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Anckaert A, Declerck S, Poussart LA, Lambert S, Helmus C, Boubsi F, Steels S, Argüelles-Arias A, Calonne-Salmon M, Ongena M. The biology and chemistry of a mutualism between a soil bacterium and a mycorrhizal fungus. Curr Biol 2024:S0960-9822(24)01230-2. [PMID: 39378881 DOI: 10.1016/j.cub.2024.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 07/26/2024] [Accepted: 09/09/2024] [Indexed: 10/10/2024]
Abstract
Arbuscular mycorrhizal (AM) fungi (e.g., Rhizophagus species) recruit specific bacterial species in their hyphosphere. However, the chemical interplay and the mutual benefit of this intricate partnership have not been investigated yet, especially as it involves bacteria known as strong producers of antifungal compounds such as Bacillus velezensis. Here, we show that the soil-dwelling B. velezensis migrates along the hyphal network of the AM fungus R. irregularis, forming biofilms and inducing cytoplasmic flow in the AM fungus that contributes to host plant root colonization by the bacterium. During hyphosphere colonization, R. irregularis modulates the biosynthesis of specialized metabolites in B. velezensis to ensure stable coexistence and as a mechanism to ward off mycoparasitic fungi and bacteria. These mutual benefits are extended into a tripartite context via the provision of enhanced protection to the host plant through the induction of systemic resistance.
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Affiliation(s)
- Adrien Anckaert
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique.
| | - Stéphane Declerck
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain-UCLouvain, Croix du Sud 2, L7.05.06, 1348 Louvain-la-Neuve, Belgique
| | - Laure-Anne Poussart
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Stéphanie Lambert
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Catherine Helmus
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Farah Boubsi
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Sébastien Steels
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Anthony Argüelles-Arias
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Earth and Life Institute, Université catholique de Louvain-UCLouvain, Croix du Sud 2, L7.05.06, 1348 Louvain-la-Neuve, Belgique
| | - Marc Ongena
- Microbial Processes and Interactions Laboratory, TERRA Teaching and Research Center, University of Liège - Gembloux Agro-Bio Tech, Avenue de la Faculté d'Agronomie, Bat. 9B, 5030 Gembloux, Belgique.
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2
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Kajihara KT, Hynson NA. Networks as tools for defining emergent properties of microbiomes and their stability. MICROBIOME 2024; 12:184. [PMID: 39342398 PMCID: PMC11439251 DOI: 10.1186/s40168-024-01868-z] [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: 05/03/2024] [Accepted: 07/04/2024] [Indexed: 10/01/2024]
Abstract
The potential promise of the microbiome to ameliorate a wide range of societal and ecological challenges, from disease prevention and treatment to the restoration of entire ecosystems, hinges not only on microbiome engineering but also on the stability of beneficial microbiomes. Yet the properties of microbiome stability remain elusive and challenging to discern due to the complexity of interactions and often intractable diversity within these communities of bacteria, archaea, fungi, and other microeukaryotes. Networks are powerful tools for the study of complex microbiomes, with the potential to elucidate structural patterns of stable communities and generate testable hypotheses for experimental validation. However, the implementation of these analyses introduces a cascade of dichotomies and decision trees due to the lack of consensus on best practices. Here, we provide a road map for network-based microbiome studies with an emphasis on discerning properties of stability. We identify important considerations for data preparation, network construction, and interpretation of network properties. We also highlight remaining limitations and outstanding needs for this field. This review also serves to clarify the varying schools of thought on the application of network theory for microbiome studies and to identify practices that enhance the reproducibility and validity of future work. Video Abstract.
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Affiliation(s)
- Kacie T Kajihara
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA.
| | - Nicole A Hynson
- Pacific Biosciences Research Center, University of Hawai'i at Mānoa, Honolulu, HI, 96822, USA
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Clark AJ, Masters-Clark E, Moratto E, Junier P, Stanley CE. Visualizing liquid distribution across hyphal networks with cellular resolution. BIOMICROFLUIDICS 2024; 18:054109. [PMID: 39381835 PMCID: PMC11460992 DOI: 10.1063/5.0231656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/24/2024] [Indexed: 10/10/2024]
Abstract
Filamentous fungi and fungal-like organisms contribute to a wide range of important ecosystem functions. Evidence has shown the movement of liquid across mycelial networks in unsaturated environments, such as soil. However, tools to investigate liquid movement along hyphae at the level of the single cell are still lacking. Microfluidic devices permit the study of fungal and fungal-like organisms with cellular resolution as they can confine hyphae to a single optical plane, which is compatible with microscopy imaging over longer timescales and allows for precise control of the microchannel environment. The aim of this study was to develop a method that enables the visualization and quantification of liquid movement on hyphae of fungal and fungal-like microorganisms. For this, the fungal-fungal interaction microfluidic device was modified to allow for the maintenance of unsaturated microchannel conditions. Fluorescein-containing growth medium solidified with agar was used to track liquid transported by hyphae via fluorescence microscopy. Our key findings highlight the suitability of this novel methodology for the visualization of liquid movement by hyphae over varying time scales and the ability to quantify the movement of liquid along hyphae. Furthermore, we showed that at the cellular level, extracellular movement of liquid along hyphae can be bidirectional and highly dynamic, uncovering a possible link between liquid movement and hyphal growth characteristics. We envisage that this method can be applied to facilitate future research probing the parameters contributing to hyphal liquid movement and is an essential step for studying the phenomenon of fungal highways.
