308 results on '"Bonkowski M"'
Search Results
2. Linking rhizosphere processes across scales: Opinion
- Author
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Schnepf, A., Carminati, A., Ahmed, M. A., Ani, M., Benard, P., Bentz, J., Bonkowski, M., Knott, M., Diehl, D., Duddek, P., Kröner, E., Javaux, M., Landl, M., Lehndorff, E., Lippold, E., Lieu, A., Mueller, C. W., Oburger, E., Otten, W., Portell, X., Phalempin, M., Prechtel, A., Schulz, R., Vanderborght, J., and Vetterlein, D.
- Published
- 2022
- Full Text
- View/download PDF
3. How to adequately represent biological processes in modeling multifunctionality of arable soils
- Author
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Vogel, Hans-Jörg, Amelung, W., Baum, C., Bonkowski, M., Blagodatsky, S., Grosch, R., Herbst, M., Kiese, R., Koch, S., Kuhwald, M., König, Sara, Leinweber, P., Lennartz, B., Müller, C.W., Pagel, H., Rillig, M.C., Rüschhoff, Judith Sophia, Russell, D., Schnepf, A., Schulz, S., Siebers, N., Vetterlein, Doris, Wachendorf, C., Weller, Ulrich, Wollschläger, Ute, Vogel, Hans-Jörg, Amelung, W., Baum, C., Bonkowski, M., Blagodatsky, S., Grosch, R., Herbst, M., Kiese, R., Koch, S., Kuhwald, M., König, Sara, Leinweber, P., Lennartz, B., Müller, C.W., Pagel, H., Rillig, M.C., Rüschhoff, Judith Sophia, Russell, D., Schnepf, A., Schulz, S., Siebers, N., Vetterlein, Doris, Wachendorf, C., Weller, Ulrich, and Wollschläger, Ute
- Abstract
Essential soil functions such as plant productivity, C storage, nutrient cycling and the storage and purification of water all depend on soil biological processes. Given this insight, it is remarkable that in modeling of these soil functions, the various biological actors usually do not play an explicit role. In this review and perspective paper we analyze the state of the art in modeling these soil functions and how biological processes could more adequately be accounted for. We do this for six different biologically driven processes clusters that are key for understanding soil functions, namely i) turnover of soil organic matter, ii) N cycling, iii) P dynamics, iv) biodegradation of contaminants v) plant disease control and vi) soil structure formation. A major conclusion is that the development of models to predict changes in soil functions at the scale of soil profiles (i.e. pedons) should be better rooted in the underlying biological processes that are known to a large extent. This is prerequisite to arrive at the predictive models that we urgently need under current conditions of Global Change.
- Published
- 2024
4. A slow-fast trait continuum at the whole community level in relation to land-use intensification
- Author
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Neyret, M., Le Provost, G., Boesing, A.L., Schneider, F.D., Baulechner, D., Bergmann, J., de Vries, F.T., Fiore-Donno, A.M., Geisen, S., Goldmann, Kezia, Merges, A., Saifutdinov, R.A., Simons, N.K., Tobias, J.A., Zaitsev, A.S., Gossner, M.M., Jung, K., Kandeler, E., Krauss, J., Penone, C., Schloter, M., Schulz, S., Staab, M., Wolters, V., Apostolakis, A., Birkhofer, K., Boch, S., Boeddinghaus, R.S., Bolliger, R., Bonkowski, M., Buscot, Francois, Dumack, K., Fischer, M., Gan, H.Y., Heinze, J., Hölzel, N., John, K., Klaus, V.H., Kleinebecker, T., Marhan, S., Müller, J., Renner, S.C., Rillig, M.C., Schenk, N.V., Schöning, I., Schrumpf, M., Seibold, S., Socher, S.A., Solly, Emily, Teuscher, M., van Kleunen, M., Wubet, Tesfaye, Manning, P., Neyret, M., Le Provost, G., Boesing, A.L., Schneider, F.D., Baulechner, D., Bergmann, J., de Vries, F.T., Fiore-Donno, A.M., Geisen, S., Goldmann, Kezia, Merges, A., Saifutdinov, R.A., Simons, N.K., Tobias, J.A., Zaitsev, A.S., Gossner, M.M., Jung, K., Kandeler, E., Krauss, J., Penone, C., Schloter, M., Schulz, S., Staab, M., Wolters, V., Apostolakis, A., Birkhofer, K., Boch, S., Boeddinghaus, R.S., Bolliger, R., Bonkowski, M., Buscot, Francois, Dumack, K., Fischer, M., Gan, H.Y., Heinze, J., Hölzel, N., John, K., Klaus, V.H., Kleinebecker, T., Marhan, S., Müller, J., Renner, S.C., Rillig, M.C., Schenk, N.V., Schöning, I., Schrumpf, M., Seibold, S., Socher, S.A., Solly, Emily, Teuscher, M., van Kleunen, M., Wubet, Tesfaye, and Manning, P.
- Abstract
Organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, whether there is synchronisation of these strategies at the entire community level is unclear. Here, we combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. The results indicate that most guilds consistently respond to these drivers through both direct and trophically mediated effects, resulting in a ‘slow-fast’ axis at the level of the entire community. Using 15 indicators of carbon and nutrient fluxes, biomass production and decomposition, we also show that fast trait communities are associated with faster rates of ecosystem functioning. These findings demonstrate that ‘slow’ and ‘fast’ strategies can be manifested at the level of whole communities, opening new avenues of ecosystem-level functional classification.
- Published
- 2024
5. Two-way NxP fertilisation experiment on barley (Hordeum vulgare) reveals shift from additive to synergistic N-P interactions at critical phosphorus fertilisation level
- Author
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Clayton, Jessica, Lemanski, K., Solbach, M.D., Temperton, V.M., Bonkowski, M., Clayton, Jessica, Lemanski, K., Solbach, M.D., Temperton, V.M., and Bonkowski, M.
- Abstract
In a pot experiment, we investigated synergistic interaction of N and P fertilisation on barley biomass (Hordeum vulgare) on both shoot and root level with the aim to determine whether N-P interaction would be the same for all levels of N and P fertilisation. We further aimed to determine whether there was a critical level of N and/or P fertilisation rate, above which, a decrease in resource allocation to roots (as nutrient availability increased) could be demonstrated. Barley plants were grown from seed on a nutrient poor substrate and subjected to a two-way NxP fertilisation gradient using a modified Hoagland fertilisation solution. We observed N-P interactions in shoot and root biomass, and N and P use-efficiencies. A synergistic response in biomass was observed only above a critical level of P fertilisation when P was not limiting growth. Furthermore, we found that the same incremental increase in N:P ratio of applied fertiliser elicited different responses in shoot and root biomass depending on P treatment and concluded that barley plants were less able to cope with increasing stoichiometric imbalance when P was deficient. We provide, for the first time, stoichiometric evidence that critical levels for synergistic interactions between N-P may exist in crop plants.
- Published
- 2024
6. Invasive earthworms shift soil microbial community structure in northern North American forest ecosystems
- Author
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Ferlian, O., Goldmann, Kezia, Bonkowski, M., Dumack, K., Wubet, Tesfaye, Eisenhauer, N., Ferlian, O., Goldmann, Kezia, Bonkowski, M., Dumack, K., Wubet, Tesfaye, and Eisenhauer, N.
- Abstract
Invasive earthworms colonize ecosystems around the globe. Compared to other species’ invasions, earthworm invasions have received little attention. Previous studies indicated their tremendous effects on resident soil biota representing a major part of the terrestrial biodiversity. We investigated effects of earthworm invasion on soil microbial communities in three forests in North America by conducting DNA sequencing of soil bacteria, fungi, and protists in two soil depths. Our study shows that microbial diversity was lower in highly invaded forest areas. While bacterial diversity was strongly affected compared to fungi and protists, fungal community composition and family dominance were strongly affected compared to bacteria and protists. We found most species specialized on invasion in fungi, mainly represented by saprotrophs. Comparably, few protist species, mostly bacterivorous, were specialized on invasion. As one of the first observational studies, we investigated earthworm invasion on three kingdoms showing distinct taxa- and trophic level-specific responses to earthworm invasion.
- Published
- 2024
7. Leaf Endophytes Affect Mycorrhizal Status and Growth of Co-Infected and Neighbouring Plants
- Author
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Omacini, M., Eggers, T., Bonkowski, M., Gange, A. C., and Jones, T. H.
