Stefan Geisen

Wageningen University & Research

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Wim H. van der Putten

Wageningen University & Research

Michael Bonkowski

University of Cologne

Qirong Shen

Nanjing Agricultural University

Rutger A. Wilschut

Wageningen University & Research

George A. Kowalchuk

Utrecht University

Wu Xiong

Nanjing Agricultural University

Alexandre Jousset

Nanjing Agricultural University

Basten L. Snoek

Utrecht University

Rong Li

Nanjing Agricultural University

Enrique Lara

Real Jardín Botánico

Cooperative Institutions

Chinese Academy of Sciences

103

Wageningen University & Research

Nanjing Agricultural University

Netherlands Institute of Ecology

University of Chinese Academy of Sciences

Centre National de la Recherche Scientifique

Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement

Consejo Superior de Investigaciones Científicas

University of Göttingen

Utrecht University

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A low proportion of rare bacterial taxa responds to abiotic changes compared with dominant taxa

Environmental Microbiology (2018)

Viola Kurm Stefan Geisen Wilhelmina H. Gera Hol

Summary In many studies, rare bacterial taxa have been found to increase in response to environmental changes. These changes have been proposed to contribute to the insurance of ecosystem functions. However, it has not been systematically tested if rare taxa are more likely to increase in abundance than dominant taxa. Here, we study whether rare soil bacterial taxa are more likely to respond to environmental disturbances and if rare taxa are more opportunistic than dominant taxa. To test this, we applied nine different disturbance treatments to a grassland soil and observed changes in bacterial community composition over 7 days. While 12% of the dominant taxa changed in abundance, only 1% of the rare taxa showed any effect. Rare taxa increased in response to a single disturbance treatment only, while dominant taxa responded to up to five treatments. We conclude that rare taxa are not more likely to contribute to community dynamics after disturbances than dominant taxa. Nevertheless, as rare taxa outnumber abundant taxa with here 230 taxa that changed significantly, the chance is high that some of these rare taxa might act as ecologically important keystone taxa. Therefore, rare and abundant taxa might both contribute to ecosystem insurance.

Rare species

10.1111/1462-2920.14492

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Citations (71)

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression

Microbiome (2020)

Chengyuan Tao Rong Li Wu Xiong Zongzhuan Shen Shanshan Liu

Abstract Background Plant diseases caused by fungal pathogen result in a substantial economic impact on the global food and fruit industry. Application of organic fertilizers supplemented with biocontrol microorganisms ( i.e. bioorganic fertilizers) has been shown to improve resistance against plant pathogens at least in part due to impacts on the structure and function of the resident soil microbiome. However, it remains unclear whether such improvements are driven by the specific action of microbial inoculants, microbial populations naturally resident to the organic fertilizer or the physical-chemical properties of the compost substrate. The aim of this study was to seek the ecological mechanisms involved in the disease suppressive activity of bio-organic fertilizers. Results To disentangle the mechanism of bio-organic fertilizer action, we conducted an experiment tracking Fusarium wilt disease of banana and changes in soil microbial communities over three growth seasons in response to the following four treatments: bio-organic fertilizer (containing Bacillus amyloliquefaciens W19), organic fertilizer, sterilized organic fertilizer and sterilized organic fertilizer supplemented with B . amyloliquefaciens W19. We found that sterilized bioorganic fertilizer to which Bacillus was re-inoculated provided a similar degree of disease suppression as the non-sterilized bioorganic fertilizer across cropping seasons. We further observed that disease suppression in these treatments is linked to impacts on the resident soil microbial communities, specifically by leading to increases in specific Pseudomonas spp.. Observed correlations between Bacillus amendment and indigenous Pseudomonas spp. that might underlie pathogen suppression were further studied in laboratory and pot experiments. These studies revealed that specific bacterial taxa synergistically increase biofilm formation and likely acted as a plant-beneficial consortium against the pathogen. Conclusion Together we demonstrate that the action of bioorganic fertilizer is a product of the biocontrol inoculum within the organic amendment and its impact on the resident soil microbiome. This knowledge should help in the design of more efficient biofertilizers designed to promote soil function.