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Affiliation(s)
- Amelia J. Clark
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Emily Masters-Clark
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Eleonora Moratto
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
| | - Pilar Junier
- Laboritoire de microbiologie, University of Neuchâtel, Neuchâtel CH-2000, Switzerland
| | - Claire E. Stanley
- Department of Bioengineering, Imperial College London, London SW7 2AZ, United Kingdom
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Kelliher JM, Johnson LYD, Robinson AJ, Longley R, Hanson BT, Cailleau G, Bindschedler S, Junier P, Chain PSG. Fabricated devices for performing bacterial-fungal interaction experiments across scales. Front Microbiol 2024; 15:1380199. [PMID: 39171270 PMCID: PMC11335632 DOI: 10.3389/fmicb.2024.1380199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Diverse and complex microbiomes are found in virtually every environment on Earth. Bacteria and fungi often co-dominate environmental microbiomes, and there is growing recognition that bacterial-fungal interactions (BFI) have significant impacts on the functioning of their associated microbiomes, environments, and hosts. Investigating BFI in vitro remains a challenge, particularly when attempting to examine interactions at multiple scales of system complexity. Fabricated devices can provide control over both biotic composition and abiotic factors within an experiment to enable the characterization of diverse BFI phenotypes such as modulation of growth rate, production of biomolecules, and alterations to physical movements. Engineered devices ranging from microfluidic chips to simulated rhizosphere systems have been and will continue to be invaluable to BFI research, and it is anticipated that such devices will continue to be developed for diverse applications in the field. This will allow researchers to address specific questions regarding the nature of BFI and how they impact larger microbiome and environmental processes such as biogeochemical cycles, plant productivity, and overall ecosystem resilience. Devices that are currently used for experimental investigations of bacteria, fungi, and BFI are discussed herein along with some of the associated challenges and several recommendations for future device design and applications.
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Affiliation(s)
- Julia M. Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Leah Y. D. Johnson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aaron J. Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Reid Longley
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Buck T. Hanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S. G. Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 PMCID: PMC11323152 DOI: 10.1016/j.mib.2024.102496] [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: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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Wang H, Xue X, Nan X, Zhai J. A comparison of the performance of bacterial biofilters and fungal-bacterial coupled biofilters in BTE p-X removal. PeerJ 2024; 12:e17452. [PMID: 38903883 PMCID: PMC11188933 DOI: 10.7717/peerj.17452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/03/2024] [Indexed: 06/22/2024] Open
Abstract
Background Conventional biofilters, which rely on bacterial activity, face challenges in eliminating hydrophobic compounds, such as aromatic compounds. This is due to the low solubility of these compounds in water, which makes them difficult to absorb by bacterial biofilms. Furthermore, biofilter operational stability is often hampered by acidification and drying out of the filter bed. Methods Two bioreactors, a bacterial biofilter (B-BF) and a fungal-bacterial coupled biofilter (F&B-BF) were inoculated with activated sludge from the secondary sedimentation tank of the Sinopec Yangzi Petrochemical Company wastewater treatment plant located in Nanjing, China. For approximately 6 months of operation, a F&B-BF was more effective than a B-BF in eliminating a gas-phase mixture containing benzene, toluene, ethylbenzene, and para-xylene (BTEp-X). Results After operating for four months, the F&B-BF showed higher removal efficiencies for toluene (T), ethylbenzene (E), benzene (B), and para-X (p-Xylene), at 96.9%, 92.6%, 83.9%, and 83.8%, respectively, compared to those of the B-BF (90.1%, 78.7%, 64.8%, and 59.3%). The degradation activity order for B-BF and F&B-BF was T > E > B > p-X. Similarly, the rates of mineralization for BTEp-X in the F&B-BF were 74.9%, 66.5%, 55.3%, and 45.1%, respectively, which were higher than those in the B-BF (56.5%, 50.8%, 43.8%, and 30.5%). Additionally, the F&B-BF (2 days) exhibited faster recovery rates than the B-BF (5 days). Conclusions It was found that a starvation protocol was beneficial for the stable operation of both the B-BF and F&B-BF. Community structure analysis showed that the bacterial genus Pseudomonas and the fungal genus Phialophora were both important in the degradation of BTEp-X. The fungal-bacterial consortia can enhance the biofiltration removal of BTEp-X vapors.
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Affiliation(s)
- Hai Wang
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, China
| | - Xiaojuan Xue
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, China
| | - Xujun Nan
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, China
| | - Jian Zhai
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, China
- Department of Printing and Packaging Engineering, Shanghai Publishing and Printing College, Shanghai, China
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7
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Zhai J, Jiang C, Xue X, Wang H. Biofiltration of toluene and ethyl acetate mixture by a fungal-bacterial biofilter: Performance and community structure analysis. Heliyon 2024; 10:e31984. [PMID: 38882306 PMCID: PMC11176807 DOI: 10.1016/j.heliyon.2024.e31984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
The inhibitory effect of hydrophilic volatile organic compounds (VOCs) on hydrophobic VOCs removal was found to be efficiently reduced by the fungal-bacterial biofilters (F&B-BFs) developed in the present study. Overall, the toluene and ethyl acetate mixture removal efficiencies (REs) and elimination capacities (ECs) of F&B-BFs were superior to those of bacterial biofilters (B-BFs). The REs for toluene and ethyl acetate were 32.5 ± 0.8 % and 74.6 ± 1.0 %, respectively, for F&B-BFs, in comparison to 8.0 ± 0.3 % and 60 ± 1.3 % for B-BFs. The ECs for toluene and ethyl acetate were 13.0 g m-3 h-1 and 149.2 g m-3 h-1, respectively, for the F&B-BF, compared to 3.2 g m-3 h-1 and 119.6 g m-3 h-1 for the B-BFs. This was achieved at a constant empty bed residence time (EBRT) of 45 s. F&B-BFs exhibited a superior mineralization efficiencies (MEs) compared to B-BFs for a VOC mixture of toluene and ethyl acetate (≈36.1 % vs ~ 29.6 %). This is attributed to the direct capture of VOCs by the presence of fungi, increased the contact time between VOCs and VOCs-degrading bacteria, and even distribution of VOCs-degrading bacteria in the F&B-BFs. Moreover, compared with B-BFs, the coupling effect of genus Pseudomonas degradation, and unclassified_f_Herpotrichiellaceae and unclassified_p_Ascomycota adsorption of F&B-BF resulted in a reduction in the impact of the presence of hydrophilic VOCs on the removal of hydrophobic VOCs, thereby enhancing the biofiltration performance of mixtures of hydrophilic and hydrophobic VOCs.
