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Ali M, Rice CA, Byrne AW, Paré PE, Beauvais W. Modelling dynamics between free-living amoebae and bacteria. Environ Microbiol 2024; 26:e16623. [PMID: 38715450 DOI: 10.1111/1462-2920.16623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/04/2024] [Indexed: 05/23/2024]
Abstract
Free-living amoebae (FLA) serve as hosts for a variety of endosymbionts, which are microorganisms that reside and multiply within the FLA. Some of these endosymbionts pose a pathogenic threat to humans, animals, or both. The symbiotic relationship with FLA not only offers these microorganisms protection but also enhances their survival outside their hosts and assists in their dispersal across diverse habitats, thereby escalating disease transmission. This review is intended to offer an exhaustive overview of the existing mathematical models that have been applied to understand the dynamics of FLA, especially concerning their interactions with bacteria. An extensive literature review was conducted across Google Scholar, PubMed, and Scopus databases to identify mathematical models that describe the dynamics of interactions between FLA and bacteria, as published in peer-reviewed scientific journals. The literature search revealed several FLA-bacteria model systems, including Pseudomonas aeruginosa, Pasteurella multocida, and Legionella spp. Although the published mathematical models account for significant system dynamics such as predator-prey relationships and non-linear growth rates, they generally overlook spatial and temporal heterogeneity in environmental conditions, such as temperature, and population diversity. Future mathematical models will need to incorporate these factors to enhance our understanding of FLA-bacteria dynamics and to provide valuable insights for future risk assessment and disease control measures.
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Affiliation(s)
- Marwa Ali
- Comparative Pathobiology Department, Purdue Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Christopher A Rice
- Comparative Pathobiology Department, Purdue Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute for Drug Discovery (PIDD), Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D), Purdue University, West Lafayette, Indiana, USA
- Regenstrief Center for Healthcare Engineering (RHCE), Purdue University, West Lafayette, Indiana, USA
| | - Andrew W Byrne
- One Health Scientific Support Unit, National Disease Control Centre, Agriculture House, Dublin, Ireland
| | - Philip E Paré
- Elmore Family School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Wendy Beauvais
- Comparative Pathobiology Department, Purdue Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease (PI4D), Purdue University, West Lafayette, Indiana, USA
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Afridi MS, Fakhar A, Kumar A, Ali S, Medeiros FHV, Muneer MA, Ali H, Saleem M. Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering. Microbiol Res 2022; 265:127199. [PMID: 36137486 DOI: 10.1016/j.micres.2022.127199] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/02/2022] [Accepted: 09/13/2022] [Indexed: 10/14/2022]
Abstract
The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.
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Affiliation(s)
- Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil.
| | - Ali Fakhar
- Division of Applied Science, Gyeongsang National University, South Korea
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour University (A Central University), Sagar 470003, MP, India
| | - Sher Ali
- NMR Lab, Department of Chemistry, Federal University of Paraná, Curitiba 81530-900, PR, Brazil
| | - Flavio H V Medeiros
- Department of Plant Pathology, Federal University of Lavras, CP3037, 37200-900 Lavras, MG, Brazil
| | - Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hina Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, Montgomery, AL 36104, USA
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Mawarda PC, Le Roux X, Acosta MU, van Elsas JD, Salles JF. The impact of protozoa addition on the survivability of Bacillus inoculants and soil microbiome dynamics. ISME COMMUNICATIONS 2022; 2:82. [PMID: 37938668 PMCID: PMC9723691 DOI: 10.1038/s43705-022-00166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/15/2022] [Accepted: 08/22/2022] [Indexed: 10/06/2023]
Abstract
Protists' selective predation of bacterial cells is an important regulator of soil microbiomes, which might influence the success of bacterial releases in soils. For instance, the survival and activity of introduced bacteria can be affected by selective grazing on resident communities or the inoculant, but this remains poorly understood. Here, we investigated the impact of the introduction in the soil of two protozoa species, Rosculus terrestris ECOP02 and/or Cerocomonas lenta ECOP01, on the survival of the inoculants Bacillus mycoides M2E15 (BM) or B. pumilus ECOB02 (BP). We also evaluated the impact of bacterial inoculation with or without protozoan addition on the abundance and diversity of native soil bacterial and protist communities. While the addition of both protozoa decreased the survival of BM, their presence contrarily increased the BP abundance. Protists' selective predation governs the establishment of these bacterial inoculants via modifying the soil microbiome structure and the total bacterial abundance. In the BP experiment, the presence of the introduced protozoa altered the soil community structures and decreased soil bacterial abundance at the end of the experiment, favouring the invader survival. Meanwhile, the introduced protozoa did not modify the soil community structures in the BM experiment and reduced the BM + Protozoa inoculants' effect on total soil bacterial abundance. Our study reinforces the view that, provided added protozoa do not feed preferentially on bacterial inoculants, their predatory behaviour can be used to steer the soil microbiome to improve the success of bacterial inoculations by reducing resource competition with the resident soil microbial communities.