- Published
- 2006
8. A fast-slow trait continuum at the level of entire communities
- Author
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Neyret, M., Le Provost, G., Boesing, A.L., Schneider, F.D., Baulechner, D., Bergmann, J., de Vries, F., Fiore-Donno, A.M., Geisen, S., Goldmann, Kezia ; orcid:0000-0003-2954-5517, Merges, A., Saifutdinov, R.A., Simons, N.K., Tobias, J.A., Zaitsev, A.S., Gossner, M.M., Jung, K., Kandeler, E., Krauss, J., Penone, C., Schloter, M., Schulz, S., Staab, M., Wolters, V., Apostolakis, A., Birkhofer, K., Boch, S., Boeddinghaus, R.S., Bolliger, R., Bonkowski, M., Buscot, Francois, Dumack, K., Fischer, M., Gan, H.Y., Heinze, J., Hölzel, N., John, K., Klaus, V.H., Kleinebecker, T., Marhan, S., Müller, J., Renner, S.C., Rillig, M., Schenk, N.V., Schöning, I., Schrumpf, M., Seibold, S., Socher, S., Solly, E.F., Teuscher, M., van Kleunen, M., Wubet, Tesfaye ; orcid:0000-0001-8572-4486, Manning, P., Neyret, M., Le Provost, G., Boesing, A.L., Schneider, F.D., Baulechner, D., Bergmann, J., de Vries, F., Fiore-Donno, A.M., Geisen, S., Goldmann, Kezia ; orcid:0000-0003-2954-5517, Merges, A., Saifutdinov, R.A., Simons, N.K., Tobias, J.A., Zaitsev, A.S., Gossner, M.M., Jung, K., Kandeler, E., Krauss, J., Penone, C., Schloter, M., Schulz, S., Staab, M., Wolters, V., Apostolakis, A., Birkhofer, K., Boch, S., Boeddinghaus, R.S., Bolliger, R., Bonkowski, M., Buscot, Francois, Dumack, K., Fischer, M., Gan, H.Y., Heinze, J., Hölzel, N., John, K., Klaus, V.H., Kleinebecker, T., Marhan, S., Müller, J., Renner, S.C., Rillig, M., Schenk, N.V., Schöning, I., Schrumpf, M., Seibold, S., Socher, S., Solly, E.F., Teuscher, M., van Kleunen, M., Wubet, Tesfaye ; orcid:0000-0001-8572-4486, and Manning, P.
- Abstract
Across the tree of life, organismal functional strategies form a continuum from slow- to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above- and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a "slow-fast" axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that "slow" and "fast" strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.
- Published
- 2023
9. Responses of root architecture and the rhizosphere microbiome assembly of maize (Zea mays L.) to a soil texture gradient
- Author
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Rüger, L., Feng, K., Chen, Y., Sun, R., Sun, B., Deng, Y., Vetterlein, Doris, Bonkowski, M., Rüger, L., Feng, K., Chen, Y., Sun, R., Sun, B., Deng, Y., Vetterlein, Doris, and Bonkowski, M.
- Abstract
Soil texture, i.e. the fractions of different sized mineral particles, is critical to root growth and an important determinant of the occurrence and distribution of soil microbiota. More recently it was shown that individual plant species and even different cultivars harbor highly distinct rhizosphere associated microbiota, but it is still an open question how soil texture and its influence on root growth feeds back on root microbial assembly. We manipulated soil texture by stepwise additions of quartz sand to an agricultural loam. We grew maize (Zea mays L.) in these soils, measured changes in root traits and sampled bulk soil and rhizosphere to apply amplicon based high-throughput sequencing. We investigated changes in root morphology of maize and the concomitant shift in prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) diversity, community composition and co-occurrence in the maize rhizosphere along the soil texture gradient. A linear relationship between loam fraction and root morphology and a shift in microbial diversity along the soil texture gradient, as well as a stronger selection effect of the rhizosphere in soils with a high sand fraction (and high bulk density) were found. Co-occurrence network analysis revealed high modularity in fine textured soil, demonstrating that bulk density and texture are important factors affecting the recruitment of the core rhizosphere microbiome of maize.
- Published
- 2023
10. Root cap is an important determinant of rhizosphere microbiome assembly
- Author
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Rüger, L., Ganther, Minh, Freudenthal, J., Jansa, J., Heintz-Buschart, A., Tarkka, Mika, Bonkowski, M., Rüger, L., Ganther, Minh, Freudenthal, J., Jansa, J., Heintz-Buschart, A., Tarkka, Mika, and Bonkowski, M.
- Abstract
Plants impact the development of their rhizosphere microbial communities. It is yet unclear to what extent the root cap and specific root zones contribute to microbial community assembly. To test the roles of root caps and root hairs in the establishment of microbiomes along maize roots (Zea mays), we compared the composition of prokaryote (archaea and bacteria) and protist (Cercozoa and Endomyxa) microbiomes of intact or decapped primary roots of maize inbred line B73 with its isogenic root hairless (rth3) mutant. In addition, we tracked gene expression along the root axis to identify molecular control points for an active microbiome assembly by roots. Absence of root caps had stronger effects on microbiome composition than the absence of root hairs and affected microbial community composition also at older root zones and at higher trophic levels (protists). Specific bacterial and cercozoan taxa correlated with root genes involved in immune response. Our results indicate a central role of root caps in microbiome assembly with ripple-on effects affecting higher trophic levels and microbiome composition on older root zones.
- Published
- 2023
11. Biotic Interactions in the Rhizosphere: Effects on Plant Growth and Herbivore Development
- Author
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Bonkowski, M., Scheu, S., Weisser, Wolfgang W., editor, and Siemann, Evan, editor
- Published
- 2008
- Full Text
- View/download PDF
12. Linking rhizosphere processes across scales: Opinion
- Author
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UCL - SST/ELI/ELIE - Environmental Sciences, Schnepf, A., Carminati, A., Ahmed, M. A., Ani, M., Benard, P., Bentz, J., Bonkowski, M., Knott, M., Diehl, D., Duddek, P., Kröner, E., Javaux, Mathieu, Landl, M., Lehndorff, E., Lippold, E., Lieu, A., Mueller, C. W., Oburger, E., Otten, W., Portell, X., Phalempin, M., Prechtel, A., Schulz, R., Vanderborght, J., Vetterlein, D., UCL - SST/ELI/ELIE - Environmental Sciences, Schnepf, A., Carminati, A., Ahmed, M. A., Ani, M., Benard, P., Bentz, J., Bonkowski, M., Knott, M., Diehl, D., Duddek, P., Kröner, E., Javaux, Mathieu, Landl, M., Lehndorff, E., Lippold, E., Lieu, A., Mueller, C. W., Oburger, E., Otten, W., Portell, X., Phalempin, M., Prechtel, A., Schulz, R., Vanderborght, J., and Vetterlein, D.
- Abstract
Purpose Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.
- Published
- 2022
13. Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs
- Author
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Yim, B., Ibrahim, Zeeshan, Krüger, L., Ganther, Minh, Maccario, L., Sørensen, S.J., Heintz-Buschart, Anna, Tarkka, Mika, Vetterlein, Doris, Bonkowski, M., Blagodatskaya, Evgenia, Smalla, K., Yim, B., Ibrahim, Zeeshan, Krüger, L., Ganther, Minh, Maccario, L., Sørensen, S.J., Heintz-Buschart, Anna, Tarkka, Mika, Vetterlein, Doris, Bonkowski, M., Blagodatskaya, Evgenia, and Smalla, K.
- Abstract
Aims Different drivers are known to shape rhizosphere microbiome assembly. How soil texture (Texture) and presence or lack of root hairs (Root Hair) of plants affect the rhizosphere microbiome assembly and soil potential extracellular enzyme activities (EEA) at defined rooting depth (Depth) is still a knowledge gap. We investigated effects of these drivers on microbial assembly in rhizosphere and on potential EEA in root-affected soil of maize. Methods Samples were taken from three depths of root hair defective mutant rth3 and wild-type WT maize planted on loam and sand in soil columns after 22 days. Rhizosphere bacterial, archaeal, fungal and cercozoan communities were analysed by sequencing of 16S rRNA gene, ITS and 18S rRNA gene fragments. Soil potential EEA of ß-glucosidase, acid phosphatase and chitinase were estimated using fluorogenic substrates. Results The bacterial, archaeal and cercozoan alpha- and beta-diversities were significantly and strongly altered by Texture, followed by Depth and Root Hair. Texture and Depth had a small impact on fungal assembly, and only fungal beta-diversity was significantly affected. Significant impacts by Depth and Root Hair on beta-diversity and relative abundances at taxonomic levels of bacteria, archaea, fungi and cercozoa were dependent on Texture. Likewise, the patterns of potential EEA followed the trends of microbial communities, and the potential EEA correlated with the relative abundances of several taxa. Conclusions Texture was the strongest driver of rhizosphere microbiome and of soil potential EEA, followed by Depth and Root Hair, similarly to findings in maize root architecture and plant gene expression studies.
- Published
- 2022
14. What drives the assembly of plant-associated protist microbiomes? Investigating the effects of crop species, soil type and bacterial microbiomes
- Author
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Dumack, K., Feng, K., Flues, S., Sapp, M., Schreiter, Susanne, Grosch, R., Rose, L.E., Deng, Y., Smalla, K., Bonkowski, M., Dumack, K., Feng, K., Flues, S., Sapp, M., Schreiter, Susanne, Grosch, R., Rose, L.E., Deng, Y., Smalla, K., and Bonkowski, M.
- Abstract
In a field experiment we investigated the influence of the environmental filters soil type (i.e. three contrasting soils) and plant species (i.e. lettuce and potato) identity on rhizosphere community assembly of Cercozoa, a dominant group of mostly bacterivorous soil protists. Plant species (14%) and rhizosphere origin (vs bulk soil) with 13%, together explained four times more variation in cercozoan beta diversity than the three soil types (7% explained variation). Our results clearly confirm the existence of plant species-specific protist communities. Network analyses of bacteria-Cercozoa rhizosphere communities identified scale-free small world topologies, indicating mechanisms of self-organization. While the assembly of rhizosphere bacterial communities is bottom-up controlled through the resource supply from root (secondary) metabolites, our results support the hypothesis that the net effect may depend on the strength of top-down control by protist grazers. Since grazing of protists has a strong impact on the composition and functioning of bacteria communities, protists expand the repertoire of plant genes by functional traits, and should be considered as ‘protist microbiomes’ in analogy to ‘bacterial microbiomes’.
