have characteristics of a competitive strategy (C‐selected) were more variable. Polytrichum strictum and Plagiomnium undulatum had intermediary life strategies. Our study revealed strong species‐specific differences in metabolite profiles between the seasons. Life strategies, growth forms, and indicator values for light and soil were among the most important ecological predictors. We demonstrate that untargeted Eco‐Metabolomics provide useful biochemical insight that improves our understanding of fundamental ecological strategies.
Publikation

Peters, K.; Worrich, A.; Weinhold, A.; Alka, O.; Balcke, G.; Birkemeyer, C.; Bruelheide, H.; Calf, O. W.; Dietz, S.; Dührkop, K.; Gaquerel, E.; Heinig, U.; Kücklich, M.; Macel, M.; Müller, C.; Poeschl, Y.; Pohnert, G.; Ristok, C.; Rodríguez, V. M.; Ruttkies, C.; Schuman, M.; Schweiger, R.; Shahaf, N.; Steinbeck, C.; Tortosa, M.; Treutler, H.; Ueberschaar, N.; Velasco, P.; Weiß, B. M.; Widdig, A.; Neumann, S.; van Dam, N. M.; Current Challenges in Plant Eco-Metabolomics Int. J. Mol. Sci. 19, 1385, (2018) DOI: 10.3390/ijms19051385

The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant–organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology
Publikation

Peters, K.; Gorzolka, K.; Bruelheide, H.; Neumann, S.; Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes Sci. Data 5, 180179, (2018) DOI: 10.1038/sdata.2018.179

In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS). Using this dataset we address the current challenges when processing Eco-Metabolomics data. Here, we also present a reproducible and reusable computational workflow implemented in Galaxy focusing on standard formats, data import, technical validation, feature detection, diversity analysis and multivariate statistics. We expect that the representative dataset and the reusable processing pipeline will facilitate future studies in the research field of Eco-Metabolomics.
Publikation

Herz, K.; Dietz, S.; Gorzolka, K.; Haider, S.; Jandt, U.; Scheel, D.; Bruelheide, H.; Linking root exudates to functional plant traits PLOS ONE 13, e0204128, (2018) DOI: 10.1371/journal.pone.0204128

Primary and secondary metabolites exuded by plant roots have mainly been studied under laboratory conditions, while knowledge of root exudate patterns of plants growing in natural communities is very limited. Focusing on ten common European grassland plant species, we asked to which degree exuded metabolite compositions are specific to species or growth forms (forbs and grasses), depend on environments and local neighbourhoods, and reflect traditional plant functional traits. Root exudates were collected under field conditions and analysed using a non-targeted gas chromatography coupled mass spectrometry (GC-MS) approach. In total, we annotated 153 compounds of which 36 were identified by structure and name as metabolites mainly derived from the primary metabolism. Here we show by using variance partitioning, that the composition of exuded polar metabolites was mostly explained by plot identity, followed by plant species identity while plant species composition of the local neighbourhood played no role. Total and root dry biomass explained the largest proportion of variance in exudate composition, with additional variance explained by traditional plant traits. Although the exudate composition was quite similar between the two growth forms, we found some metabolites that occurred only in one of the two growth forms. Our study demonstrated the feasibility of measuring polar exudates under non-sterile field conditions by mass spectrometry, which opens new avenues of research for functional plant ecology.
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