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Affiliation(s)
- Panji Cahya Mawarda
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
- Research Center for Environment and Clean Technology, National Research and Innovation Agency Republic of Indonesia (BRIN), Komplek LIPI Bandung, Jalan Sangkuriang Gedung 50, Bandung, 40135, Indonesia.
| | - Xavier Le Roux
- Laboratoire d'Ecologie Microbienne, INRAE, CNRS, Université de Lyon, Université Lyon 1, UMR INRAE 1418, UMR CNRS 5557, 43 Boulevard du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Melissa Uribe Acosta
- Plant-Microbe Interactions Group, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Pollution Diagnostics and Control Group (GDCON), Biology Institute, University Research Campus (SIU), University of Antioquia (UdeA), Calle 70 No. 52-21, Medellín, Colombia
| | - Jan Dirk van Elsas
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology Cluster, Expertise Group GREEN, Groningen Institute of Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Sanya DRA, Syed-Ab-Rahman SF, Jia A, Onésime D, Kim KM, Ahohuendo BC, Rohr JR. A review of approaches to control bacterial leaf blight in rice. World J Microbiol Biotechnol 2022; 38:113. [PMID: 35578069 DOI: 10.1007/s11274-022-03298-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/29/2022] [Indexed: 01/16/2023]
Abstract
The Gram-negative bacteria Xanthomonas oryzae pv. oryzae, the causative agent of bacterial leaf blight (BLB), received attention for being an economically damaging pathogen of rice worldwide. This damage prompted efforts to better understand the molecular mechanisms governing BLB disease progression. This research revealed numerous virulence factors that are employed by this vascular pathogen to invade the host, outcompete host defence mechanisms, and cause disease. In this review, we emphasize the virulence factors and molecular mechanisms that X. oryzae pv. oryzae uses to impair host defences, recent insights into the cellular and molecular mechanisms underlying host-pathogen interactions and components of pathogenicity, methods for developing X. oryzae pv. oryzae-resistant rice cultivars, strategies to mitigate disease outbreaks, and newly discovered genes and tools for disease management. We conclude that the implementation and application of cutting-edge technologies and tools are crucial to avoid yield losses from BLB and ensure food security.
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Affiliation(s)
| | | | - Aiqun Jia
- School of Environmental & Biological Engineering, Nanjing University of Science and Technology, Xiaolingwei No. 200, Xuanwu District, 210014, Nanjing, Jiangsu, China
| | - Djamila Onésime
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Kyung-Min Kim
- School of Applied BioSciences, College of Agriculture & Life Sciences, Kyungpook National University, 80 Daehak-ro, Buk-Gu, 41566, Daegu, Korea
| | - Bonaventure Cohovi Ahohuendo
- Faculty of Agricultural Sciences, University of Abomey-Calavi, 526 Recette Principale, Cotonou 01, 01 BP, Abomey-Calavi, Benin
| | - Jason R Rohr
- Department of Biological Sciences, University of Notre Dame, Eck Institute of Global Health, Environmental Change Initiative, 178 Galvin Life Science Center, 46556, Notre Dame, IN, USA
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Wu C, Chao Y, Shu L, Qiu R. Interactions between soil protists and pollutants: An unsolved puzzle. JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128297. [PMID: 35077968 DOI: 10.1016/j.jhazmat.2022.128297] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
Soil protists are essential but often overlooked in soils, although they play crucial functional roles in the terrestrial ecosystem. While soil protists have drawn increased attention to their functional role in soils, their interaction with soil pollutants remains unresolved. This review provides a first overview of the current understanding of interactions between soil protists and major pollutants (heavy metals, organic pollutants, nanoparticles, and soil pathogens). We summarize how soil pollutants affect protists and vice versa, showing that we are just beginning to understand their complex interactions. In addition, we identify five research gaps, including hidden diversity, adaptive mechanisms, species interactions, soil bioindicators and environmental applications, and we hope that our review will help promote and build research guidelines for the future. In conclusion, a better understanding of soil pollutant-protist interactions will significantly increase our knowledge of the pollution ecology in the soil and how soil organisms respond and adapt to environmental pollution, which will contribute to the bioremediation and environmental applications of protists in soil.