- Published
- 2022
15. Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests
- Author
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Dumack, K., Ferlian, O., Morselli Gysi, D., Degrune, F., Jauss, R.-T., Walden, S., Öztoprak, H., Wubet, Tesfaye, Bonkowski, M., Eisenhauer, N., Dumack, K., Ferlian, O., Morselli Gysi, D., Degrune, F., Jauss, R.-T., Walden, S., Öztoprak, H., Wubet, Tesfaye, Bonkowski, M., and Eisenhauer, N.
- Abstract
Earthworms are considered ecosystem engineers due to their fundamental impact on soil structure, soil processes and on other soil biota. An invasion of non-native earthworm species has altered soils of North America since European settlement, a process currently expanding into still earthworm-free forest ecosystems due to continuous spread and increasing soil temperatures owing to climate change. Although earthworms are known to modify soil microbial diversity and activity, it is as yet unclear how eukaryote consumers in soil microbial food webs will be affected. Here, we investigated how earthworm invasion affects the diversity of Cercozoa, one of the most dominant protist taxa in soils. Although the composition of the native cercozoan community clearly shifted in response to earthworm invasion, the communities of the different forests showed distinct responses. We identified 39 operational taxonomic units (OTUs) exclusively indicating earthworm invasion, hinting at an earthworm-associated community of Cercozoa. In particular, Woronina pythii, a hyper-parasite of plant-parasitic Oomycota in American forests, increased strongly in the presence of invasive earthworms, indicating an influence of invasive earthworms on oomycete communities and potentially on forest health, which requires further research.
- Published
- 2022
16. Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands
- Author
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European Research Council, Ministerio de Economía y Competitividad (España), Generalitat Valenciana, Ministerio de Ciencia e Innovación (España), European Commission, Junta de Andalucía, Australian Research Council, Pescador, David S. [0000-0003-0395-9543], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Singh, Brajesh K. [0000-0003-4413-4185], Maestre, Fernando T. [0000-0002-7434-4856], Pescador, David S., Delgado-Baquerizo, Manuel, Fiore-Donno, Anna M., Singh, Brajesh K., Bonkowski, M., Maestre, Fernando T., European Research Council, Ministerio de Economía y Competitividad (España), Generalitat Valenciana, Ministerio de Ciencia e Innovación (España), European Commission, Junta de Andalucía, Australian Research Council, Pescador, David S. [0000-0003-0395-9543], Delgado-Baquerizo, Manuel [0000-0002-6499-576X], Singh, Brajesh K. [0000-0003-4413-4185], Maestre, Fernando T. [0000-0002-7434-4856], Pescador, David S., Delgado-Baquerizo, Manuel, Fiore-Donno, Anna M., Singh, Brajesh K., Bonkowski, M., and Maestre, Fernando T.
- Abstract
Determining the influence of climate in driving the global distribution of soil microbial communities is fundamental to help predict potential shifts in soil food webs and ecosystem functioning under global change scenarios. Herein, we used a global survey including 80 dryland ecosystems from six continents, and found that the relative abundance of ecological clusters formed by taxa involved in bacteria-fungi and bacteria-cercozoa bipartite networks was highly sensitive to changes in temperature and aridity. Importantly, such a result was maintained when controlling for soil, geographical location and vegetation attributes, being pH and soil organic carbon important determinants of the relative abundance of the ecological clusters. We also identified potential global associations between important soil microbial taxa, which can be useful to support the conservation of terrestrial ecosystems under global change scenarios. Our results suggest that increases in temperature and aridity such as those forecasted for the next decades in drylands could potentially lead to drastic changes in the community composition of functionally important bipartite networks within soil food webs. This could have important but unknown implications for the provision of key ecosystem functions and associated services driven by the organisms forming these networks if other taxa cannot cope with them. This article is part of the theme issue 'Ecological complexity and the biosphere: the next 30 years'
- Published
- 2022
17. Linking rhizosphere processes across scales:Opinion
- Author
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Schnepf, A., Carminati, A., Ahmed, M. A., Ani, M., Benard, P., Bentz, J., Bonkowski, M., Knott, M., Diehl, D., Duddek, P., Kröner, E., Javaux, M., Landl, M., Lehndorff, E., Lippold, E., Lieu, A., Mueller, C. W., Oburger, E., Otten, W., Portell, X., Phalempin, M., Prechtel, A., Schulz, R., Vanderborght, J., Vetterlein, D., Schnepf, A., Carminati, A., Ahmed, M. A., Ani, M., Benard, P., Bentz, J., Bonkowski, M., Knott, M., Diehl, D., Duddek, P., Kröner, E., Javaux, M., Landl, M., Lehndorff, E., Lippold, E., Lieu, A., Mueller, C. W., Oburger, E., Otten, W., Portell, X., Phalempin, M., Prechtel, A., Schulz, R., Vanderborght, J., and Vetterlein, D.
- Abstract
Purpose: Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods: We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results: Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion: Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.
- Published
- 2022
18. Soil bacteria and protozoa affect root branching via effects on the auxin and cytokinin balance in plants
- Author
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Krome, K., Rosenberg, K., Dickler, C., Kreuzer, K., Ludwig-Müller, J., Ullrich-Eberius, C., Scheu, S., and Bonkowski, M.
- Published
- 2010
19. Nitrogen Enrichment Modifies Plant Community Structure via Changes to Plant-Soil Feedback
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Manning, P., Morrison, S. A., Bonkowski, M., and Bardgett, R. D.
- Published
- 2008
- Full Text
- View/download PDF
20. Secondary Metabolite Production Facilitates Establishment of Rhizobacteria by Reducing Both Protozoan Predation and the Competitive Effects of Indigenous Bacteria
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Jousset, A., Scheu, S., and Bonkowski, M.
- Published
- 2008
- Full Text
- View/download PDF
21. Linking rhizosphere processes across scales: Opinion
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Schnepf, A., primary, Carminati, A., additional, Ahmed, M. A., additional, Ani, M., additional, Benard, P., additional, Bentz, J., additional, Bonkowski, M., additional, Brax, M., additional, Diehl, D., additional, Duddek, P., additional, Kröner, E., additional, Javaux, M., additional, Landl, M., additional, Lehndorff, E., additional, Lippold, E., additional, Lieu, A., additional, Mueller, C. W., additional, Oburger, E., additional, Otten, W., additional, Portell, X., additional, Phalempin, M., additional, Prechtel, A., additional, Schulz, R., additional, Vanderborght, J., additional, and Vetterlein, D., additional
- Published
- 2021
- Full Text
- View/download PDF
22. Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.)
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Rüger, L., Feng, K., Dumack, K., Freudenthal, J., Chen, Y., Sun, R., Wilson, M., Yu, P., Sun, B., Deng, Y., Hochholdinger, F., Vetterlein, Doris, Bonkowski, M., Rüger, L., Feng, K., Dumack, K., Freudenthal, J., Chen, Y., Sun, R., Wilson, M., Yu, P., Sun, B., Deng, Y., Hochholdinger, F., Vetterlein, Doris, and Bonkowski, M.
- Abstract
It is by now well proven that different plant species within their specific root systems select for distinct subsets of microbiota from bulk soil – their individual rhizosphere microbiomes. In maize, root growth advances several centimeters each day, with the locations, quality and quantity of rhizodeposition changing. We investigated the assembly of communities of prokaryotes (archaea and bacteria) and their protistan predators (Cercozoa, Rhizaria) along the longitudinal root axis of maize (Zea mays L.). We grew maize plants in an agricultural loam and sampled rhizosphere soil at distinct locations along maize roots. We applied high-throughput sequencing, followed by diversity and network analyses in order to track changes in relative abundances, diversity and co-occurrence of rhizosphere microbiota along the root axis. Apart from a reduction of OTU richness and a strong shift in community composition between bulk soil and root tips, patterns of microbial community assembly along maize-roots were more complex than expected. High variation in beta diversity at root tips and the root hair zone indicated substantial randomness of community assembly. Root hair zone communities were characterized by massive co-occurrence of microbial taxa, likely fueled by abundant resource supply from rhizodeposition. Deterministic processes of community assembly (through competition and predation) only occurred further up the root where lateral roots emerged. They were revealed by low variability of beta diversity, changes in network topology, and the appearance of regular phylogenetic co-occurrence patterns in bipartite networks between prokaryotes and their potential protistan predators. Deterministic processes were strongest in regions with fully developed laterals, suggesting that a consistent rhizosphere microbiome finally assembled. For the targeted improvement of microbiome function, such knowledge on the processes of microbiome assembly on roots and its temporal and spatial va
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- 2021
23. Spatiotemporal dynamics of maize (Zea mays L.) root growth and its potential consequences for the assembly of the rhizosphere microbiota
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Bonkowski, M., Tarkka, Mika, Razavi, B.S., Schmidt, H., Blagodatskaya, Evgenia, Koller, R., Yu, P., Knief, C., Hochholdinger, F., Vetterlein, Doris, Bonkowski, M., Tarkka, Mika, Razavi, B.S., Schmidt, H., Blagodatskaya, Evgenia, Koller, R., Yu, P., Knief, C., Hochholdinger, F., and Vetterlein, Doris
- Abstract
Numerous studies have shown that plants selectively recruit microbes from the soil to establish a complex, yet stable and quite predictable microbial community on their roots – their “microbiome.” Microbiome assembly is considered as a key process in the self-organization of root systems. A fundamental question for understanding plant-microbe relationships is where a predictable microbiome is formed along the root axis and through which microbial dynamics the stable formation of a microbiome is challenged. Using maize as a model species for which numerous data on dynamic root traits are available, this mini-review aims to give an integrative overview on the dynamic nature of root growth and its consequences for microbiome assembly based on theoretical considerations from microbial community ecology.