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Affiliation(s)
- Jian Zhai
- Department of Printing and Packaging Engineering, Shanghai Publishing and Printing College, Shanghai, People's Republic of China
| | - Chunhua Jiang
- Department of Printing and Packaging Engineering, Shanghai Publishing and Printing College, Shanghai, People's Republic of China
| | - Xiaojuan Xue
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, Gansu Province, People's Republic of China
| | - Hai Wang
- School of Environmental Engineering, Gansu Forestry Polytechnic, Tianshui, Gansu Province, People's Republic of China
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Pérez‐Pazos E, Beidler KV, Narayanan A, Beatty BH, Maillard F, Bancos A, Heckman KA, Kennedy PG. Fungi rather than bacteria drive early mass loss from fungal necromass regardless of particle size. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13280. [PMID: 38922748 PMCID: PMC11194057 DOI: 10.1111/1758-2229.13280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/30/2024] [Indexed: 06/28/2024]
Abstract
Microbial necromass is increasingly recognized as an important fast-cycling component of the long-term carbon present in soils. To better understand how fungi and bacteria individually contribute to the decomposition of fungal necromass, three particle sizes (>500, 250-500, and <250 μm) of Hyaloscypha bicolor necromass were incubated in laboratory microcosms inoculated with individual strains of two fungi and two bacteria. Decomposition was assessed after 15 and 28 days via necromass loss, microbial respiration, and changes in necromass pH, water content, and chemistry. To examine how fungal-bacterial interactions impact microbial growth on necromass, single and paired cultures of bacteria and fungi were grown in microplates containing necromass-infused media. Microbial growth was measured after 5 days through quantitative PCR. Regardless of particle size, necromass colonized by fungi had higher mass loss and respiration than both bacteria and uninoculated controls. Fungal colonization increased necromass pH, water content, and altered chemistry, while necromass colonized by bacteria remained mostly unaltered. Bacteria grew significantly more when co-cultured with a fungus, while fungal growth was not significantly affected by bacteria. Collectively, our results suggest that fungi act as key early decomposers of fungal necromass and that bacteria may require the presence of fungi to actively participate in necromass decomposition.
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Affiliation(s)
- Eduardo Pérez‐Pazos
- Ecology, Evolution, and Behavior Graduate ProgramUniversity of MinnesotaSt. PaulMinnesotaUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Katilyn V. Beidler
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Achala Narayanan
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Briana H. Beatty
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - François Maillard
- Microbial Ecology Group, Department of BiologyLund UniversityLundSweden
| | - Alexandra Bancos
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
| | | | - Peter G. Kennedy
- Department of Plant and Microbial BiologyUniversity of MinnesotaSt. PaulMinnesotaUSA
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9
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Richter A, Blei F, Hu G, Schwitalla JW, Lozano-Andrade CN, Xie J, Jarmusch SA, Wibowo M, Kjeldgaard B, Surabhi S, Xu X, Jautzus T, Phippen CBW, Tyc O, Arentshorst M, Wang Y, Garbeva P, Larsen TO, Ram AFJ, van den Hondel CAM, Maróti G, Kovács ÁT. Enhanced surface colonisation and competition during bacterial adaptation to a fungus. Nat Commun 2024; 15:4486. [PMID: 38802389 PMCID: PMC11130161 DOI: 10.1038/s41467-024-48812-1] [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: 06/05/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Bacterial-fungal interactions influence microbial community performance of most ecosystems and elicit specific microbial behaviours, including stimulating specialised metabolite production. Here, we use a co-culture experimental evolution approach to investigate bacterial adaptation to the presence of a fungus, using a simple model of bacterial-fungal interactions encompassing the bacterium Bacillus subtilis and the fungus Aspergillus niger. We find in one evolving population that B. subtilis was selected for enhanced production of the lipopeptide surfactin and accelerated surface spreading ability, leading to inhibition of fungal expansion and acidification of the environment. These phenotypes were explained by specific mutations in the DegS-DegU two-component system. In the presence of surfactin, fungal hyphae exhibited bulging cells with delocalised secretory vesicles possibly provoking an RlmA-dependent cell wall stress. Thus, our results indicate that the presence of the fungus selects for increased surfactin production, which inhibits fungal growth and facilitates the competitive success of the bacterium.
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Affiliation(s)
- Anne Richter
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Felix Blei
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department Pharmaceutical Microbiology, Hans-Knöll-Institute, Friedrich-Schiller-Universität, Jena, Germany
| | - Guohai Hu
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Environmental Microbial Genomics and Application, BGI-Shenzhen, Shenzhen, China
| | - Jan W Schwitalla
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jiyu Xie
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Scott A Jarmusch
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Mario Wibowo
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research, Singapore, Republic of Singapore
| | - Bodil Kjeldgaard
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Surabhi Surabhi
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Xinming Xu
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Theresa Jautzus
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Christopher B W Phippen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Olaf Tyc
- Netherlands Institute of Ecology, Wageningen, The Netherlands
- Department of Internal Medicine I, Goethe University Hospital, Frankfurt, Germany
| | - Mark Arentshorst
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Yue Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Wageningen, The Netherlands
| | - Thomas Ostenfeld Larsen
- Natural Product Discovery Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Arthur F J Ram
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | | | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby, Denmark.
