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Nieto EE, Jurburg SD, Steinbach N, Festa S, Morelli IS, Coppotelli BM, Chatzinotas A. DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories. MICROBIOME 2024; 12:146. [PMID: 39113100 PMCID: PMC11305082 DOI: 10.1186/s40168-024-01865-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/26/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND Bioaugmentation is considered a sustainable and cost-effective methodology to recover contaminated environments, but its outcome is highly variable. Predation is a key top-down control mechanism affecting inoculum establishment, however, its effects on this process have received little attention. This study focused on the impact of trophic interactions on bioaugmentation success in two soils with different pollution exposure histories. We inoculated a 13C-labelled pollutant-degrading consortium in these soils and tracked the fate of the labelled biomass through stable isotope probing (SIP) of DNA. We identified active bacterial and eukaryotic inoculum-biomass consumers through amplicon sequencing of 16S rRNA and 18S rRNA genes coupled to a novel enrichment factor calculation. RESULTS Inoculation effectively increased PAH removal in the short-term, but not in the long-term polluted soil. A decrease in the relative abundance of the inoculated genera was observed already on day 15 in the long-term polluted soil, while growth of these genera was observed in the short-term polluted soil, indicating establishment of the inoculum. In both soils, eukaryotic genera dominated as early incorporators of 13C-labelled biomass, while bacteria incorporated the labelled biomass at the end of the incubation period, probably through cross-feeding. We also found different successional patterns between the two soils. In the short-term polluted soil, Cercozoa and Fungi genera predominated as early incorporators, whereas Ciliophora, Ochrophyta and Amoebozoa were the predominant genera in the long-term polluted soil. CONCLUSION Our results showed differences in the inoculum establishment and predator community responses, affecting bioaugmentation efficiency. This highlights the need to further study predation effects on inoculum survival to increase the applicability of inoculation-based technologies. Video Abstract.
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Affiliation(s)
- Esteban E Nieto
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina.
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
| | - Stephanie D Jurburg
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nicole Steinbach
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Sabrina Festa
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Irma S Morelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
- Comisión de Investigaciones Científicas de La Provincia de Buenos Aires, La Plata, Argentina
| | - Bibiana M Coppotelli
- Centro de Investigación y Desarrollo en Fermentaciones Industriales, CONICET), CINDEFI (UNLP, CCT-La Plata Street 50 N°227, 1900, La Plata, Argentina
| | - Antonis Chatzinotas
- Department of Applied Microbial Ecology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany.
- Institute of Biology, Leipzig University, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
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Vandermaesen J, Daly AJ, Mawarda PC, Baetens JM, De Baets B, Boon N, Springael D. Cooperative interactions between invader and resident microbial community members weaken the negative diversity-invasion relationship. Ecol Lett 2024; 27:e14433. [PMID: 38712704 DOI: 10.1111/ele.14433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]
Abstract
The negative diversity-invasion relationship observed in microbial invasion studies is commonly explained by competition between the invader and resident populations. However, whether this relationship is affected by invader-resident cooperative interactions is unknown. Using ecological and mathematical approaches, we examined the survival and functionality of Aminobacter niigataensis MSH1 to mineralize 2,6-dichlorobenzamide (BAM), a groundwater micropollutant affecting drinking water production, in sand microcosms when inoculated together with synthetic assemblies of resident bacteria. The assemblies varied in richness and in strains that interacted pairwise with MSH1, including cooperative and competitive interactions. While overall, the negative diversity-invasion relationship was retained, residents engaging in cooperative interactions with the invader had a positive impact on MSH1 survival and functionality, highlighting the dependency of invasion success on community composition. No correlation existed between community richness and the delay in BAM mineralization by MSH1. The findings suggest that the presence of cooperative residents can alleviate the negative diversity-invasion relationship.
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Affiliation(s)
| | - Aisling J Daly
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Panji Cahya Mawarda
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
- Research Center for Applied Microbiology, National Research and Innovation Agency Republic of Indonesia (BRIN), Bandung, Indonesia
| | - Jan M Baetens
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Bernard De Baets
- Department of Data Analysis and Mathematical Modelling, Ghent University, Gent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Gent, Belgium
| | - Dirk Springael
- Division of Soil and Water Management, KU Leuven, Heverlee, Belgium
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Liu X, Salles JF. Drivers and consequences of microbial community coalescence. THE ISME JOURNAL 2024; 18:wrae179. [PMID: 39288091 PMCID: PMC11447283 DOI: 10.1093/ismejo/wrae179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/14/2024] [Accepted: 09/16/2024] [Indexed: 09/19/2024]
Abstract
Microbial communities are undergoing unprecedented dispersion and amalgamation across diverse ecosystems, thereby exerting profound and pervasive influences on microbial assemblages and ecosystem dynamics. This review delves into the phenomenon of community coalescence, offering an ecological overview that outlines its four-step process and elucidates the intrinsic interconnections in the context of community assembly. We examine pivotal mechanisms driving community coalescence, with a particular emphasis on elucidating the fates of both source and resident microbial communities and the consequential impacts on the ecosystem. Finally, we proffer recommendations to guide researchers in this rapidly evolving domain, facilitating deeper insights into the ecological ramifications of microbial community coalescence.