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- 2021
24. Editorial: Rhizosphere spatiotemporal organisation
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Tarkka, Mika, Bonkowski, M., Ge, T., Knief, C., Razavi, B.S., Vetterlein, Doris, Tarkka, Mika, Bonkowski, M., Ge, T., Knief, C., Razavi, B.S., and Vetterlein, Doris
- Abstract
Formation of the rhizosphere, interface between living plant roots and soil, leads to changes in soil properties, nutrient and water distribution and biogeochemical cycling, and to a selection of unique populations of microorganisms and invertebrates. Dynamic feedback processes between the plant, the soil and the biota govern rhizosphere formation. The Frontiers Research Topic on “Rhizosphere Spatiotemporal Organization” presents contributions which aim to advance our understanding of rhizosphere processes. All of the six articles took the challenge to elaborate on the dynamic interactions and feedback processes in both spatial and temporal contexts.
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- 2021
25. Contrasting responses of above- and belowground diversity to multiple components of land-use intensity
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Le Provost, G., Thiele, J., Westphal, C., Penone, C., Allan, E., Neyret, M., van der Plas, F., Ayasse, M., Bardgett, R.D., Birkhofer, K., Boch, S., Bonkowski, M., Buscot, Francois, Feldhaar, H., Gaulton, R., Goldmann, Kezia, Gossner, M.M., Klaus, V.H., Kleinebecker, T., Krauss, J., Renner, S., Scherreiks, P., Sikorski, J., Baulechner, D., Blüthgen, N., Bolliger, R., Börschig, C., Busch, V., Chisté, M., Fiore-Donno, A.M., Fischer, M., Arndt, H., Hoelzel, N., John, K., Jung, K., Lange, M., Marzini, C., Overmann, J., Paŝalić, E., Perović, D.J., Prati, D., Schäfer, D., Schöning, I., Schrumpf, M., Sonnemann, I., Steffan-Dewenter, I., Tschapka, M., Türke, M., Vogt, J., Wehner, K., Weiner, C., Weisser, W., Wells, K., Werner, M., Wolters, V., Wubet, Tesfaye, Wurst, S., Zaitsev, A.S., Manning, P., Le Provost, G., Thiele, J., Westphal, C., Penone, C., Allan, E., Neyret, M., van der Plas, F., Ayasse, M., Bardgett, R.D., Birkhofer, K., Boch, S., Bonkowski, M., Buscot, Francois, Feldhaar, H., Gaulton, R., Goldmann, Kezia, Gossner, M.M., Klaus, V.H., Kleinebecker, T., Krauss, J., Renner, S., Scherreiks, P., Sikorski, J., Baulechner, D., Blüthgen, N., Bolliger, R., Börschig, C., Busch, V., Chisté, M., Fiore-Donno, A.M., Fischer, M., Arndt, H., Hoelzel, N., John, K., Jung, K., Lange, M., Marzini, C., Overmann, J., Paŝalić, E., Perović, D.J., Prati, D., Schäfer, D., Schöning, I., Schrumpf, M., Sonnemann, I., Steffan-Dewenter, I., Tschapka, M., Türke, M., Vogt, J., Wehner, K., Weiner, C., Weisser, W., Wells, K., Werner, M., Wolters, V., Wubet, Tesfaye, Wurst, S., Zaitsev, A.S., and Manning, P.
- Abstract
Land-use intensification is a major driver of biodiversity loss. However, understanding how different components of land use drive biodiversity loss requires the investigation of multiple trophic levels across spatial scales. Using data from 150 agricultural grasslands in central Europe, we assess the influence of multiple components of local- and landscape-level land use on more than 4,000 above- and belowground taxa, spanning 20 trophic groups. Plot-level land-use intensity is strongly and negatively associated with aboveground trophic groups, but positively or not associated with belowground trophic groups. Meanwhile, both above- and belowground trophic groups respond to landscape-level land use, but to different drivers: aboveground diversity of grasslands is promoted by diverse surrounding land-cover, while belowground diversity is positively related to a high permanent forest cover in the surrounding landscape. These results highlight a role of landscape-level land use in shaping belowground communities, and suggest that revised agroecosystem management strategies are needed to conserve whole-ecosystem biodiversity.
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- 2021
26. Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) Sheds Light on Euglyphida’s Dark Matter
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Dumack, K., Duckert, C., Meinhardt, R., Lara, Enrique, Bonkowski, M., Dumack, K., Duckert, C., Meinhardt, R., Lara, Enrique, and Bonkowski, M.
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The majority of Euglyphida species are characterised by shells with imbricated silica scales. Environmental surveys indicate a large unexplored diversity and recent efforts hinted at a certain diversity of yet undescribed, inconspicuous, scale-lacking Euglyphida. Here we describe Phaeobola aeris gen. nov., sp. nov. that shows a variety of morphological characters typical for the Euglyphida but lacks silica scales-instead, this species bears an agglutinated test. Neither its morphology nor phylogenetic placement allows its assignment to any currently described family. We erected the yet monospecific genus Phaeobola gen. nov., which with yet available data remain Euglyphida incertae sedis.
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- 2021
27. A global database of soil nematode abundance and functional group composition [Data paper]
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van den Hoogen, J., Geisen, S., Wall, D. H., Wardle, D. A., Traunspurger, W., de Goede, R. G. M., Adams, B. J., Ahmad, W., Ferris, H., Bardgett, R. D., Bonkowski, M., Campos-Herrera, R., Cares, J. E., Caruso, T., Caixeta, L. D., Chen, X. Y., Costa, S. R., Creamer, R., Castro, Jmde, Dam, M., Djigal, D., Escuer, M., Griffiths, B. S., Gutierrez, C., Hohberg, K., Kalinkina, D., Kardol, P., Kergunteuil, A., Korthals, G., Krashevska, V., Kudrin, A. A., Li, Qi, Liang, W. J., Magilton, M., Marais, M., Martin, J. A. R., Matveeva, E., Mayad, E., Mzough, E., Mulder, C., Mullin, P., Neilson, R., Nguyen, T. A. D., Nielsen, U. N., Okada, H., Rius, J. E. P., Pan, K. W., Peneva, V., Pellissier, L., da Silva, J. C. P., Pitteloud, C., Powers, T. O., Powers, K., Quist, C. W., Rasmann, S., Moreno, S. S., Scheu, S., Setala, H., Sushchuk, A., Tiunov, A. V., Trap, Jean, Vestergard, M., Villenave, C., Waeyenberge, L., Wilschut, R. A., Wright, D. G., Keith, A. M., Yang, J. I., Schmidt, O., Bouharroud, R., Ferji, Z., van der Putten, W. H., Routh, D., and Crowther, T. W.
- Abstract
Measurement(s)Abundance center dot Nematoda center dot environmental factorTechnology Type(s)Elutriative Centrifugation center dot computational modeling techniqueFactor Type(s)geographic locationSample Characteristic - OrganismNematodaSample Characteristic - Environmentsoil environment center dot climateSample Characteristic - LocationEarth (planet) Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11925843 As the most abundant animals on earth, nematodes are a dominant component of the soil community. They play critical roles in regulating biogeochemical cycles and vegetation dynamics within and across landscapes and are an indicator of soil biological activity. Here, we present a comprehensive global dataset of soil nematode abundance and functional group composition. This dataset includes 6,825 georeferenced soil samples from all continents and biomes. For geospatial mapping purposes these samples are aggregated into 1,933 unique 1-km pixels, each of which is linked to 73 global environmental covariate data layers. Altogether, this dataset can help to gain insight into the spatial distribution patterns of soil nematode abundance and community composition, and the environmental drivers shaping these patterns.
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- 2020
28. Land-use intensity alters networks between biodiversity, ecosystem functions, and services
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Felipe-Lucia, Maria, Soliveres, S., Penone, C., Fischer, M., Ammer, C., Boch, S., Boeddinghaus, R.S., Bonkowski, M., Buscot, Francois, Fiore-Donno, A.M., Frank, K., Goldmann, Kezia, Gossner, M.M., Hölzel, N., Jochum, M., Kandeler, E., Klaus, V.H., Kleinebecker, T., Leimer, S., Manning, P., Oelmann, Y., Saiz, H., Schall, P., Schloter, M., Schöning, I., Schrumpf, M., Solly, E.F., Stempfhuber, B., Weisser, W.W., Wilcke, W., Wubet, T., Allan, E., Felipe-Lucia, Maria, Soliveres, S., Penone, C., Fischer, M., Ammer, C., Boch, S., Boeddinghaus, R.S., Bonkowski, M., Buscot, Francois, Fiore-Donno, A.M., Frank, K., Goldmann, Kezia, Gossner, M.M., Hölzel, N., Jochum, M., Kandeler, E., Klaus, V.H., Kleinebecker, T., Leimer, S., Manning, P., Oelmann, Y., Saiz, H., Schall, P., Schloter, M., Schöning, I., Schrumpf, M., Solly, E.F., Stempfhuber, B., Weisser, W.W., Wilcke, W., Wubet, T., and Allan, E.
