1
|
Li E, Ryo M, Kowalchuk GA, Bakker PAHM, Jousset A. Rapid evolution of trait correlation networks during bacterial adaptation to the rhizosphere. Evolution 2021; 75:1218-1229. [PMID: 33634862 PMCID: PMC8252368 DOI: 10.1111/evo.14202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 02/04/2021] [Accepted: 02/12/2021] [Indexed: 12/22/2022]
Abstract
There is a growing awareness that traits do not evolve individually but rather are organized as modular networks of covarying traits. Although the importance of multi-trait correlation has been linked to the ability to evolve in response to new environmental conditions, the evolvability of the network itself has to date rarely been assessed experimentally. By following the evolutionary dynamics of a model bacterium adapting to plant roots, we demonstrate that the whole structure of the trait correlation network is highly dynamic. We experimentally evolved Pseudomonas protegens, a common rhizosphere dweller, on the roots of Arabidopsis thaliana. We collected bacteria at regular intervals and determined a range of traits linked to growth, stress resistance, and biotic interactions. We observed a rapid disintegration of the original trait correlation network. Ancestral populations showed a modular network, with the traits linked to resource use and stress resistance forming two largely independent modules. This network rapidly was restructured during adaptation, with a loss of the stress resistance module and the appearance of new modules out of previously disconnected traits. These results show that evolutionary dynamics can involve a deep restructuring of phenotypic trait organization, pointing to the emergence of novel life history strategies not represented in the ancestral phenotype.
Collapse
Affiliation(s)
- Erqin Li
- Department of Biology, Plant‐Microbe InteractionsUtrecht UniversityUtrechtCH3584The Netherlands
- Institut für BiologieFreie Universität BerlinBerlinD‐14195Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinD‐14195Germany
| | - Masahiro Ryo
- Institut für BiologieFreie Universität BerlinBerlinD‐14195Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity ResearchBerlinD‐14195Germany
- Leibniz Centre for Agricultural Landscape Research (ZALF)Müncheberg15374Germany
- Institute of Environmental SciencesBrandenburg University of TechnologyCottbus03046Germany
| | - George A. Kowalchuk
- Department of Biology, Ecology, and BiodiversityUtrecht UniversityUtrechtCH3584The Netherlands
| | - Peter A. H. M. Bakker
- Department of Biology, Plant‐Microbe InteractionsUtrecht UniversityUtrechtCH3584The Netherlands
| | - Alexandre Jousset
- Department of Biology, Ecology, and BiodiversityUtrecht UniversityUtrechtCH3584The Netherlands
| |
Collapse
|
2
|
Bonkowski M, Tarkka M, Razavi BS, Schmidt H, Blagodatskaya E, Koller R, Yu P, Knief C, Hochholdinger F, Vetterlein D. Spatiotemporal Dynamics of Maize ( Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Front Microbiol 2021; 12:619499. [PMID: 33815308 PMCID: PMC8010349 DOI: 10.3389/fmicb.2021.619499] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
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.
Collapse
Affiliation(s)
- Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Mika Tarkka
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Bahar S Razavi
- Department of Soil and Plant Microbiome, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Evgenia Blagodatskaya
- Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany
| | - Robert Koller
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Peng Yu
- Emmy Noether Group Root Functional Biology, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Claudia Knief
- Institute of Crop Science and Resource Conservation - Molecular Biology of the Rhizosphere, University of Bonn, Bonn, Germany
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Doris Vetterlein
- Department of Soil System Science, Helmholtz Centre for Environmental Research - UFZ, Halle, Germany.,Soil Science, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
3
|
Pavlova AS, Leontieva MR, Smirnova TA, Kolomeitseva GL, Netrusov AI, Tsavkelova EA. Colonization strategy of the endophytic plant growth-promoting strains of Pseudomonas fluorescens and Klebsiella oxytoca on the seeds, seedlings and roots of the epiphytic orchid, Dendrobium nobile Lindl. J Appl Microbiol 2017; 123:217-232. [PMID: 28457004 DOI: 10.1111/jam.13481] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/17/2017] [Accepted: 04/24/2017] [Indexed: 11/26/2022]
Abstract
AIMS Orchids form strong mycorrhizal associations, but their interactions with bacteria are poorly understood. We aimed to investigate the distribution of plant growth promoting rhizobacteria (PGPR) at different stages of orchid development and to study if there is any selective specificity in choosing PGPR partners. METHODS AND RESULTS Colonization patterns of gfp-tagged Pseudomonas fluorescens and Klebsiella oxytoca were studied on roots, seeds, and seedlings of Dendrobium nobile. Endophytic rhizobacteria rapidly colonized velamen and core parenchyma entering through exodermis and the passage cells, whereas at the early stages, they stayed restricted to the surface and the outer layers of the protocorms and rhizoids. The highest amounts of auxin (indole-3-acetic acid) were produced by K. oxytoca and P. fluorescens in the nitrogen-limiting and NO3 -containing media respectively. Bacterization of D. nobile seeds resulted in promotion of their in vitro germination. The plant showed no selective specificity to the tested strains. Klebsiella oxytoca demonstrated more intense colonization activity and more efficient growth promoting impact under tryptophan supplementation, while P. fluorescens revealed its growth-promoting capacity without tryptophan. CONCLUSIONS Both strategies are regarded as complementary, improving adaptive potentials of the orchid when different microbial populations colonize the plant. SIGNIFICANCE AND IMPACT OF THE STUDY This study enlarges our knowledge on orchid-microbial interactions, and provides new features on application of the nonorchid PGPR in orchid seed germination and conservation.
