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1. Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification.

Author

Qiao, Mengjie, Sun, Ruibo, Wang, Zixuan, Dumack, Kenneth, Xie, Xingguang, Dai, Chuanchao, Wang, Ertao, Sun, Bo, Peng, Xinhua, Bonkowski, Michael, Chen, Yan, and Zhou, Jizhong

Subjects
Nitrogen Fixation, Fabaceae, Plant Root Nodulation, Soil, Soil Microbiology, Symbiosis, Arachis, Vegetables, Nitrogen, Root Nodules, Plant
Abstract

Biological nitrogen fixation by free-living bacteria and rhizobial symbiosis with legumes plays a key role in sustainable crop production. Here, we study how different crop combinations influence the interaction between peanut plants and their rhizosphere microbiota via metabolite deposition and functional responses of free-living and symbiotic nitrogen-fixing bacteria. Based on a long-term (8 year) diversified cropping field experiment, we find that peanut co-cultured with maize and oilseed rape lead to specific changes in peanut rhizosphere metabolite profiles and bacterial functions and nodulation. Flavonoids and coumarins accumulate due to the activation of phenylpropanoid biosynthesis pathways in peanuts. These changes enhance the growth and nitrogen fixation activity of free-living bacterial isolates, and root nodulation by symbiotic Bradyrhizobium isolates. Peanut plant root metabolites interact with Bradyrhizobium isolates contributing to initiate nodulation. Our findings demonstrate that tailored intercropping could be used to improve soil nitrogen availability through changes in the rhizosphere microbiome and its functions.

Published
2024

2. Publisher Correction: Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification

Author

Qiao, Mengjie, Sun, Ruibo, Wang, Zixuan, Dumack, Kenneth, Xie, Xingguang, Dai, Chuanchao, Wang, Ertao, Zhou, Jizhong, Sun, Bo, Peng, Xinhua, Bonkowski, Michael, and Chen, Yan

Subjects
Agricultural, Veterinary and Food Sciences, Crop and Pasture Production, Microbiome
Abstract

Correction to: Nature Communicationshttps://doi.org/10.1038/s41467-024-47159-x, published online 04 April 2024 In this article the affiliation ‘State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China’ for Xinhua Peng was missing. The original article has been corrected.

Published
2024

4. Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability

Author

Zhu, Lingyue, Chen, Yan, Sun, Ruibo, Zhang, Jiabao, Hale, Lauren, Dumack, Kenneth, Geisen, Stefan, Deng, Ye, Duan, Yinghua, Zhu, Bo, Li, Yan, Liu, Wenzhao, Wang, Xiaoyue, Griffiths, Bryan S, Bonkowski, Michael, Zhou, Jizhong, and Sun, Bo

Subjects
Ecosystem, Biodiversity, Biomass, Soil, Nutritional Status, Soil biodiversity, Within trophic interactions, Cross-trophic interactions, Agroecosystem, Ecosystem functioning, Ecology, Microbiology, Medical Microbiology
Abstract

BackgroundFor achieving long-term sustainability of intensive agricultural practices, it is pivotal to understand belowground functional stability as belowground organisms play essential roles in soil biogeochemical cycling. It is commonly believed that resource availability is critical for controlling the soil biodiversity and belowground organism interactions that ultimately lead to the stabilization or collapse of terrestrial ecosystem functions, but evidence to support this belief is still limited. Here, we leveraged field experiments from the Chinese National Ecosystem Research Network (CERN) and two microcosm experiments mimicking high and low resource conditions to explore how resource availability mediates soil biodiversity and potential multi-trophic interactions to control functional trait stability.ResultsWe found that agricultural practice-induced higher resource availability increased potential cross-trophic interactions over 316% in fields, which in turn had a greater effect on functional trait stability, while low resource availability made the stability more dependent on the potential within trophic interactions and soil biodiversity. This large-scale pattern was confirmed by fine-scale microcosm systems, showing that microcosms with sufficient nutrient supply increase the proportion of potential cross-trophic interactions, which were positively associated with functional stability. Resource-driven belowground biodiversity and multi-trophic interactions ultimately feedback to the stability of plant biomass.ConclusionsOur results indicated the importance of potential multi-trophic interactions in supporting belowground functional trait stability, especially when nutrients are sufficient, and also suggested the ecological benefits of fertilization programs in modern agricultural intensification. Video Abstract.