- Abstract
Land-use intensification can increase provisioning ecosystem services, such as food and timber production, but it also drives changes in ecosystem functioning and biodiversity loss, which may ultimately compromise human wellbeing. To understand how changes in land-use intensity affect the relationships between biodiversity, ecosystem functions, and services, we built networks from correlations between the species richness of 16 trophic groups, 10 ecosystem functions, and 15 ecosystem services. We evaluated how the properties of these networks varied across land-use intensity gradients for 150 forests and 150 grasslands. Land-use intensity significantly affected network structure in both habitats. Changes in connectance were larger in forests, while changes in modularity and evenness were more evident in grasslands. Our results show that increasing land-use intensity leads to more homogeneous networks with less integration within modules in both habitats, driven by the belowground compartment in grasslands, while forest responses to land management were more complex. Land-use intensity strongly altered hub identity and module composition in both habitats, showing that the positive correlations of provisioning services with biodiversity and ecosystem functions found at low land-use intensity levels, decline at higher intensity levels. Our approach provides a comprehensive view of the relationships between multiple components of biodiversity, ecosystem functions, and ecosystem services and how they respond to land use. This can be used to identify overall changes in the ecosystem, to derive mechanistic hypotheses, and it can be readily applied to further global change drivers.
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- 2020
29. Molecular investigation of Phryganella acropodia Hertwig et Lesser, 1874 (Arcellinida, Amoebozoa)
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Dumack, K., Görzen, D., González-Miguéns, R., Siemensma, F., Lahr, D.J.G., Lara, Enrique, Bonkowski, M., Dumack, K., Görzen, D., González-Miguéns, R., Siemensma, F., Lahr, D.J.G., Lara, Enrique, and Bonkowski, M.
- Abstract
Phryganella acropodia Hertwig and Lesser, 1874, is one of the most common and abundant testate amoeba species. It represents the type species of the genus Phryganella Penard, 1902, which in turn is the type genus for the suborder Phryganellina (Arcellinida) Bovee, 1985, but despite its taxonomic importance it was not yet analyzed with molecular methods. We established two cultures of putative Phryganella acropodia, designed Phryganellina-specific primers, amplified SSU rDNA data and subjected these sequences to phylogenetic analyses. Morphological and genetic differences were found between both strains. With SSU rDNA phylogenetic analyses we confirm that Phryganella acropodia branches with Phryganella paradoxa Penard, 1902 and Cryptodifflugia Penard, 1890 in the Phryganellina. We thus give further evidence that pseudopodia morphology in the Arcellinida is a character of high taxonomic value, as suggested by Bovee and Jung when erecting the suborder Phryganellina. Moreover, we provide evidence for cryptic diversity and for the first time confirm the existence of a naked life stage in Arcellinida by molecular means.
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- 2020
30. Impacts of soil faunal community composition on model grassland ecosystems. (Reports)
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Bradford, M.A., Jones, T.H., Bardgett, R.D., Black, H.I.J., Boag, B., Bonkowski, M., Cook, R., Eggers, T., Gange, A.C., Grayston, S.J., Kandeler, E., McCaig, A.E., Newington, J.E., Prosser, J.I., Setala, H., Staddon, P.L., Tordoff, G.M., Tscherko, D., and Lawton, J.H.
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Soil microbiology -- Research -- Environmental aspects -- Models ,Grasslands -- Environmental aspects -- Research -- Models ,Science and technology ,Models ,Research ,Environmental aspects - Abstract
Human impacts, including global change, may alter the composition of soil faunal communities, but consequences for ecosystem functioning are poorly understood. We constructed model grassland systems in the Ecotron controlled environment facility and manipulated soil community composition through assemblages of different animal body sizes. Plant community composition, microbial and root biomass, decomposition rate, and mycorrhizal colonization were all markedly affected. However, two key ecosystem processes, aboveground net primary productivity and net ecosystem productivity, were surprisingly resistant to these changes. We hypothesize that positive and negative faunal-mediated effects in soil communities cancel each other out, causing no net ecosystem effects., Soil fauna are essential to efficient nutrient cycling, organic matter turnover, and maintenance of soil physical structure, processes that are key determinants of primary production and ecosystem carbon storage (1-3). [...]
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- 2002
31. Microbial biomass and respiratory activity in soil aggregates of different sizes from three beechwood sites on a basalt hill
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Scheu, S., Maraun, M., Bonkowski, M., and Alphei, J.
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- 1996
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32. IN VIVO CELLULAR REPROGRAMMING FOR TISSUE REGENERATION AND AGE REVERSAL
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Lu, Y, Yu, D, Bonkowski, M, Schultz, M, Tian, X, Yang, J, He, Z, and Sinclair, D
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Abstracts - Abstract
Partial reprogramming without changing cellular identity has enormous potential to improve tissue regeneration and to reverse aspects of aging. The optic nerve injury is an excellent model for assessing the effects of age on axon regeneration in the central nervous system. In newborn rodents, optic nerves readily extend axons and regenerate after injury. In adults, however, this regenerative capacity is rapidly lost, at least partially due to epigenetic changes. Whether partial reprogramming can be achieved through an in vivo delivery approach to improve tissue regeneration is unknown. We have developed a dual adeno-associated viral (AAV) vector system allowing for the overexpression of reprogramming factors under the control of doxycycline, without any detectable leakiness. Our preliminary results showed that such AAVs are able to induce partial reprogramming safely without generating teratoma in vivo, and dramatically improve axon regeneration in adult mice. Thus, in vivo partial reprogramming through AAV delivery increases the regeneration capacity of axons after damage, and holds potential to reprogram cells in any tissue to be epigenetically younger.
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- 2018
33. Biotic interactions, community assembly, and ecoevolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships
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Eisenhauer, N., Bonkowski, M., Brose, U., Buscot, Francois, Durka, Walter, Ebeling, A., Fischer, M., Gleixner, G., Heintz-Buschart, A., Hines, J., Jesch, A., Lange, M., Meyer, S., Roscher, Christiane, Scheu, S., Schielzeth, H., Schloter, M., Schulz, S., Unsicker, S., van Dam, N.M., Weigelt, A., Weisser, W.W., Wirth, C., Wolf, J., Schmid, B., Eisenhauer, N., Bonkowski, M., Brose, U., Buscot, Francois, Durka, Walter, Ebeling, A., Fischer, M., Gleixner, G., Heintz-Buschart, A., Hines, J., Jesch, A., Lange, M., Meyer, S., Roscher, Christiane, Scheu, S., Schielzeth, H., Schloter, M., Schulz, S., Unsicker, S., van Dam, N.M., Weigelt, A., Weisser, W.W., Wirth, C., Wolf, J., and Schmid, B.