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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10
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Li J, Hong M, Lv J, Tang R, Wang R, Yang Y, Liu N. Enhancement on migration and biodegradation of Diaphorobacter sp. LW2 mediated by Pythium ultimum in soil with different particle sizes. Front Microbiol 2024; 15:1391553. [PMID: 38841075 PMCID: PMC11150788 DOI: 10.3389/fmicb.2024.1391553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction The composition and structure of natural soil are very complex, leading to the difficult contact between hydrophobic organic compounds and degrading-bacteria in contaminated soil, making pollutants hard to be removed from the soil. Several researches have reported the bacterial migration in unsaturated soil mediated by fungal hyphae, but bacterial movement in soil of different particle sizes or in heterogeneous soil was unclear. The remediation of contaminated soil enhanced by hyphae still needs further research. Methods In this case, the migration and biodegradation of Diaphorobacter sp. LW2 in soil was investigated in presence of Pythium ultimum. Results Hyphae could promote the growth and migration of LW2 in culture medium. It was also confirmed that LW2 was able to migrate in the growth direction and against the growth direction along hyphae. Mediated by hyphae, motile strain LW2 translocated over 3 cm in soil with different particle size (CS1, 1.0-2.0 mm; CS2, 0.5-1.0mm; MS, 0.25-0.5 mm and FS, <0.25 mm), and it need shorter time in bigger particle soils. In inhomogeneous soil, hyphae participated in the distribution of introduced bacteria, and the total number of bacteria increased. Pythium ultimum enhanced the migration and survival of LW2 in soil, improving the bioremediation of polluted soil. Discussion The results of this study indicate that the mobilization of degrading bacteria mediated by Pythium ultimum in soil has great potential for application in bioremediation of contaminated soil.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Ruofan Wang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, China
- National and Local Joint Engineering Laboratory for Petrochemical Contaminated Site Control and Remediation Technology, Jilin University, Changchun, China
| | - Yadong Yang
- School of Environmental Science and Engineering, Jiangsu Engineering Research Center of Biomass Waste Pyrolytic Carbonization & Application, Yancheng Institute of Technology, Yancheng, China
| | - Na Liu
- Department of Ecology, College of Life Science and Technology, Jinan University, Guangzhou, Guangdong, China
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11
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Thomas VE, Antony-Babu S. Core hyphosphere microbiota of Fusarium oxysporum f. sp. niveum. ENVIRONMENTAL MICROBIOME 2024; 19:14. [PMID: 38461269 PMCID: PMC10924372 DOI: 10.1186/s40793-024-00558-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Bacteria and fungi are dynamically interconnected, leading to beneficial or antagonistic relationships with plants. Within this interkingdom interaction, the microbial community directly associated with the pathogen make up the pathobiome. While the overall soil bacterial community associated with Fusarium wilt diseases has been widely examined, the specific bacterial populations that directly interact with the Fusarium wilt pathogens are yet to be discovered. In this study, we define the bacterial community associated with the hyphae of Fusarium oxysporum f. sp. niveum race 2 (FON2). Using the 16S rRNA gene metabarcoding, we describe the hyphosphere pathobiome of three isolates of FON2. RESULTS Our results show a core microbiome that is shared among the three tested hyphospheres. The core hyphosphere community was made up of 15 OTUs (Operational Taxonomic Units) that were associated with all three FON2 isolates. This core consisted of bacterial members of the families, Oxalobacteraceae, Propionibacteriaceae, Burkholderiaceae, Micrococcaceae, Bacillaceae, Comamonadaceae, Pseudomonadaceae and unclassified bacteria. The hyphosphere of FON2 was dominated by order Burkholderiales. While all three isolate hyphospheres were dominated by these taxa, the specific OTU differed. We also note that while the dominant OTU of one hyphosphere might not be the largest OTU for other hyphospheres, they were still present across all the three isolate hyphospheres. Additionally, in the correlation and co-occurrence analysis the most abundant OTU was negatively correlated with most of the other OTU populations within the hyphosphere. CONCLUSIONS The study indicates a core microbiota associated with FON2. These results provide insights into the microbe-microbe dynamic of the pathogen's success and its ability to recruit a core pathobiome. Our research promotes the concept of pathogens not being lone invaders but recruits from the established host microbiome to form a pathobiome.
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Affiliation(s)
- Vanessa E Thomas
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA
| | - Sanjay Antony-Babu
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, 77843, USA.
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12
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Maucourt F, Doumèche B, Nazaret S, Fraissinet-Tachet L. Under explored roles of microbial ligninolytic enzymes in aerobic polychlorinated biphenyl transformation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:19071-19084. [PMID: 38372925 DOI: 10.1007/s11356-024-32291-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/28/2024] [Indexed: 02/20/2024]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants in the environment that are responsible for many adverse health effects. Bioremediation appears to be a healthy and cost-effective alternative for remediating PCB-contaminated environments. While some microbial species have been observed to be capable of transforming PCBs, only two different microbial pathways (rdh and bph pathways) have been described to be involved in PCB transformations. Ligninolytic enzymes have been observed or are under suspicion in some microbial PCB transformations. However, the role of these promising PCB-transforming enzymes, which are produced by fungi and some aerobic bacteria, is still unclear. The present review describes their role by identifying microbial PCB-transforming species and their reported ligninolytic enzymes whether proven or suspected to be involved in PCB transformations. There are several lines of evidence that ligninolytic enzymes are responsible for PCB transformations such as (1) the ability of purified laccases from Myceliophthora thermophila, Pycnoporus cinnabarinus, Trametes versicolor, Cladosporium sp, and Coprinus cumatus to transform hydroxy-PCBs; (2) the increased production of laccases and peroxidases by many fungi in the presence of PCBs; and (3) the enhanced PCB transformation by Pseudomonas stutzeri and Sinorhizobium meliloti NM after the addition of ligninolytic enzyme enhancers. However, if the involvement of ligninolytic enzymes in PCB transformation is clearly demonstrated in some fungal species, it does not seem to be implicated in all microbial species suggesting other still unknown metabolic pathways involved in PCB transformation and different from the bph and rdh pathways. Therefore, PCB transformation may involve several metabolic pathways, some involving ligninolytic enzymes, bph or rdh genes, and some still unknown, depending on the microbial species. In addition, current knowledge does not fully clarify the role of ligninolytic enzymes in PCB oxidation and dechlorination. Therefore, further studies focusing on purified ligninolytic enzymes are needed to clearly elucidate their role in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
- ENVISOL, 2-4 rue Hector Berlioz, F-38110, La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-7 69622, Villeurbanne, France
| | - Sylvie Nazaret
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-7 69622, Villeurbanne, France.