Published
2023

7. The multiple-mechanisms hypothesis of biodiversity–stability relationships

Author

Eisenhauer, Nico, Mueller, Kevin, Ebeling, Anne, Gleixner, Gerd, Huang, Yuanyuan, Madaj, Anna-Maria, Roscher, Christiane, Weigelt, Alexandra, Bahn, Michael, Bonkowski, Michael, Brose, Ulrich, Cesarz, Simone, Feilhauer, Hannes, Guimaraes-Steinicke, Claudia, Heintz-Buschart, Anna, Hines, Jes, Lange, Markus, Meyer, Sebastian T., Mohanbabu, Neha, Mommer, Liesje, Neuhauser, Sigrid, Oelmann, Yvonne, Rahmanian, Soroor, Sasaki, Takehiro, Scheu, Stefan, Schielzeth, Holger, Schmid, Bernhard, Schloter, Michael, Schulz, Stefanie, Unsicker, Sybille B., Vogel, Cordula, Weisser, Wolfgang W., and Isbell, Forest

Published
2024
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9. A slow-fast trait continuum at the whole community level in relation to land-use intensification

Author

Neyret, Margot, Le Provost, Gaëtane, Boesing, Andrea Larissa, Schneider, Florian D., Baulechner, Dennis, Bergmann, Joana, de Vries, Franciska T., Fiore-Donno, Anna Maria, Geisen, Stefan, Goldmann, Kezia, Merges, Anna, Saifutdinov, Ruslan A., Simons, Nadja K., Tobias, Joseph A., Zaitsev, Andrey S., Gossner, Martin M., Jung, Kirsten, Kandeler, Ellen, Krauss, Jochen, Penone, Caterina, Schloter, Michael, Schulz, Stefanie, Staab, Michael, Wolters, Volkmar, Apostolakis, Antonios, Birkhofer, Klaus, Boch, Steffen, Boeddinghaus, Runa S., Bolliger, Ralph, Bonkowski, Michael, Buscot, François, Dumack, Kenneth, Fischer, Markus, Gan, Huei Ying, Heinze, Johannes, Hölzel, Norbert, John, Katharina, Klaus, Valentin H., Kleinebecker, Till, Marhan, Sven, Müller, Jörg, Renner, Swen C., Rillig, Matthias C., Schenk, Noëlle V., Schöning, Ingo, Schrumpf, Marion, Seibold, Sebastian, Socher, Stephanie A., Solly, Emily F., Teuscher, Miriam, van Kleunen, Mark, Wubet, Tesfaye, and Manning, Peter

Published
2024
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10. A global database of soil nematode abundance and functional group composition.

Author

van den Hoogen, Johan, Geisen, Stefan, Wall, Diana H, Wardle, David A, Traunspurger, Walter, de Goede, Ron GM, Adams, Byron J, Ahmad, Wasim, Ferris, Howard, Bardgett, Richard D, Bonkowski, Michael, Campos-Herrera, Raquel, Cares, Juvenil E, Caruso, Tancredi, de Brito Caixeta, Larissa, Chen, Xiaoyun, Costa, Sofia R, Creamer, Rachel, da Cunha E Castro, José Mauro, Dam, Marie, Djigal, Djibril, Escuer, Miguel, Griffiths, Bryan S, Gutiérrez, Carmen, Hohberg, Karin, Kalinkina, Daria, Kardol, Paul, Kergunteuil, Alan, Korthals, Gerard, Krashevska, Valentyna, Kudrin, Alexey A, Li, Qi, Liang, Wenju, Magilton, Matthew, Marais, Mariette, Martín, José Antonio Rodríguez, Matveeva, Elizaveta, Mayad, El Hassan, Mzough, E, Mulder, Christian, Mullin, Peter, Neilson, Roy, Nguyen, TA Duong, Nielsen, Uffe N, Okada, Hiroaki, Rius, Juan Emilio Palomares, Pan, Kaiwen, Peneva, Vlada, Pellissier, Loïc, da Silva, Julio Carlos Pereira, Pitteloud, Camille, Powers, Thomas O, Powers, Kirsten, Quist, Casper W, Rasmann, Sergio, Moreno, Sara Sánchez, Scheu, Stefan, Setälä, Heikki, Sushchuk, Anna, Tiunov, Alexei V, Trap, Jean, Vestergård, Mette, Villenave, Cecile, Waeyenberge, Lieven, Wilschut, Rutger A, Wright, Daniel G, Keith, Aidan M, Yang, Jiue-In, Schmidt, Olaf, Bouharroud, R, Ferji, Z, van der Putten, Wim H, Routh, Devin, and Crowther, Thomas W

Abstract

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.