- Abstract
The functioning and service provisioning of ecosystems in the face of anthropogenic environmental and biodiversity change is a cornerstone of ecological research. The last three decades of biodiversity–ecosystem functioning (BEF) research have provided compelling evidence for the significant positive role of biodiversity in the functioning of many ecosystems. Despite broad consensus of this relationship, the underlying ecological and evolutionary mechanisms have not been well understood. This complicates the transition from a description of patterns to a predictive science. The proposed Research Unit aims at filling this gap of knowledge by applying novel experimental and analytical approaches in one of the longest-running biodiversity experiments in the world: the Jena Experiment. The central aim of the Research Unit is to uncover the mechanisms that determine BEF relationships in the short- and in the long-term. Increasing BEF relationships with time in long-term experiments do not only call for a paradigm shift in the appreciation of the relevance of biodiversity change, they likely are key to understanding the mechanisms of BEF relationships in general. The subprojects of the proposed Research Unit fall into two tightly linked main categories with two research areas each that aim at exploring variation in community assembly processes and resulting differences in biotic interactions as determinants of the long-term BEF relationship. Subprojects under “Microbial community assembly” and “Assembly and functions of animal communities” mostly focus on plant diversity effects on the assembly of communities and their feedback effects on biotic interactions and ecosystem functions. Subprojects under “Mediators of plant-biotic interactions” and “Intraspecific diversity and micro-evolutionary changes” mostly focus on plant diversity effects on plant trait expression and micro-evolutionary adaptation, and subsequent feedback effects on biotic interactions and ecosystem func
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- 2019
34. Networking Our Way to Better Ecosystem Service Provision
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Bohan, D. A., Landuyt, D., Ma, A., Macfadyen, S., Martinet, V., Massol, F., McInerny, G., Montoya, J. M., Mulder, C., Pascual, U., Pocock, M. J. O., White, P., Blanchemanche, S., Bonkowski, M., Bretagnolle, V., Bronmark, C., Dicks, L., Dumbrell, A., Eisenhauer, N., Friberg, N., Gessner, M. O., Gill, R. J., Gray, C., Haughton, A., Ibanez, S., Jensen, J., Jeppesen, E., Jokela, J., Lacroix, G., Lannou, C., Lavorel, S., Le Galliard, J. F., Lescourret, F., Liu, S., Loeuille, N., McLaughlin, O., Muggleton, S., Penuelas, J., Petanidou, T., Petit, S., Pomati, F., Raffaelli, D., Rasmussen, J., Raybould, A., Reboud, X., Richard, G., Scherber, C., Scheu, S., Sutherland, W. J., Tamaddoni-Nezhad, A., ter Braak, C., Termansen, M., Thompson, M. S., Tscharntke, T., Vacher, C., van der Geest, H., Voigt, W., Vonk, J. A., Zhou, X., Woodward, G., Quintessence Consortium, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratory of Plant Ecology, Department of Applied Ecology and Environmental Biology, Universiteit Gent = Ghent University [Belgium] (UGENT), School of Electronic Engineering and Computer Science (EECS), Queen Mary University of London (QMUL), CSIRO Agriculture and Food (CSIRO), Economie Publique (ECO-PUB), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), EconomiX, Université Paris Nanterre (UPN)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique et Evolution des Populations Végétales, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Department of Computer Science [Oxford], University of Oxford [Oxford], Station d'écologie théorique et expérimentale (SETE), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD), National Institute for Public Health and the Environment [Bilthoven] (RIVM), Basque Centre for Climate Change (BC3), Centre for Ecology and Hydrology [Wallingford] (CEH), Natural Environment Research Council (NERC), Environment Department [York], University of York [York, UK], Cologne Biocenter, Institute of Developmental Biology, Institute of Developmental Biology, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Department of Zoology [Cambridge], University of Cambridge [UK] (CAM), School of Biological Sciences [Colchester], University of Essex, German Centre for Integrative Biodiversity Research (iDiv), Norwegian Institute for Water Research (NIVA), Imperial College London, Rothamsted Research, Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), IBED Other Research (FNWI), Faculty of Science, Aquatic Environmental Ecology (IBED, FNWI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Universiteit Gent = Ghent University (UGENT), University of Oxford, Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), and Biotechnology and Biological Sciences Research Council (BBSRC)
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ECOLOGICAL NETWORKS ,0106 biological sciences ,Value (ethics) ,01 natural sciences ,Ecosystem services ,WORLD ,Models ,Natural (music) ,PERSPECTIVE ,Environmental Restoration and Remediation ,Genetics & Heredity ,PREDATION ,Ecology ,SCIENCE ,Biological Sciences ,PE&RC ,Conservation of Natural Resources / economics ,010601 ecology ,Biometris ,[SDE]Environmental Sciences ,Life Sciences & Biomedicine ,BEHAVIOR ,Ecology (disciplines) ,Ecological and Environmental Phenomena ,Environmental Sciences & Ecology ,Context (language use) ,010603 evolutionary biology ,SYSTEMS ,FOOD-WEB STRUCTURE ,Natural science ,Life Science ,Animals ,Humans ,Ecosystem ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Science & Technology ,Scale (chemistry) ,15. Life on land ,Biological ,Data science ,Ecological network ,SIZE ,Socioeconomic Factors ,13. Climate action ,Earth and Environmental Sciences ,Conservation of Natural Resources / methods ,Environmental science ,BIODIVERSITY ,Environmental Sciences - Abstract
International audience; The ecosystem services (EcoS) concept is being used increasingly to attach values to natural systems and the multiple benefits they provide to human societies. Ecosystem processes or functions only become EcoS if they are shown to have social and/or economic value. This should assure an explicit connection between the natural and social sciences, but EcoS approaches have been criticized for retaining little natural science. Preserving the natural, ecological science context within EcoS research is challenging because the multiple disciplines involved have very different traditions and vocabularies (common-language challenge) and span many organizational levels and temporal and spatial scales (scale challenge) that define the relevant interacting entities (interaction challenge). We propose a network-based approach to transcend these discipline challenges and place the natural science context at the heart of EcoS research.
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- 2016
35. IMPAIRMENT OF AN ENDOTHELIAL NAD+-H2S SIGNALING NETWORK IS A REVERSIBLE CAUSE OF VASCULAR AGING
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Bonkowski, M S, primary, Das, A, additional, Schultz, M, additional, Lu, Y, additional, Mitchell, J, additional, Wu, L, additional, Guarente, L, additional, and Sinclair, D, additional
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- 2018
- Full Text
- View/download PDF
36. DIVERGENT REGULATION OF SIRT1 MEDIATES THE ENDOCRINE RESPONSE TO CALORIE RESTRICTION
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Bonkowski, M, primary, Shawn, D, additional, Lu, Y, additional, Schultz, M, additional, Reyes, J, additional, Guarente, L, additional, and Sinclair, D, additional
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- 2018
- Full Text
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37. NAD+ DEPLETION AS A CAUSE OF INFLAMMAGING
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Schultz, M B, primary, Bochaton, T, additional, Bonkowski, M, additional, Li, J, additional, Lokitiyakul, D, additional, Colville, A, additional, Gomes, A, additional, and Sinclair, D, additional
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- 2018
- Full Text
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38. Soil networks become more connected and take up more carbon as nature restoration progresses
- Author
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Morriën, E., Hannula, S.E., Snoek, Basten, Helmsing, N.R., Zweers, H., De Hollander, M., Lujan Soto, Raquel, Bouffaud, M.L., Buée, M., Dimmers, Wim, Duyts, H., Geisen, S., Girlanda, M., Griffiths, R.I., Jørgensen, H-B., Jensen, J., Plassart, Pierre, Redecker, Dirk, Schmelz, R.M., Schmidt, O., Thomson, B.C., Tisserant, Emilie, Uroz, S., Winding, A., Bailey, M.J., Bonkowski, M., Faber, Jack H., Martin, F., Lemanceau, P., De Boer, W., van Veen, Hans, van der Putten, W.H., Morriën, E., Hannula, S.E., Snoek, Basten, Helmsing, N.R., Zweers, H., De Hollander, M., Lujan Soto, Raquel, Bouffaud, M.L., Buée, M., Dimmers, Wim, Duyts, H., Geisen, S., Girlanda, M., Griffiths, R.I., Jørgensen, H-B., Jensen, J., Plassart, Pierre, Redecker, Dirk, Schmelz, R.M., Schmidt, O., Thomson, B.C., Tisserant, Emilie, Uroz, S., Winding, A., Bailey, M.J., Bonkowski, M., Faber, Jack H., Martin, F., Lemanceau, P., De Boer, W., van Veen, Hans, and van der Putten, W.H.
- Abstract
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered
- Published
- 2017
39. Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters
- Author
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Shang, Y., Sikorski, J., Bonkowski, M., Fiore-Donno, A.-M., Kandeler, E., Marhan, S., Boeddinghaus, R.S., Solly, E.F., Schrumpf, M., Schöning, I., Wubet, Tesfaye, Buscot, Francois, Overmann, J., Shang, Y., Sikorski, J., Bonkowski, M., Fiore-Donno, A.-M., Kandeler, E., Marhan, S., Boeddinghaus, R.S., Solly, E.F., Schrumpf, M., Schöning, I., Wubet, Tesfaye, Buscot, Francois, and Overmann, J.
- Abstract
Interactions occur between two or more organisms affecting each other. Interactions are decisive for the ecology of the organisms. Without direct experimental evidence the analysis of interactions is difficult. Correlation analyses that are based on co-occurrences are often used to approximate interaction. Here, we present a new mathematical model to estimate the interaction strengths between taxa, based on changes in their relative abundances across environmental gradients.
- Published
- 2017
40. Soil protistology rebooted: 30 fundamental questions to start with
- Author
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Geisen, S., Mitchell, E.A.D., Wilkinson, D.M., Adl, S., Bonkowski, M., Brown, M.W., Fiore-Donno, A.M., Heger, T.J., Jassey, V.E.J., Krashevska, V., Lahr, D.J.G., Marcisz, K., Mulot, M., Payne, R., Singer, D., Anderson, O.R., Charman, D.J., Ekelund, F., Griffiths, B.S., Rønn, R., Smirnov, A., Bass, ´D., Belbahri, L., Berney, C., Blandenier, Q., Chatzinotas, Antonis, Clarholm, M., Dunthorn, M., Feest, A., Fernández, L.D., Foissner, W., Fournier, B., Gentekaki, E., Hájek, M., Helder, J., Jousset, A., Koller, R., Kumar, S., La Terza, A., Lamentowicz, M., Mazei, Y., Santos, S.S., Seppey, C.V.W., Spiegel, F.W., Walochnik, J., Winding, A., Lara, E., Geisen, S., Mitchell, E.A.D., Wilkinson, D.M., Adl, S., Bonkowski, M., Brown, M.W., Fiore-Donno, A.M., Heger, T.J., Jassey, V.E.J., Krashevska, V., Lahr, D.J.G., Marcisz, K., Mulot, M., Payne, R., Singer, D., Anderson, O.R., Charman, D.J., Ekelund, F., Griffiths, B.S., Rønn, R., Smirnov, A., Bass, ´D., Belbahri, L., Berney, C., Blandenier, Q., Chatzinotas, Antonis, Clarholm, M., Dunthorn, M., Feest, A., Fernández, L.D., Foissner, W., Fournier, B., Gentekaki, E., Hájek, M., Helder, J., Jousset, A., Koller, R., Kumar, S., La Terza, A., Lamentowicz, M., Mazei, Y., Santos, S.S., Seppey, C.V.W., Spiegel, F.W., Walochnik, J., Winding, A., and Lara, E.