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Affiliation(s)
- Chenyuan Wu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanqing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Longfei Shu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Environmental Microbiomics Research Center, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou 510006, China.
| | - Rongliang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China.
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Jia T, Liang X, Guo T, Chai B. Impact of Nutrients on Protozoa Community Diversity and Structure in Litter of Two Natural Grass Species in a Copper Tailings Dam, China. Microorganisms 2021; 9:microorganisms9112250. [PMID: 34835372 PMCID: PMC8624916 DOI: 10.3390/microorganisms9112250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022] Open
Abstract
In nature, protists directly participate in litter decomposition and indirectly affect litter decomposition processes by means of their influence on litter microbial communities. To date, relevant studies on litter microbial communities have primarily focused on bacteria and fungi, while relatively little attention has been paid to the characteristics of protozoan communities within damaged ecosystems. Two dominant grass species (Bothriochloa ischaemum and Imperata cylindrica) were selected from China’s “Eighteenth” River tailings dam to explore protozoan community composition and diversity in a degraded mining area and to clarify the influence among key ecological factors and protozoan community characteristics in litter. High-throughput sequencing was used to analyze protozoan community composition and diversity, while correlation analysis was used to explore the relationships between protozoan communities and litter nutrient characteristics, including associative enzyme degradation. Although protozoan communities in litter shared a dominant group at an order level (Colpodida), they differed at a genus level (i.e., Hausmanniella and Tychosporium). Moreover, although the order Cryomonadida positively correlated to total nitrogen (TN) and sucrose, it exhibited an extreme negative correlation to total carbon (TC) and cellulase. Colpodida and Oomycota_X significantly and negatively correlated to litter urease activity. Nutrient characteristics of grass litter in copper tailing dams are important ecological factors that affect protozoan community characteristics. Notable differences were observed among protozoan communities of these two grass species, while litter enzyme activities were closely correlated to protozoan community diversity. The results suggested that Colpodida may play important roles in litter decomposition and nutrient cycling in mining areas.
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Affiliation(s)
- Tong Jia
- Correspondence: ; Tel.: +86-155-1369-4458
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Environmental Free-Living Amoebae Can Predate on Diverse Antibiotic-Resistant Human Pathogens. Appl Environ Microbiol 2021; 87:e0074721. [PMID: 34232736 PMCID: PMC8388808 DOI: 10.1128/aem.00747-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here, we sought to test the resistance of human pathogens to unaltered environmental free-living amoebae. Amoebae are ubiquitous eukaryotic microorganisms and important predators of bacteria. Environmental amoebae have also been proposed to serve as both potential reservoirs and training grounds for human pathogens. However, studies addressing their relationships with human pathogens often rely on a few domesticated amoebae that have been selected to feed on rich medium, thereby possibly overestimating the resistance of pathogens to these predatory phagocytes. From an open-air composting site, we recovered over 100 diverse amoebae that were able to feed on Acinetobacter baumannii and Klebsiella pneumoniae. In a standardized and quantitative assay for predation, the isolated amoebae showed a broad predation spectrum, killing clinical isolates of A. baumannii, K. pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Interestingly, A. baumannii, which was previously reported to resist predation by laboratory strains of Acanthamoeba, was efficiently consumed by closely related environmental amoebae. The isolated amoebae were capable of feeding on highly virulent carbapenem-resistant or methicillin-resistant clinical isolates. In conclusion, the natural environment is a rich source of amoebae with broad-spectrum bactericidal activities, including against antibiotic-resistant isolates. IMPORTANCE Free-living amoebae have been proposed to play an important role in hosting and disseminating various human pathogens. The resistance of human pathogens to predation by amoebae is often derived from in vitro experiments using model amoebae. Here, we sought to isolate environmental amoebae and to test their predation on diverse human pathogens, with results that challenge conclusions based on model amoebae. We found that the natural environment is a rich source of diverse amoebae with broad-spectrum predatory activities against human pathogens, including highly virulent and antibiotic-resistant clinical isolates.