Published
2020

11. Loss of epigenetic information as a cause of mammalian aging

Author

Yang, Jae-Hyun, Hayano, Motoshi, Griffin, Patrick T., Amorim, João A., Bonkowski, Michael S., Apostolides, John K., Salfati, Elias L., Blanchette, Marco, Munding, Elizabeth M., Bhakta, Mital, Chew, Yap Ching, Guo, Wei, Yang, Xiaojing, Maybury-Lewis, Sun, Tian, Xiao, Ross, Jaime M., Coppotelli, Giuseppe, Meer, Margarita V., Rogers-Hammond, Ryan, Vera, Daniel L., Lu, Yuancheng Ryan, Pippin, Jeffrey W., Creswell, Michael L., Dou, Zhixun, Xu, Caiyue, Mitchell, Sarah J., Das, Abhirup, O’Connell, Brendan L., Thakur, Sachin, Kane, Alice E., Su, Qiao, Mohri, Yasuaki, Nishimura, Emi K., Schaevitz, Laura, Garg, Neha, Balta, Ana-Maria, Rego, Meghan A., Gregory-Ksander, Meredith, Jakobs, Tatjana C., Zhong, Lei, Wakimoto, Hiroko, El Andari, Jihad, Grimm, Dirk, Mostoslavsky, Raul, Wagers, Amy J., Tsubota, Kazuo, Bonasera, Stephen J., Palmeira, Carlos M., Seidman, Jonathan G., Seidman, Christine E., Wolf, Norman S., Kreiling, Jill A., Sedivy, John M., Murphy, George F., Green, Richard E., Garcia, Benjamin A., Berger, Shelley L., Oberdoerffer, Philipp, Shankland, Stuart J., Gladyshev, Vadim N., Ksander, Bruce R., Pfenning, Andreas R., Rajman, Luis A., and Sinclair, David A.

Published
2023
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13. Land-use intensity alters networks between biodiversity, ecosystem functions, and services

Author

Felipe-Lucia, María R., Soliveres, Santiago, Penone, Caterina, Fischer, Markus, Ammer, Christian, Boch, Steffen, Boeddinghaus, Runa S., Bonkowski, Michael, Buscot, François, Fiore-Donno, Anna Maria, Franki, Kevin, Goldmann, Kezia, Gossner, Martin M., Hölzel, Norbert, Jochum, Malte, Kandeler, Ellen, Klaus, Valentin H., Kleinebecker, Till, Leimer, Sophia, Manning, Peter, Oelmann, Yvonne, Saiz, Hugo, Schall, Peter, Schloter, Michael, Schöning, Ingo, Schrumpf, Marion, Solly, Emily F., Stempfhuber, Barbara, Weisser, Wolfgang W., Wilcke, Wolfgang, Wubet, Tesfaye, and Allan, Eric

Published
2020

19. Reprogramming to recover youthful epigenetic information and restore vision

Author

Lu, Yuancheng, Brommer, Benedikt, Tian, Xiao, Krishnan, Anitha, Meer, Margarita, Wang, Chen, Vera, Daniel L., Zeng, Qiurui, Yu, Doudou, Bonkowski, Michael S., Yang, Jae-Hyun, Zhou, Songlin, Hoffmann, Emma M., Karg, Margarete M., Schultz, Michael B., Kane, Alice E., Davidsohn, Noah, Korobkina, Ekaterina, Chwalek, Karolina, Rajman, Luis A., Church, George M., Hochedlinger, Konrad, Gladyshev, Vadim N., Horvath, Steve, Levine, Morgan E., Gregory-Ksander, Meredith S., Ksander, Bruce R., He, Zhigang, and Sinclair, David A.