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13
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Li J, Hong M, Tang R, Cui T, Yang Y, Lv J, Liu N, Lei Y. Isolation of Diaphorobacter sp. LW2 capable of degrading Phenanthrene and its migration mediated by Pythium ultimum. ENVIRONMENTAL TECHNOLOGY 2024; 45:1497-1507. [PMID: 36384417 DOI: 10.1080/09593330.2022.2145914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Phenanthrene, one of the polycyclic aromatic hydrocarbons, is stubborn and persistent and exists widely in petroleum-contaminated soil. Filamentous fungi are good assistants to bacterial transport, by hyphae passing through soil pores and reaching further positions. An isolated bacterial strain, from the contaminated soil of the coking plant, was identified as Diaphorobacter and named LW2, which could use phenanthrene as the only carbon source and energy for its growth. LW2 could degrade phenanthrene in a wide range of pH, temperature and initial concentration. When pH was 6 and 10, the removal rate of phenanthrene was 38.59% and 76.44%, respectively, and the removal rate of phenanthrene was 68.25% at 15 ℃. And LW2 could degrade 86.64% phenanthrene when the initial concentration was 100 mg L-1. The detection of DI-N-octyl phthalate, phthalic acid and p-hydroxybenzoic acid revealed that the strain LW2 metabolised phenanthrene through the phthalic acid pathway. Meanwhile, swimming and swarming test results suggested that LW2 was motile. The auxiliary effect of Pythium ultimum on LW2 migration was assessed. In the presence of Pythium ultimum, LW2 could migrate within the range of centimters by its mycelium, which was also observed by fluorescence microscopy. Meanwhile, the degradation ability of LW2 after the migration was also explored. The results proved that the migration process had no significant effect on its degradation ability, and LW2 still showed good phenanthrene metabolism ability. This study provides more possibilities for the bioremediation of phenanthrene-contaminated soil by screening the degradation bacteria and testing the effect of fungi on its migration.
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Affiliation(s)
- Jialu Li
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Mei Hong
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Rui Tang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Tingchen Cui
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Yadong Yang
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Jing Lv
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, College of New Energy and Environment, Jilin University, Changchun, People's Republic of China
| | - Na Liu
- Institute of Groundwater and Earth Science, Jinan University, Guangzhou City, People's Republic of China
| | - Yutao Lei
- South China Institute of Environmental Sciences, MEP, Guangzhou, People's Republic of China
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14
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Périat C, Kuhn T, Buffi M, Corona-Ramirez A, Fatton M, Cailleau G, Chain PS, Stanley CE, Wick LY, Bindschedler S, Gonzalez D, Li Richter XY, Junier P. Host and nonhost bacteria support bacteriophage dissemination along mycelia and abiotic dispersal networks. MICROLIFE 2024; 5:uqae004. [PMID: 38463165 PMCID: PMC10924533 DOI: 10.1093/femsml/uqae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
Bacteriophages play a crucial role in shaping bacterial communities, yet the mechanisms by which nonmotile bacteriophages interact with their hosts remain poorly understood. This knowledge gap is especially pronounced in structured environments like soil, where spatial constraints and air-filled zones hinder aqueous diffusion. In soil, hyphae of filamentous microorganisms form a network of 'fungal highways' (FHs) that facilitate the dispersal of other microorganisms. We propose that FHs also promote bacteriophage dissemination. Viral particles can diffuse in liquid films surrounding hyphae or be transported by infectable (host) or uninfectable (nonhost) bacterial carriers coexisting on FH networks. To test this, two bacteriophages that infect Pseudomonas putida DSM291 (host) but not KT2440 (nonhost) were used. In the absence of carriers, bacteriophages showed limited diffusion on 3D-printed abiotic networks, but diffusion was significantly improved in Pythium ultimum-formed FHs when the number of connecting hyphae exceeded 20. Transport by both host and nonhost carriers enhanced bacteriophage dissemination. Host carriers were five times more effective in transporting bacteriophages, particularly in FHs with over 30 connecting hyphae. This study enhances our understanding of bacteriophage dissemination in nonsaturated environments like soils, highlighting the importance of biotic networks and bacterial hosts in facilitating this process.
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Affiliation(s)
- Claire Périat
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Andrea Corona-Ramirez
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Mathilda Fatton
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Patrick S Chain
- Los Alamos National Laboratory, Bioscience Division, P.O. Box 1663, NM 87545, Los Alamos, United States
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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15
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Mei Y, Zhang M, Cao G, Zhu J, Zhang A, Bai H, Dai C, Jia Y. Endofungal bacteria and ectomycorrhizal fungi synergistically promote the absorption of organic phosphorus in Pinus massoniana. PLANT, CELL & ENVIRONMENT 2024; 47:600-610. [PMID: 37885374 DOI: 10.1111/pce.14742] [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: 04/26/2023] [Revised: 09/02/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023]
Abstract
Ectomycorrhizal fungi (ECMFs) that are involved in phosphorus mobilisation and turnover have limited ability to mineralise phytate alone. The endofungal bacteria in the ectomycorrhizal fruiting body may contribute to achieving this ecological function of ECMFs. We investigated the synergistic effect and mechanisms of endofungal bacteria and ECMF Suillus grevillea on phytate mineralisation. The results showed that soluble phosphorus content in the combined system of endofungal bacterium Cedecea lapagei and S. grevillea was 1.8 times higher than the sum of C. lapagei and S. grevillea alone treatment under the phytate mineralisation experiment. The S. grevillea could first chemotactically assist C. lapagei in adhering to the surface of S. grevillea. Then, the mineralisation of phytate was synergistically promoted by increasing the biomass of C. lapagei and the phosphatase and phytase activities of S. grevillea. The expression of genes related to chemotaxis, colonisation, and proliferation of C. lapagei and genes related to phosphatase and phytase activity of S. grevillea was also significantly upregulated. Furthermore, in the pot experiment, we verified that there might exist a ternary symbiotic system in the natural forest in which endofungal bacteria and ECMFs could synergistically promote phytate uptake in the plant Pinus massoniana via the ectomycorrhizal system.