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Martin KH, Borlee GI, Wheat WH, Jackson M, Borlee BR. Busting biofilms: free-living amoebae disrupt preformed methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis biofilms. MICROBIOLOGY-SGM 2020; 166:695-706. [PMID: 32459167 PMCID: PMC7641382 DOI: 10.1099/mic.0.000933] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Biofilm-associated infections are difficult to eradicate because of their ability to tolerate antibiotics and evade host immune responses. Amoebae and/or their secreted products may provide alternative strategies to inhibit and disperse biofilms on biotic and abiotic surfaces. We evaluated the potential of five predatory amoebae – Acanthamoeba castellanii, Acanthamoeba lenticulata, Acanthamoeba polyphaga, Vermamoeba vermiformis and Dictyostelium discoideum – and their cell-free secretions to disrupt biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis. The biofilm biomass produced by MRSA and M. bovis was significantly reduced when co-incubated with A. castellanii, A. lenticulata and A. polyphaga, and their corresponding cell-free supernatants (CFS). Acanthamoeba spp. generally produced CFS that mediated biofilm dispersal rather than directly killing the bacteria; however, A. polyphaga CFS demonstrated active killing of MRSA planktonic cells when the bacteria were present at low concentrations. The active component(s) of the A. polyphaga CFS is resistant to freezing, but can be inactivated to differing degrees by mechanical disruption and exposure to heat. D. discoideum and its CFS also reduced preformed M. bovis biofilms, whereas V. vermiformis only decreased M. bovis biofilm biomass when amoebae were added. These results highlight the potential of using select amoebae species or their CFS to disrupt preformed bacterial biofilms.
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Affiliation(s)
- Kevin H Martin
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Grace I Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - William H Wheat
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Bradley R Borlee
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
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Long JJ, Luna EK, Jackson M, Wheat W, Jahn CE, Leach JE. Interactions of free-living amoebae with the rice fungal pathogen, Rhizoctonia solani. BMC Res Notes 2019; 12:746. [PMID: 31730018 PMCID: PMC6858675 DOI: 10.1186/s13104-019-4802-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 11/12/2019] [Indexed: 11/13/2022] Open
Abstract
Objective Rhizoctonia solani is a soil-borne fungal pathogen of many important crop plants. In rice, R. solani causes sheath blight disease, which results in devastating grain yield and quality losses. Few methods are available to control this pathogen and classic single gene resistance mechanisms in rice plants have not been identified. We hypothesize that alternate means of control are available in the environment including free-living amoebae. Amoebae are soil-, water- and air-borne microorganisms that are predominantly heterotrophic. Many amoeba species are mycophagous, and several harm their prey using mechanisms other than phagocytosis. Here, we used light and scanning electron microscopy to survey the interactions of R. solani with four amoeba species, with the goal of identifying amoebae species with potential for biocontrol. Results We observed a wide range of responses during interactions of R. solani with four different free-living amoebae. Two Acanthamoeba species encyst in co-cultures with R. solani at higher rates than medium without R. solani. Vermamoeba vermiformis (formerly Hartmanella vermiformis) attach to R. solani mycelium and are associated with mycelial shriveling and perforations of fungal cell walls, indicating an antagonistic interaction. No phenotypic changes were observed in co-cultures of Dictyostelium discoideum and R. solani.
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Affiliation(s)
- John J Long
- Department of Plant Pathology, The Ohio State University, Columbus, OH, USA.,Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Emily K Luna
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - William Wheat
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Courtney E Jahn
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.
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Gao Z, Karlsson I, Geisen S, Kowalchuk G, Jousset A. Protists: Puppet Masters of the Rhizosphere Microbiome. TRENDS IN PLANT SCIENCE 2019; 24:165-176. [PMID: 30446306 DOI: 10.1016/j.tplants.2018.10.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 05/18/2023]
Abstract
The rhizosphere microbiome is a central determinant of plant performance. Microbiome assembly has traditionally been investigated from a bottom-up perspective, assessing how resources such as root exudates drive microbiome assembly. However, the importance of predation as a driver of microbiome structure has to date largely remained overlooked. Here we review the importance of protists, a paraphyletic group of unicellular eukaryotes, as a key regulator of microbiome assembly. Protists can promote plant-beneficial functions within the microbiome, accelerate nutrient cycling, and remove pathogens. We conclude that protists form an essential component of the rhizosphere microbiome and that accounting for predator-prey interactions would greatly improve our ability to predict and manage microbiome function at the service of plant growth and health.
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Affiliation(s)
- Zhilei Gao
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; These authors contributed equally
| | - Ida Karlsson
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; Dept. of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 75007 Uppsala, Sweden; These authors contributed equally
| | - Stefan Geisen
- Department of Terrestrial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands
| | - George Kowalchuk
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Alexandre Jousset
- Institute of Environmental Biology, Ecology & Biodiversity, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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