Published
2020
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20. Contrasting responses of above- and belowground diversity to multiple components of land-use intensity

Author

Le Provost, Gaëtane, Thiele, Jan, Westphal, Catrin, Penone, Caterina, Allan, Eric, Neyret, Margot, van der Plas, Fons, Ayasse, Manfred, Bardgett, Richard D., Birkhofer, Klaus, Boch, Steffen, Bonkowski, Michael, Buscot, Francois, Feldhaar, Heike, Gaulton, Rachel, Goldmann, Kezia, Gossner, Martin M., Klaus, Valentin H., Kleinebecker, Till, Krauss, Jochen, Renner, Swen, Scherreiks, Pascal, Sikorski, Johannes, Baulechner, Dennis, Blüthgen, Nico, Bolliger, Ralph, Börschig, Carmen, Busch, Verena, Chisté, Melanie, Fiore-Donno, Anna Maria, Fischer, Markus, Arndt, Hartmut, Hoelzel, Norbert, John, Katharina, Jung, Kirsten, Lange, Markus, Marzini, Carlo, Overmann, Jörg, Paŝalić, Esther, Perović, David J., Prati, Daniel, Schäfer, Deborah, Schöning, Ingo, Schrumpf, Marion, Sonnemann, Ilja, Steffan-Dewenter, Ingolf, Tschapka, Marco, Türke, Manfred, Vogt, Juliane, Wehner, Katja, Weiner, Christiane, Weisser, Wolfgang, Wells, Konstans, Werner, Michael, Wolters, Volkmar, Wubet, Tesfaye, Wurst, Susanne, Zaitsev, Andrey S., and Manning, Peter

Published
2021
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23. Soil nematode abundance and functional group composition at a global scale

Author

van den Hoogen, Johan, Geisen, Stefan, Routh, Devin, Ferris, Howard, Traunspurger, Walter, Wardle, David A., de Goede, Ron G. M., Adams, Byron J., Ahmad, Wasim, Andriuzzi, Walter S., Bardgett, Richard D., Bonkowski, Michael, Campos-Herrera, Raquel, Cares, Juvenil E., Caruso, Tancredi, de Brito Caixeta, Larissa, Chen, Xiaoyun, Costa, Sofia R., Creamer, Rachel, Mauro da Cunha Castro, José, Dam, Marie, Djigal, Djibril, Escuer, Miguel, Griffiths, Bryan S., Gutiérrez, Carmen, Hohberg, Karin, Kalinkina, Daria, Kardol, Paul, Kergunteuil, Alan, Korthals, Gerard, Krashevska, Valentyna, Kudrin, Alexey A., Li, Qi, Liang, Wenju, Magilton, Matthew, Marais, Mariette, Martín, José Antonio Rodríguez, Matveeva, Elizaveta, Mayad, El Hassan, Mulder, Christian, Mullin, Peter, Neilson, Roy, Nguyen, T. A. Duong, Nielsen, Uffe N., Okada, Hiroaki, Rius, Juan Emilio Palomares, Pan, Kaiwen, Peneva, Vlada, Pellissier, Loïc, Carlos Pereira da Silva, Julio, Pitteloud, Camille, Powers, Thomas O., Powers, Kirsten, Quist, Casper W., Rasmann, Sergio, Moreno, Sara Sánchez, Scheu, Stefan, Setälä, Heikki, Sushchuk, Anna, Tiunov, Alexei V., Trap, Jean, van der Putten, Wim, Vestergård, Mette, Villenave, Cecile, Waeyenberge, Lieven, Wall, Diana H., Wilschut, Rutger, Wright, Daniel G., Yang, Jiue-in, and Crowther, Thomas Ward

Published
2019
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32. Straw amendment and nitrification inhibitor controlling N losses and immobilization in a soil cooling-warming experiment

Author

Chen, Hao, Rosinger, Christoph, Blagodatsky, Sergey, Reichel, Rüdiger, Li, Bo, Kumar, Amit, Rothardt, Steffen, Luo, Jie, Brüggemann, Nicolas, Kage, Henning, and Bonkowski, Michael

Subjects
Nitrogen use efficiency, Environmental Engineering, Ecosystems Research, 15N labelling, Temperature effect, Soil microbial biomass, Environmental Chemistry, ddc:610, N immobilization, Nitrification, Pollution, Waste Management and Disposal
Abstract