Collapse
Affiliation(s)
- A S Pavlova
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - M R Leontieva
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - T A Smirnova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - G L Kolomeitseva
- The Stock Greenhouse, Tsitsin Main Botanical Garden, Russian Academy of Sciences, Moscow, Russia
| | - A I Netrusov
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - E A Tsavkelova
- Department of Microbiology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| |
Collapse
|
4
|
van Bruggen AHC, Gamliel A, Finckh MR. Plant disease management in organic farming systems. PEST MANAGEMENT SCIENCE 2016; 72:30-44. [PMID: 26331771 DOI: 10.1002/ps.4145] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 08/07/2015] [Accepted: 08/27/2015] [Indexed: 05/14/2023]
Abstract
Organic farming (OF) has significantly increased in importance in recent decades. Disease management in OF is largely based on the maintenance of biological diversity and soil health by balanced crop rotations, including nitrogen-fixing and cover crops, intercrops, additions of manure and compost and reductions in soil tillage. Most soil-borne diseases are naturally suppressed, while foliar diseases can sometimes be problematic. Only when a severe disease outbreak is expected are pesticides used that are approved for OF. A detailed overview is given of cultural and biological control measures. Attention is also given to regulated pesticides. We conclude that a systems approach to disease management is required, and that interdisciplinary research is needed to solve lingering disease problems, especially for OF in the tropics. Some of the organic regulations are in need of revision in close collaboration with various stakeholders.
Collapse
Affiliation(s)
- Ariena H C van Bruggen
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Abraham Gamliel
- Agriculture Research Organization, ARO Volcani Center , Bet Dagan, Israel
| | - Maria R Finckh
- Faculty of Organic Agricultural Sciences, Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| |
Collapse
|
5
|
Pershina E, Valkonen J, Kurki P, Ivanova E, Chirak E, Korvigo I, Provorov N, Andronov E. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems. PLoS One 2015; 10:e0145072. [PMID: 26684619 PMCID: PMC4684275 DOI: 10.1371/journal.pone.0145072] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 11/28/2015] [Indexed: 02/01/2023] Open
Abstract
One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.
Collapse
Affiliation(s)
- Elizaveta Pershina
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Saint-Petersburg State University, Saint-Petersburg, Russia
- * E-mail:
| | - Jari Valkonen
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Päivi Kurki
- Natural Resources Institute Finland, Mikkeli, Finland
| | - Ekaterina Ivanova
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Laboratory of biology and biochemistry of soils, V.V. Dokuchaev Soil Science Institute, Moscow, Russia
| | - Evgeny Chirak
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Ilia Korvigo
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Nykolay Provorov
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
| | - Evgeny Andronov
- Laboratory of microbiological monitoring and bioremediation of soils, All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, Russia
- Saint-Petersburg State University, Saint-Petersburg, Russia
| |
Collapse
|
6
|
|
7
|
Semenov AV, Franz E, van Bruggen AH. COLIWAVE a simulation model for survival of E. coli O157:H7 in dairy manure and manure-amended soil. Ecol Modell 2010. [DOI: 10.1016/j.ecolmodel.2009.10.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|