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Affiliation(s)
- Xipeng Liu
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- Ecologie Microbienne Lyon, Centre National de la Recherche Scientifique (CNRS) UMR5557, Bâtiment Grégoire Mendel, 69100 Villeurbanne, France
| | - Joana Falcão Salles
- Microbial Ecology cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Nguyen TBA, Bonkowski M, Dumack K, Chen QL, He JZ, Hu HW. Protistan predation selects for antibiotic resistance in soil bacterial communities. THE ISME JOURNAL 2023; 17:2182-2189. [PMID: 37794244 PMCID: PMC10689782 DOI: 10.1038/s41396-023-01524-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
Understanding how antibiotic resistance emerges and evolves in natural habitats is critical for predicting and mitigating antibiotic resistance in the context of global change. Bacteria have evolved antibiotic production as a strategy to fight competitors, predators and other stressors, but how predation pressure of their most important consumers (i.e., protists) affects soil antibiotic resistance genes (ARGs) profiles is still poorly understood. To address this gap, we investigated responses of soil resistome to varying levels of protistan predation by inoculating low, medium and high concentrations of indigenous soil protist suspensions in soil microcosms. We found that an increase in protistan predation pressure was strongly associated with higher abundance and diversity of soil ARGs. High protist concentrations significantly enhanced the abundances of ARGs encoding multidrug (oprJ and ttgB genes) and tetracycline (tetV) efflux pump by 608%, 724% and 3052%, respectively. Additionally, we observed an increase in the abundance of numerous bacterial genera under high protistan pressure. Our findings provide empirical evidence that protistan predation significantly promotes antibiotic resistance in soil bacterial communities and advances our understanding of the biological driving forces behind the evolution and development of environmental antibiotic resistance.
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Affiliation(s)
- Thi Bao-Anh Nguyen
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Michael Bonkowski
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - Kenneth Dumack
- Terrestrial Ecology, Institute of Zoology, University of Cologne, Köln, Germany
| | - Qing-Lin Chen
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Cardoni M, Mercado-Blanco J. Confronting stresses affecting olive cultivation from the holobiont perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1261754. [PMID: 38023867 PMCID: PMC10661416 DOI: 10.3389/fpls.2023.1261754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
The holobiont concept has revolutionized our understanding of plant-associated microbiomes and their significance for the development, fitness, growth and resilience of their host plants. The olive tree holds an iconic status within the Mediterranean Basin. Innovative changes introduced in olive cropping systems, driven by the increasing demand of its derived products, are not only modifying the traditional landscape of this relevant commodity but may also imply that either traditional or emerging stresses can affect it in ways yet to be thoroughly investigated. Incomplete information is currently available about the impact of abiotic and biotic pressures on the olive holobiont, what includes the specific features of its associated microbiome in relation to the host's structural, chemical, genetic and physiological traits. This comprehensive review consolidates the existing knowledge about stress factors affecting olive cultivation and compiles the information available of the microbiota associated with different olive tissues and organs. We aim to offer, based on the existing evidence, an insightful perspective of diverse stressing factors that may disturb the structure, composition and network interactions of the olive-associated microbial communities, underscoring the importance to adopt a more holistic methodology. The identification of knowledge gaps emphasizes the need for multilevel research approaches and to consider the holobiont conceptual framework in future investigations. By doing so, more powerful tools to promote olive's health, productivity and resilience can be envisaged. These tools may assist in the designing of more sustainable agronomic practices and novel breeding strategies to effectively face evolving environmental challenges and the growing demand of high quality food products.
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Affiliation(s)
- Martina Cardoni
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Jesús Mercado-Blanco
- Departamento de Microbiología del Suelo y la Planta, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
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Hu S, Li G, Berlinches de Gea A, Teunissen J, Geisen S, Wilschut RA, Schwelm A, Wang Y. Microbiome predators in changing soils. Environ Microbiol 2023; 25:2057-2067. [PMID: 37438930 DOI: 10.1111/1462-2920.16461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
Microbiome predators shape the soil microbiome and thereby soil functions. However, this knowledge has been obtained from small-scale observations in fundamental rather than applied settings and has focused on a few species under ambient conditions. Therefore, there are several unaddressed questions on soil microbiome predators: (1) What is the role of microbiome predators in soil functioning? (2) How does global change affect microbiome predators and their functions? (3) How can microbiome predators be applied in agriculture? We show that there is sufficient evidence for the vital role of microbiome predators in soils and stress that global changes impact their functions, something that urgently needs to be addressed to better understand soil functioning as a whole. We are convinced that there is a potential for the application of microbiome predators in agricultural settings, as they may help to sustainably increase plant growth. Therefore, we plea for more applied research on microbiome predators.
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Affiliation(s)
- Shunran Hu
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Guixin Li
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Alejandro Berlinches de Gea
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Joliese Teunissen
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Stefan Geisen
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Rutger A Wilschut
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
| | - Arne Schwelm
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
- Department of Environment, Soils and Landuse, Teagasc Johnstown Castle, Wexford, Ireland
| | - Yuxin Wang
- Laboratory of Nematology, Plant Science Group, Wageningen University & Research (WU), Wageningen, The Netherlands
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Geller AM, Levy A. "What I cannot create, I do not understand": elucidating microbe-microbe interactions to facilitate plant microbiome engineering. Curr Opin Microbiol 2023; 72:102283. [PMID: 36868050 DOI: 10.1016/j.mib.2023.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
Plant-microbe interactions are important for both physiological and pathological processes. Despite the significance of plant-microbe interactions, microbe-microbe interactions themselves represent an important, complex, dynamic network that warrants deeper investigation. To understand how microbe-microbe interactions affect plant microbiomes, one approach is to systematically understand all the factors involved in successful engineering of a microbial community. This follows the physicist Richard Feynman's declaration: "what I cannot create, I do not understand". This review highlights recent studies that focus on aspects that we believe are important for building (ergo understanding) microbe-microbe interactions in the plant environment, including pairwise screening, intelligent application of cross-feeding models, spatial distributions of microbes, and understudied interactions between bacteria and fungi, phages, and protists. We offer a framework for systematic collection and centralized integration of data of plant microbiomes that could organize all the factors that can help ecologists understand microbiomes and help synthetic ecologists engineer beneficial microbiomes.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
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