- Abstract
Protists are the most diverse eukaryotes. These microbes are keystone organisms of soil ecosystems and regulate essential processes of soil fertility such as nutrient cycling and plant growth. Despite this, protists have received little scientific attention, especially compared to bacteria, fungi and nematodes in soil studies. Recent methodological advances, particularly in molecular biology techniques, have made the study of soil protists more accessible, and have created a resurgence of interest in soil protistology. This ongoing revolution now enables comprehensive investigations of the structure and functioning of soil protist communities, paving the way to a new era in soil biology. Instead of providing an exhaustive review, we provide a synthesis of research gaps that should be prioritized in future studies of soil protistology to guide this rapidly developing research area. Based on a synthesis of expert opinion we propose 30 key questions covering a broad range of topics including evolution, phylogenetics, functional ecology, macroecology, paleoecology, and methodologies. These questions highlight a diversity of topics that will establish soil protistology as a hub discipline connecting different fundamental and applied fields such as ecology, biogeography, evolution, plant-microbe interactions, agronomy, and conservation biology. We are convinced that soil protistology has the potential to be one of the most exciting frontiers in biology.
- Published
- 2017
41. Soil networks become more connected and take up more carbon as nature restoration progresses
- Author
-
Morriën, W.E., Hannula, S.E., Snoek, L.B., Helmsing, N.R., Zweers, Hans, de Hollander, M., Soto, Raquel Luján, Bouffaud, Marie Lara, Buée, M., Dimmers, W.J., Duyts, Henk, Geisen, Stefan, Girlanda, Mariangela, Griffiths, R.I., Jorgensen, H.B., Jensen, J., Plassart, P., Redecker, Dirk, Schmelz, R.M., Schmidt, Olaf, Thomson, Bruce C., Tisserant, Emilie, Uroz, Stephane, Winding, Anne, Bailey, M.J., Bonkowski, M., Faber, J.H., Martin, F., Lemanceau, Philippe, de Boer, W., van Veen, J.A., van der Putten, W.H., Morriën, W.E., Hannula, S.E., Snoek, L.B., Helmsing, N.R., Zweers, Hans, de Hollander, M., Soto, Raquel Luján, Bouffaud, Marie Lara, Buée, M., Dimmers, W.J., Duyts, Henk, Geisen, Stefan, Girlanda, Mariangela, Griffiths, R.I., Jorgensen, H.B., Jensen, J., Plassart, P., Redecker, Dirk, Schmelz, R.M., Schmidt, Olaf, Thomson, Bruce C., Tisserant, Emilie, Uroz, Stephane, Winding, Anne, Bailey, M.J., Bonkowski, M., Faber, J.H., Martin, F., Lemanceau, Philippe, de Boer, W., van Veen, J.A., and van der Putten, W.H.
- Abstract
Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
- Published
- 2017
42. Decoupling the direct and indirect effects of nitrogen deposition on ecosystem function
- Author
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Manning, P, Newington, JE, Robson, HR, Saunders, M, Eggers, T, Bradford, MA, Bardgett, RD, Bonkowski, M, Ellis, RJ, Gange, AC, Grayston, SJ, Kandeler, E, Marhan, S, Reid, E, Tscherko, D, Godfray, HC, and Rees, M
- Subjects
fungi ,food and beverages ,sense organs ,skin and connective tissue diseases - Abstract
Elevated nitrogen (N) inputs into terrestrial ecosystems are causing major changes to the composition and functioning of ecosystems. Understanding these changes is challenging because there are complex interactions between 'direct' effects of N on plant physiology and soil biogeochemistry, and 'indirect' effects caused by changes in plant species composition. By planting high N and low N plant community compositions into high and low N deposition model terrestrial ecosystems we experimentally decoupled direct and indirect effects and quantified their contribution to changes in carbon, N and water cycling. Our results show that direct effects on plant growth dominate ecosystem response to N deposition, although long-term carbon storage is reduced under high N plant-species composition. These findings suggest that direct effects of N deposition on ecosystem function could be relatively strong in comparison with the indirect effects of plant community change.
- Published
- 2016
43. Soil biodiversity and carbon dynamics in the long-term (50 years) experiment V140/00 in Müncheberg, Germany
- Author
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Joschko M., Barkusky D., Franko U., Reinhold J., Lentzsch P., Haubold-Rosar M., Siewert C., Graefe U., Willms M., Wiemer M., Emmerling C., Ciancio A., Gholami S., Rühlmann J., Bonkowski M., Fox C. A., Bellingrath-Kimura S., and Rogasik J.
- Subjects
soil ,biodiversity ,organic matter - Abstract
The relationships between primary organic matter, soil biota and soil organic matter are still insufficiently understood, even though knowledge thereof is crucial for both understanding and optimizing sustainable management systems. Long-term field experiments, such as the 50 year V140/00 experiment on sandy soil in Müncheberg, provide the opportunity to analyse soil biota and long-term carbon dynamics in variants subjected to different management. The aim of this study was to relate soil carbon dynamics to soil biodiversity using a combined monitoring and modelling approach. Selected taxa from different functional groups (ecosystem engineers, litter transformers, microfoodwebs) were studied between 2010 and 2013 in treatments with different input of straw, manure and N-fertilizer. In addition, some integrated measures of soil quality were taken. We, inter alia, hypothesized that increased carbon sequestration would coincide with increased soil biodiversity, especially with respect to soil fauna. The results revealed that no simple relationship exists between soil biodiversity and carbon dynamics in the studied soil. The results are discussed in the framework of the ecosystem services concept.
- Published
- 2016
44. Many previously incertae sedis amoebozoans find a home within the Centramoebida
- Author
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TICE A.K., SHADWICK L.L., SPIEGEL F.W., GEISEN S., FIORE-DONNO A.M., BONKOWSKI M., DUMACK K., KANG S., and BROWN M.W.
- Published
- 2016
45. Pack hunting by a common soil amoeba on nematodes
- Author
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Geisen, Stefan, Rosengarten, J., Koller, R., Mulder, Christian, Urich, T., Bonkowski, M., and Terrestrial Ecology (TE)
- Subjects
Ribosomal ,Amoeba ,Animals ,Europe ,Food Chain ,Host-Parasite Interactions ,Nematoda ,Predatory Behavior ,RNA, Ribosomal, 18S ,Soil ,Species Specificity ,Transcriptome ,Microbiology ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Evolution ,18S ,Behavior and Systematics ,international ,Life Science ,RNA - Abstract
Soils host the most complex communities on Earth,including the most diverse and abundant eukaryotes,i.e. heterotrophic protists. Protists are generally con-sidered as bacterivores, but evidence for negativeinteractions with nematodes both from laboratory andfield studies exist. However, direct impacts of protistson nematodes remain unknown. We isolated the soil-borne testate amoebaCryptodifflugia operculata andfound a highly specialized and effective pack-huntingstrategy to prey on bacterivorous nematodes.Enhanced reproduction in presence of prey nema-todes suggests a beneficial predatory life history ofthese omnivorous soil amoebae.Cryptodifflugiaoperculata appears to selectively impact the nema-tode community composition as reductions of nema-tode numbers were species specific. Furthermore, weinvestigated 12 soil metatranscriptomes from five dis-tinct locations throughout Europe for 18S ribosomalRNA transcripts of C. operculata. The presence ofC. operculata transcripts in all samples, representingup to 4% of the active protist community, indicates apotential ecological importance of nematophagy per-formed byC. operculata in soil food webs. The uniquepack-hunting strategy on nematodes that was previously unknown from protists, together with molecularevidence that these pack hunters are likely to beabundant and widespread in soils, imply a consider-able importance of the hitherto neglected trophic link‘nematophagous protists’ in soil food webs
- Published
- 2015
46. A method of establishing a transect for biodiversity and ecosystem function monitoring across Europe
- Author
-
Stone, D., Blomkvist, P., Hendriksen, N. Bohse, Bonkowski, M., Jorgensen, H. Bracht, Carvalho, F., Dunbar, M. B., Gardi, C., Geisen, S., Griffiths, R., Hug, A. S., Jensen, J., Laudon, H., Mendes, S., Morais, P. V., Orgiazzi, A., Plassart, P., Roembke, J., Rutgers, M., Schmelz, R. M., Sousa, J. P., Steenbergen, E., Suhadolc, M., Winding, A., Zupan, M., Lemanceau, P., Creamer, R. E., Stone, D., Blomkvist, P., Hendriksen, N. Bohse, Bonkowski, M., Jorgensen, H. Bracht, Carvalho, F., Dunbar, M. B., Gardi, C., Geisen, S., Griffiths, R., Hug, A. S., Jensen, J., Laudon, H., Mendes, S., Morais, P. V., Orgiazzi, A., Plassart, P., Roembke, J., Rutgers, M., Schmelz, R. M., Sousa, J. P., Steenbergen, E., Suhadolc, M., Winding, A., Zupan, M., Lemanceau, P., and Creamer, R. E.