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Affiliation(s)
- Yan Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
- College of Life Sciences, Nanjing University, Nanjing, China
| | - Meiling Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Gengyue Cao
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jiale Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Aiyue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hongyan Bai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialisation of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, China
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16
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Zhang C, van der Heijden MGA, Dodds BK, Nguyen TB, Spooren J, Valzano-Held A, Cosme M, Berendsen RL. A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization. MICROBIOME 2024; 12:13. [PMID: 38243337 PMCID: PMC10799531 DOI: 10.1186/s40168-023-01726-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 11/18/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Plant microbiomes play crucial roles in nutrient cycling and plant growth, and are shaped by a complex interplay between plants, microbes, and the environment. The role of bacteria as mediators of the 400-million-year-old partnership between the majority of land plants and, arbuscular mycorrhizal (AM) fungi is still poorly understood. Here, we test whether AM hyphae-associated bacteria influence the success of the AM symbiosis. RESULTS Using partitioned microcosms containing field soil, we discovered that AM hyphae and roots selectively assemble their own microbiome from the surrounding soil. In two independent experiments, we identified several bacterial genera, including Devosia, that are consistently enriched on AM hyphae. Subsequently, we isolated 144 pure bacterial isolates from a mycorrhiza-rich sample of extraradical hyphae and isolated Devosia sp. ZB163 as root and hyphal colonizer. We show that this AM-associated bacterium synergistically acts with mycorrhiza on the plant root to strongly promote plant growth, nitrogen uptake, and mycorrhization. CONCLUSIONS Our results highlight that AM fungi do not function in isolation and that the plant-mycorrhiza symbiont can recruit beneficial bacteria that support the symbiosis. Video Abstract.
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Affiliation(s)
- Changfeng Zhang
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marcel G A van der Heijden
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Bethany K Dodds
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Thi Bich Nguyen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Jelle Spooren
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Alain Valzano-Held
- Plant Soil Interactions, Division Agroecology and Environment, Agroscope, Reckenholzstrasse 191, CH-8046, Zürich, Switzerland
| | - Marco Cosme
- Mycology, Earth and Life Institute, Université Catholique de Louvain, Louvain-La-Neuve, Belgium
- Plants and Ecosystems, Biology Department, University of Antwerp, Antwerp, Belgium
| | - Roeland L Berendsen
- Plant-Microbe Interactions, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands.
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17
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Hu G, Zhou Y, Mou D, Qu J, Luo L, Duan L, Xu Z, Zou X. Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen. Microbiol Spectr 2024; 12:e0117923. [PMID: 38099615 PMCID: PMC10783027 DOI: 10.1128/spectrum.01179-23] [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: 03/19/2023] [Accepted: 11/04/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.
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Affiliation(s)
- Gongping Hu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yeming Zhou
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Dan Mou
- Department of Humanities, Business College of Guizhou University of Finance and Economics, Qiannan, Guizhou, China
| | - Jiaojiao Qu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
- Tea College, Guizhou University, Guiyang, Guizhou, China
| | - Li Luo
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Lin Duan
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Zhongshun Xu
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Xiao Zou
- Institute of Fungal Resources, College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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18
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Simon E, Guseva K, Darcy S, Alteio L, Pjevac P, Schmidt H, Jenab K, Ranits C, Kaiser C. Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates. THE ISME JOURNAL 2024; 18:wrae156. [PMID: 39105276 PMCID: PMC11325450 DOI: 10.1093/ismejo/wrae156] [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: 04/18/2024] [Revised: 06/29/2024] [Accepted: 08/05/2024] [Indexed: 08/07/2024]
Abstract
Soils provide essential ecosystem services and represent the most diverse habitat on Earth. It has been suggested that the presence of various physico-chemically heterogeneous microhabitats supports the enormous diversity of microbial communities in soil. However, little is known about the relationship between microbial communities and their immediate environment at the micro- to millimetre scale. In this study, we examined whether bacteria, archaea, and fungi organize into distinct communities in individual 2-mm-sized soil aggregates and compared them to communities of homogenized bulk soil samples. Furthermore, we investigated their relationship to their local environment by concomitantly determining microbial community structure and physico-chemical properties from the same individual aggregates. Aggregate communities displayed exceptionally high beta-diversity, with 3-4 aggregates collectively capturing more diversity than their homogenized parent soil core. Up to 20%-30% of ASVs (particularly rare ones) were unique to individual aggregates selected within a few centimetres. Aggregates and bulk soil samples showed partly different dominant phyla, indicating that taxa that are potentially driving biogeochemical processes at the small scale may not be recognized when analysing larger soil volumes. Microbial community composition and richness of individual aggregates were closely related to aggregate-specific carbon and nitrogen content, carbon stable-isotope composition, and soil moisture, indicating that aggregates provide a stable environment for sufficient time to allow co-development of communities and their environment. We conclude that the soil microbiome is a metacommunity of variable subcommunities. Our study highlights the necessity to study small, spatially coherent soil samples to better understand controls of community structure and community-mediated processes in soils.
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Affiliation(s)
- Eva Simon
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Ksenia Guseva
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Sean Darcy
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Lauren Alteio
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, 3430 Tulln, Austria
| | - Petra Pjevac
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
| | - Hannes Schmidt
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Kian Jenab
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christian Ranits
- Doctoral School in Microbiology and Environmental Science, University of Vienna, 1030 Vienna, Austria
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1030 Vienna, Austria
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19
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Dreyling L, Penone C, Schenk NV, Schmitt I, Dal Grande F. Biotic interactions outweigh abiotic factors as drivers of bark microbial communities in Central European forests. ISME COMMUNICATIONS 2024; 4:ycae012. [PMID: 38500703 PMCID: PMC10945369 DOI: 10.1093/ismeco/ycae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Indexed: 03/20/2024]
Abstract
Bark surfaces are extensive areas within forest ecosystems, which provide an ideal habitat for microbial communities, through their longevity and seasonal stability. Here we provide a comprehensive account of the bark surface microbiome of living trees in Central European forests, and identify drivers of diversity and community composition. We examine algal, fungal, and bacterial communities and their interactions using metabarcoding on samples from over 750 trees collected in the Biodiversity Exploratories in northern, central, and southern Germany. We show that mutual biotic influence is more important than the abiotic environment with regard to community composition, whereas abiotic conditions and geography are more important for alpha diversity. Important abiotic factors are the relative humidity and light availability, which decrease the algal and bacterial alpha diversity but strongly increase fungal alpha diversity. In addition, temperature is important in shaping the microbial community, with higher temperature leading to homogeneous communities of dominant fungi, but high turnover in bacterial communities. Changes in the community dissimilarity of one organismal group occur in close relation to changes in the other two, suggesting that there are close interactions between the three major groups of the bark surface microbial communities, which may be linked to beneficial exchange. To understand the functioning of the forest microbiome as a whole, we need to further investigate the functionality of interactions within the bark surface microbiome and combine these results with findings from other forest habitats such as soil or canopy.