Bacillus amyloliquefaciens

Organic fertilizer

Beneficial organism

Biofertilizer

Plant disease

Chlamydospore

10.1186/s40168-020-00892-z

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Deciphering Underlying Drivers of Disease Suppressiveness Against Pathogenic Fusarium oxysporum

Frontiers in Microbiology (2019)

Yannan Ou C. Ryan Penton Stefan Geisen Zongzhuan Shen Yifei Sun

Soil-borne diseases, especially those caused by fungal pathogens, lead to profound annual yield losses. One key example for such a disease is Fusarium wilt disease in banana. In some soils, plants do not show disease symptoms, even if the disease-causing pathogens are present. However, the underlying agents that make soils suppressive against Fusarium wilt remain elusive. In this study, we aimed to determine the underlying microbial agents governing soil disease-suppressiveness. We traced the shift of microbiomes during the invasion of disease-causing Fusarium oxysporum f. sp. cubense in disease-suppressive and disease-conducive soils. We found distinct microbiome structures in the suppressive and conducive soils after pathogen invasion. The alpha diversity indices increased (or did not significantly change) and decreased, respectively, in the suppressive and conducive soils, indicating that the shift pattern of the microbiome with pathogen invasion was notably different between the suppressive and conductive soils. Microbiome networks were more complex with higher numbers of links and revealed more negative links, especially between bacterial taxa and the disease-causing Fusarium, in suppressive soils than in conducive soils. We identified the bacterial genera Chryseolinea, Terrimonas, and Ohtaekwangia as key groups that likely confer suppressiveness against disease-causing Fusarium. Overall, our study provides the first insights into agents potentially underlying the disease suppressiveness of soils against Fusarium wilt pathogen invasion. The results of this study may help to guide efforts for targeted cultivation and application of these potential biocontrol agents, which might lead to the development of effective biocontrol agents against Fusarium wilt disease.

Wilt disease

Plant disease

10.3389/fmicb.2019.02535

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Citations (50)

Species-specific impact of protists in controlling litter decomposition

Soil Biology and Biochemistry (2024)

Yuxin Wang Thomas Edison E. dela Cruz James Kennard Sanz Jacob Stefan Geisen

Litter

10.1016/j.soilbio.2024.109598

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Protists as main indicators and determinants of plant performance

Microbiome (2021)

Sai Guo Wu Xiong Xinnan Hang Zhilei Gao Zixuan Jiao

Abstract Background Microbiomes play vital roles in plant health and performance, and the development of plant beneficial microbiomes can be steered by organic fertilizer inputs. Especially well-studied are fertilizer-induced changes on bacteria and fungi and how changes in these groups alter plant performance. However, impacts on protist communities, including their trophic interactions within the microbiome and consequences on plant performance remain largely unknown. Here, we tracked the entire microbiome, including bacteria, fungi, and protists, over six growing seasons of cucumber under different fertilization regimes (conventional, organic, and Trichoderma bio-organic fertilization) and linked microbial data to plant yield to identify plant growth-promoting microbes. Results Yields were higher in the (bio-)organic fertilization treatments. Soil abiotic conditions were altered by the fertilization regime, with the prominent effects coming from the (bio-)organic fertilization treatments. Those treatments also led to the pronounced shifts in protistan communities, especially microbivorous cercozoan protists. We found positive correlations of these protists with plant yield and the density of potentially plant-beneficial microorganisms. We further explored the mechanistic ramifications of these relationships via greenhouse experiments, showing that cercozoan protists can positively impact plant growth, potentially via interactions with plant-beneficial microorganisms including Trichoderma, the biological agent delivered by the bio-fertilizer. Conclusions We show that protists may play central roles in stimulating plant performance through microbiome interactions. Future agricultural practices might aim to specifically enhance plant beneficial protists or apply those protists as novel, sustainable biofertilizers.

Trichoderma

10.1186/s40168-021-01025-w

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Citations (96)

Arbuscular mycorrhizal inoculation and plant response strongly shape bacterial and eukaryotic soil community trajectories

Soil Biology and Biochemistry (2021)

Johan De Gruyter James T. Weedon Evelyne M. Elst Stefan Geisen Marcel G. A. van der Heijden

Holcus lanatus

Glomeromycota

10.1016/j.soilbio.2021.108524

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Citations (17)