It is common practice in agriculture to apply high‑carbon amendments, e.g. straw, or nitrification inhibitors (NI) to reduce soil nitrogen (N) losses. However, little is known on the combined effects of straw and NI and how seasonal soil temperature variations further affect N immobilization. We conducted a 113-day mesocosm experiment with different levels of 15N-fertilizer application (N0: control; N1: 125 kg N ha−1; N2: 250 kg N ha−1) in an agricultural soil, amended with either wheat straw, NI or a combination of both in order to investigate N retention and loss from soil after a cooling-warming phase simulating a seasonal temperature shift, i.e., 30 days cooling phase at 7 °C and 10 days warming phase at 21 °C. Subsequently, soils were planted with barley as phytometers to study 15N-transfer to a following crop.Straw addition significantly reduced soil N-losses due to microbial N immobilization. Although carbon added as straw led to increased N2O emissions at high N fertilization, this was partly counterbalanced by NI. Soil cooling-warming strongly increased ammonification (+77 %), while nitrification was suppressed, and straw-induced microbial N immobilization dominated. N immobilized after straw addition was mineralized at the end of the experiment as indicated by structural equation models. Re-mineralization in N2 was sufficient, but still suboptimal in N0 and N1 at critical times of early barley growth. N-use efficiency of the 15N tracer decreased with fertilization intensity from 50 % in N1 to 35 % in N2, and straw amendment reduced NUE to 25 % at both fertilization rates. Straw amendment was most powerful in reducing N-losses (−41 %), in particular under variable soil temperature conditions, but NI enforced its effects by reducing N2O emission (−40 %) in N2 treatment. Sufficient N-fertilization coupled with straw application is required to adjust the timely re-mineralization of N for subsequent crops.

Published
2023

34. Root cap is an important determinant of rhizosphere microbiome assembly.

Author

Rüger, Lioba, Ganther, Minh, Freudenthal, Jule, Jansa, Jan, Heintz‐Buschart, Anna, Tarkka, Mika Tapio, and Bonkowski, Michael

Subjects
RHIZOSPHERE, FOOD chains, MICROBIAL communities, PLANT development, CORN, GRAIN yields
Abstract

Summary: 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. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Appendix S1. Materials and Methods - Figs. S1 to S5 - Tables S1 to S3 from Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands

Author

Pescador, David S., Delgado-Baquerizo, Manuel, Fiore-Donno, Anna Maria, Singh, Brajesh K., Bonkowski, Michael, 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 them.This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.

Published
2022
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44. Editorial: Rhizosphere Spatiotemporal Organisation

Author

Tarkka, Mika T., Bonkowski, Michael, Ge, Tida, Knief, Claudia, Razavi, Bahar S., and Vetterlein, Doris

Subjects
process rate, Editorial, soil properties, community assembly, modeling, Plant Science, biosensor, network analysis
Published
2021

50. Taxonomic and Functional Diversity of Heterotrophic Protists (Cercozoa and Endomyxa) from Biological Soil Crusts

Author

Khanipour Roshan, Samira, Dumack, Kenneth, Bonkowski, Michael, Leinweber, Peter, Karsten, Ulf, and Glaser, Karin

Subjects
lcsh:Biology (General), soil food web, feeding behavior, eukaryvory, functional traits, Cercozoa, lcsh:QH301-705.5, Article
Abstract

Biological soil crusts (biocrusts) accommodate diverse communities of phototrophic and heterotrophic microorganisms. Heterotrophic protists have critical roles in the microbial food webs of soils, with Cercozoa and Endomyxa often being dominant groups. Still, the diversity, community composition, and functions of Cercozoa and Endomyxa in biocrusts have been little explored. In this study, using a high-throughput sequencing method with taxon-specific barcoded primers, we studied cercozoan and endomyxan communities in biocrusts from two unique habitats (subarctic grassland and temperate dunes). The communities differed strongly, with the grassland and dunes being dominated by Sarcomonadea (69%) and Thecofilosea (43%), respectively. Endomyxa and Phytomyxea were the minor components in dunes. Sandonidae, Allapsidae, and Rhogostomidae were the most abundant taxa in both habitats. In terms of functionality, up to 69% of the grassland community was constituted by bacterivorous Cercozoa. In contrast, cercozoan and endomyxan communities in dunes consisted of 31% bacterivores, 25% omnivores, and 20% eukaryvores. Facultative and obligate eukaryvores mostly belonged to the families Rhogostomidae, Fiscullidae, Euglyphidae, Leptophryidae, and Cercomonadidae, most of which are known to feed mainly on algae. Biocrust edaphic parameters such as pH, total organic carbon, nitrogen, and phosphorus did not have any significant influence on shaping cercozoan communities within each habitat, which confirms previous results from dunes.

Published
2021

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