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Affiliation(s)
- Lukas Dreyling
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Goethe University Frankfurt, Institute of Ecology, Evolution and Diversity, Frankfurt am Main 60438, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main 60325, Germany
- Department of Biology, University of Padova, Padua 35122, Italy
- National Biodiversity Future Center (NBFC), Palermo 90133, Italy
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20
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Burz SD, Causevic S, Dal Co A, Dmitrijeva M, Engel P, Garrido-Sanz D, Greub G, Hapfelmeier S, Hardt WD, Hatzimanikatis V, Heiman CM, Herzog MKM, Hockenberry A, Keel C, Keppler A, Lee SJ, Luneau J, Malfertheiner L, Mitri S, Ngyuen B, Oftadeh O, Pacheco AR, Peaudecerf F, Resch G, Ruscheweyh HJ, Sahin A, Sanders IR, Slack E, Sunagawa S, Tackmann J, Tecon R, Ugolini GS, Vacheron J, van der Meer JR, Vayena E, Vonaesch P, Vorholt JA. From microbiome composition to functional engineering, one step at a time. Microbiol Mol Biol Rev 2023; 87:e0006323. [PMID: 37947420 PMCID: PMC10732080 DOI: 10.1128/mmbr.00063-23] [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] [Indexed: 11/12/2023] Open
Abstract
SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.
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Affiliation(s)
- Sebastian Dan Burz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Senka Causevic
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Alma Dal Co
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Marija Dmitrijeva
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institut de microbiologie, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | | | | | - Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Soon-Jae Lee
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Julien Luneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Bidong Ngyuen
- Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Omid Oftadeh
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences, CHUV University Hospital Lausanne, Lausanne, Switzerland
| | | | - Asli Sahin
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Ian R. Sanders
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Emma Slack
- Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | | | - Janko Tackmann
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Robin Tecon
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, EPF Lausanne, Lausanne, Switzerland
| | - Pascale Vonaesch
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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21
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Antón-Herrero R, Chicca I, García-Delgado C, Crognale S, Lelli D, Gargarello RM, Herrero J, Fischer A, Thannberger L, Eymar E, Petruccioli M, D’Annibale A. Main Factors Determining the Scale-Up Effectiveness of Mycoremediation for the Decontamination of Aliphatic Hydrocarbons in Soil. J Fungi (Basel) 2023; 9:1205. [PMID: 38132804 PMCID: PMC10745009 DOI: 10.3390/jof9121205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/07/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Soil contamination constitutes a significant threat to the health of soil ecosystems in terms of complexity, toxicity, and recalcitrance. Among all contaminants, aliphatic petroleum hydrocarbons (APH) are of particular concern due to their abundance and persistence in the environment and the need of remediation technologies to ensure their removal in an environmentally, socially, and economically sustainable way. Soil remediation technologies presently available on the market to tackle soil contamination by petroleum hydrocarbons (PH) include landfilling, physical treatments (e.g., thermal desorption), chemical treatments (e.g., oxidation), and conventional bioremediation. The first two solutions are costly and energy-intensive approaches. Conversely, bioremediation of on-site excavated soil arranged in biopiles is a more sustainable procedure. Biopiles are engineered heaps able to stimulate microbial activity and enhance biodegradation, thus ensuring the removal of organic pollutants. This soil remediation technology is currently the most environmentally friendly solution available on the market, as it is less energy-intensive and has no detrimental impact on biological soil functions. However, its major limitation is its low removal efficiency, especially for long-chain hydrocarbons (LCH), compared to thermal desorption. Nevertheless, the use of fungi for remediation of environmental contaminants retains the benefits of bioremediation treatments, including low economic, social, and environmental costs, while attaining removal efficiencies similar to thermal desorption. Mycoremediation is a widely studied technology at lab scale, but there are few experiences at pilot scale. Several factors may reduce the overall efficiency of on-site mycoremediation biopiles (mycopiles), and the efficiency detected in the bench scale. These factors include the bioavailability of hydrocarbons, the selection of fungal species and bulking agents and their application rate, the interaction between the inoculated fungi and the indigenous microbiota, soil properties and nutrients, and other environmental factors (e.g., humidity, oxygen, and temperature). The identification of these factors at an early stage of biotreatability experiments would allow the application of this on-site technology to be refined and fine-tuned. This review brings together all mycoremediation work applied to aliphatic petroleum hydrocarbons (APH) and identifies the key factors in making mycoremediation effective. It also includes technological advances that reduce the effect of these factors, such as the structure of mycopiles, the application of surfactants, and the control of environmental factors.
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Affiliation(s)
- Rafael Antón-Herrero
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | | | - Carlos García-Delgado
- Department of Geology and Geochemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Silvia Crognale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Davide Lelli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Romina Mariel Gargarello
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | - Jofre Herrero
- Water, Air and Soil Unit, Eurecat, Centre Tecnològic de Catalunya, 08242 Manresa, Spain; (R.M.G.); (J.H.)
| | | | | | - Enrique Eymar
- Department of Agricultural Chemistry and Food Science, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (R.A.-H.); (E.E.)
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
| | - Alessandro D’Annibale
- Department for Innovation in Biological, Agri-Food and Forestry Systems, University of Tuscia, 01100 Tuscia, Italy; (S.C.); (D.L.); (M.P.); (A.D.)
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22
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Wippel K. Plant and microbial features governing an endophytic lifestyle. CURRENT OPINION IN PLANT BIOLOGY 2023; 76:102483. [PMID: 37939457 DOI: 10.1016/j.pbi.2023.102483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/10/2023]
Abstract
Beneficial microorganisms colonizing internal plant tissues, the endophytes, support their host through plant growth promotion, pathogen protection, and abiotic stress alleviation. Their efficient application in agriculture requires the understanding of the molecular mechanisms and environmental conditions that facilitate in planta accommodation. Accumulating evidence reveals that commensal microorganisms employ similar colonization strategies as their pathogenic counterparts. Fine-tuning of immune response, motility, and metabolic crosstalk accounts for their differentiation. For a holistic perspective, in planta experiments with microbial collections and comprehensive genome data exploration are crucial. This review describes the most recent findings on factors involved in endophytic colonization processes, focusing on bacteria and fungi, and discusses required methodological approaches to unravel their relevance within a community context.