- Abstract
The establishment of the range of soil biodiversity found within European soils is needed to guide EU policy development regarding the protection of soil. Such a base-line should be collated from a wide-ranging sampling campaign to ensure that soil biodiversity from the majority of soil types, land-use or management systems, and European climatic (bio-geographical zones) were included. This paper reports the design and testing of a method to achieve the large scale sampling associated with the establishment of such a baseline, carried out within the remit of the EcoFINDERS project, and outlines points to consider when such a task is undertaken. Applying a GIS spatial selection process, a sampling campaign was undertaken by 13 EcoFINDERS partners across 11 countries providing data on the range of indicators of biodiversity and ecosystem functions including; micro and meso fauna biodiversity, extracellular enzyme activity, PLEA and community level physiological profiling (MicroResp (TM) and Biolog (TM)). Physical, chemical and bio-geographical parameters of the 81 sites sampled were used to determine whether the model predicted a wide enough range of sites to allow assessment of the biodiversity indicators tested. Discrimination between the major bio-geographical zones of Atlantic and Continental was possible for all land-use types. Boreal and Alpine zones only allowed discrimination in the most common land-use type for that area e.g. forestry and grassland sites, respectively, while the Mediterranean zone did not have enough sites sampled to draw conclusions across all land-use types. The method used allowed the inclusion of a range of land-uses in both the model prediction stage and the final sites sampled. The establishment of the range of soil biodiversity across Europe is possible, though a larger targeted campaign is recommended. The techniques applied within the EcoFINDERS sampling would be applicable to a larger campaign. (C) 2015 Elsevier B.V. All rights rese
- Published
- 2016
47. Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function
- Author
-
Griffiths, B. S., Roembke, J., Schmelz, R. M., Scheffczyk, A., Faber, J. H., Bloem, J., Peres, G., Cluzeau, D., Chabbi, A., Suhadolc, M., Sousa, J. P., Martins da Silva, P., Carvalho, F., Mendes, S., Morais, P., Francisco, R., Pereira, C., Bonkowski, M., Geisen, S., Bardgett, R. D., de Vries, F. T., Bolger, T., Dirilgen, T., Schmidt, O., Winding, A., Hendriksen, N. B., Johansen, A., Philippot, L., Plassart, P., Bru, D., Thomson, B., Griffiths, R. I., Bailey, M. J., Keith, A., Rutgers, M., Mulder, C., Hannula, S. E., Creamer, R., Stone, D., Griffiths, B. S., Roembke, J., Schmelz, R. M., Scheffczyk, A., Faber, J. H., Bloem, J., Peres, G., Cluzeau, D., Chabbi, A., Suhadolc, M., Sousa, J. P., Martins da Silva, P., Carvalho, F., Mendes, S., Morais, P., Francisco, R., Pereira, C., Bonkowski, M., Geisen, S., Bardgett, R. D., de Vries, F. T., Bolger, T., Dirilgen, T., Schmidt, O., Winding, A., Hendriksen, N. B., Johansen, A., Philippot, L., Plassart, P., Bru, D., Thomson, B., Griffiths, R. I., Bailey, M. J., Keith, A., Rutgers, M., Mulder, C., Hannula, S. E., Creamer, R., and Stone, D.
- Abstract
Soils provide many ecosystem services that are ultimately dependent on the local diversity and below ground abundance of organisms. Soil biodiversity is affected negatively by many threats and there is a perceived policy requirement for the effective biological monitoring of soils at the European level. The aim of this study was to evaluate and recommend policy relevant, cost-effective soil biological indicators for biodiversity and ecosystem function across Europe. A total of 18 potential indicators were selected using a logical-sieve based approach. This paper considers the use of indicators from the 'top down' (i.e. concerned with the process of indicator selection), rather than from the 'bottom up' detail of how individual indicators perform at specific sites and with specific treatments. The indicators assessed a range of microbial, faunal and functional attributes, newer nucleic acids based techniques, morphological approaches and process based measurements. They were tested at 6 European experimental sites already in operation and chosen according to land-use, climatic zone and differences in land management intensity. These were 4 arable sites, one each in Atlantic, Continental, Mediterranean and Pannonian climate zones, and 2 grassland sites, one each in Atlantic and Continental zones. At each site we sampled three replicated plots of contrasting management intensity and, while the treatments varied from site to site, their disturbance effects were quantified in terms of land use intensity. The field sampling and laboratory analysis were standardised through a combination of ISO protocols, or standard operating procedures if the former were not available. Sites were sampled twice, in autumn 2012 and spring or autumn 2013, with relative costs of the different indicators being determined each time. A breakdown of the cost effectiveness of the indicators showed the expected trade-off between effort required in the field and effort required in the laboratory. A
- Published
- 2016
48. EFFECTS OF LAND-USE INTENSITY ON THE COMMUNITY COMPOSITION OF NEMATODES FROM CAO BANG PROVINCE IN VIETNAM
- Author
-
Nguyen, T. A. D., Abolafia, J., Pena-Santiago, R., Bonkowski, M., Nguyen, T. A. D., Abolafia, J., Pena-Santiago, R., and Bonkowski, M.
- Published
- 2016
49. Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function
- Author
-
Griffiths, B.s., Römbke, J., Schmelz, R.m., Scheffczyk, A., Faber, J.h., Bloem, Jaap, Pérès, G., Cluzeau, D., Chabbi, A., Suhadolc, M., Sousa, J.p., Martins Da Silva, P., Carvalho, F., Mendes, S., Morais, P., Francisco, R., Pereira, C., Bonkowski, M., Geisen, S., Bardgett, R.d., De Vries, F.t., Bolger, T., Dirilgen, T., Schmidt, O., Winding, A., Hendriksen, N.b., Johansen, A., Philippot, L., Plassart, P., Bru, D., Thomson, B., Griffiths, R.i., Bailey, M.j., Keith, A., Rutgers, M., Mulder, C., Hannula, S.e., Creamer, R., Stone, D., Griffiths, B.s., Römbke, J., Schmelz, R.m., Scheffczyk, A., Faber, J.h., Bloem, Jaap, Pérès, G., Cluzeau, D., Chabbi, A., Suhadolc, M., Sousa, J.p., Martins Da Silva, P., Carvalho, F., Mendes, S., Morais, P., Francisco, R., Pereira, C., Bonkowski, M., Geisen, S., Bardgett, R.d., De Vries, F.t., Bolger, T., Dirilgen, T., Schmidt, O., Winding, A., Hendriksen, N.b., Johansen, A., Philippot, L., Plassart, P., Bru, D., Thomson, B., Griffiths, R.i., Bailey, M.j., Keith, A., Rutgers, M., Mulder, C., Hannula, S.e., Creamer, R., and Stone, D.
- Abstract
Soils provide many ecosystem services that are ultimately dependent on the local diversity and below ground abundance of organisms. Soil biodiversity is affected negatively by many threats and there is a perceived policy requirement for the effective biological monitoring of soils at the European level. The aim of this study was to evaluate and recommend policy relevant, cost-effective soil biological indicators for biodiversity and ecosystem function across Europe. A total of 18 potential indicators were selected using a logical-sieve based approach. This paper considers the use of indicators from the 'top down' (i.e. concerned with the process of indicator selection), rather than from the 'bottom up' detail of how individual indicators perform at specific sites and with specific treatments. The indicators assessed a range of microbial, faunal and functional attributes, newer nucleic acids based techniques, morphological approaches and process based measurements. They were tested at 6 European experimental sites already in operation and chosen according to land-use, climatic zone and differences in land management intensity. These were 4 arable sites, one each in Atlantic, Continental, Mediterranean and Pannonian climate zones, and 2 grassland sites, one each in Atlantic and Continental zones. At each site we sampled three replicated plots of contrasting management intensity and, while the treatments varied from site to site, their disturbance effects were quantified in terms of land use intensity. The field sampling and laboratory analysis were standardised through a combination of ISO protocols, or standard operating procedures if the former were not available. Sites were sampled twice, in autumn 2012 and spring or autumn 2013, with relative costs of the different indicators being determined each time. A breakdown of the cost effectiveness of the indicators showed the expected trade-off between effort required in the field and effort required in the laboratory. A
- Published
- 2016
50. Resource partitioning between bacteria, fungi, and protists in the detritusphere of an agricultural soil
- Author
-
Kramer, S., Dibbern, D., Moll, Julia, Huenninghaus, M., Koller, R., Krueger, Dirk, Marhan, S., Urich, T., Wubet, Tesfaye, Bonkowski, M., Buscot, Francois, Lueders, T., Kandeler, E., Kramer, S., Dibbern, D., Moll, Julia, Huenninghaus, M., Koller, R., Krueger, Dirk, Marhan, S., Urich, T., Wubet, Tesfaye, Bonkowski, M., Buscot, Francois, Lueders, T., and Kandeler, E.
- Abstract
The flow of plant-derived carbon in soil is a key component of global carbon cycling. Conceptual models of trophic carbon fluxes in soil have assumed separate bacterial and fungal energy channels in the detritusphere, controlled by both substrate complexity and recalcitrance. However, detailed understanding of the key populations involved and niche-partitioning between them is limited. Here, a microcosm experiment was performed to trace the flow of detritusphere C from substrate analogs (glucose, cellulose) and plant biomass amendments (maize leaves, roots) in an agricultural soil. Carbon flow was traced by rRNA stable isotope probing and amplicon sequencing across three microbial kingdoms. Distinct lineages within the Actinobacteria, Bacteroidetes, Gammaproteobacteria, Basidiomycota, Ascomycota as well as Peronosporomycetes were identified as important primary substrate consumers. A dynamic succession of primary consumers was observed especially in the cellulose treatments, but also in plant amendments over time. While intra-kingdom niche partitioning was clearly observed, distinct bacterial and fungal energy channels were not apparent. Furthermore, while the diversity of primary substrate consumers did not notably increase with substrate complexity, consumer succession and secondary trophic links to bacterivorous and fungivorous microbes resulted in increased food web complexity in the more recalcitrant substrates. This suggests that rather than substrate-defined energy channels, consumer succession as well as intra- and inter-kingdom cross-feeding should be considered as mechanisms supporting food web complexity in the detritusphere.
- Published
- 2016
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