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Affiliation(s)
- Kathrin Wippel
- Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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23
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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24
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Buffi M, Cailleau G, Kuhn T, Li Richter XY, Stanley CE, Wick LY, Chain PS, Bindschedler S, Junier P. Fungal drops: a novel approach for macro- and microscopic analyses of fungal mycelial growth. MICROLIFE 2023; 4:uqad042. [PMID: 37965130 PMCID: PMC10642649 DOI: 10.1093/femsml/uqad042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
This study presents an inexpensive approach for the macro- and microscopic observation of fungal mycelial growth. The 'fungal drops' method allows to investigate the development of a mycelial network in filamentous microorganisms at the colony and hyphal scales. A heterogeneous environment is created by depositing 15-20 µl drops on a hydrophobic surface at a fixed distance. This system is akin to a two-dimensional (2D) soil-like structure in which aqueous-pockets are intermixed with air-filled pores. The fungus (spores or mycelia) is inoculated into one of the drops, from which hyphal growth and exploration take place. Hyphal structures are assessed at different scales using stereoscopic and microscopic imaging. The former allows to evaluate the local response of regions within the colony (modular behaviour), while the latter can be used for fractal dimension analyses to describe the hyphal network architecture. The method was tested with several species to underpin the transferability to multiple species. In addition, two sets of experiments were carried out to demonstrate its use in fungal biology. First, mycelial reorganization of Fusarium oxysporum was assessed as a response to patches containing different nutrient concentrations. Second, the effect of interactions with the soil bacterium Pseudomonas putida on habitat colonization by the same fungus was assessed. This method appeared as fast and accessible, allowed for a high level of replication, and complements more complex experimental platforms. Coupled with image analysis, the fungal drops method provides new insights into the study of fungal modularity both macroscopically and at a single-hypha level.
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Affiliation(s)
- Matteo Buffi
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Thierry Kuhn
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Department of Bioengineering, Imperial College London, B304, Bessemer Building, South Kensington Campus, SW7 2AZ, London, United Kingdom
| | - Lukas Y Wick
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Patrick S Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, P.O. Box 1663, NM 87545, United States
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland
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25
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Maucourt F, Cébron A, Budzinski H, Le Menach K, Peluhet L, Czarnes S, Melayah D, Chapulliot D, Vallon L, Plassart G, Hugoni M, Fraissinet-Tachet L. Prokaryotic, Microeukaryotic, and Fungal Composition in a Long-Term Polychlorinated Biphenyl-Contaminated Brownfield. MICROBIAL ECOLOGY 2023; 86:1696-1708. [PMID: 36646913 DOI: 10.1007/s00248-022-02161-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.
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Affiliation(s)
- Flavien Maucourt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- ENVISOL, 2-4 Rue Hector Berlioz, 38110, La Tour du Pin, France
| | - Aurélie Cébron
- Université de Lorraine, CNRS, LIEC, 54000, Nancy, France
| | | | | | | | - Sonia Czarnes
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Delphine Melayah
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation Et Pathogénie, 69621, Villeurbanne, France
| | - David Chapulliot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Laurent Vallon
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
| | - Gaël Plassart
- ENVISOL, 2-4 Rue Hector Berlioz, 38110, La Tour du Pin, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France
- Univ Lyon, INSA Lyon, CNRS, UMR 5240 Microbiologie Adaptation Et Pathogénie, 69621, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Laurence Fraissinet-Tachet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622, Villeurbanne, France.
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26
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Yao D, Wang N, Dai W, Liu Y, Tian K, Wang H, Liu Y. Degradation of benzo [a] pyrene in the soil enhanced by soapwort: The role of soapwort and functional microbial community. JOURNAL OF HAZARDOUS MATERIALS 2023; 458:131993. [PMID: 37423134 DOI: 10.1016/j.jhazmat.2023.131993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/20/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
The limited bioavailability of polycyclic aromatic hydrocarbons (PAHs) in soils poses a challenge for their biodegradation. We hypotheses soapwort (Saponaria officinalis L.) as a factory in-situ providing biosurfactant, which could effectively promote the BaP removal by exogenous or native functional microbes. Rhizo-box and microcosm experiments were conducted to analyze the phyto-microbial remediation mechanism of soapwort, a plant that excretes biosurfactants known as saponins, and combined with two exogenous strains (P. chrysosporium and/or B. subtilis) for benzo[a]pyrene (BaP)-contaminated soils. The results revealed that the natural attenuation treatment (CK) BaP achieved only a 15.90% BaP removal rate after 100 days. In contrast, soapwort (SP), soapwort-bacteria (SPB), soapwort-fungus (SPF), soapwort- bacteria - fungus (SPM) mediated rhizosphere soils treatments yielded removal rates of 40.48%, 42.42%, 52.37%, and 62.57%, respectively. The analysis of the microbial community structure suggested that soapwort stimulated the introduction and native functional microorganisms, such as Rhizobiales, Micrococcales, and Clostridiales, which contributed to BaP removal via metabolic pathways. Furthermore, the efficient BaP removal was attributed to saponins, amino acids, and carbohydrates, which facilitated mobilization, solubilization of BaP, and microbial activity. In conclusion, our study highlights the potential of soapwort and specific microbial strains to effectively remediate PAH-contaminated soils.
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Affiliation(s)
- Dandan Yao
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Ning Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Wei Dai
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Yang Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Kun Tian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
| | - Hui Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China.
| | - Yun Liu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China; University of Chinese Academy of Sciences, Nanjing, 211135, China
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27
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AbuQamar SF, Abd El-Fattah HI, Nader MM, Zaghloul RA, Abd El-Mageed TA, Selim S, Omar BA, Mosa WF, Saad AM, El-Tarabily KA, El-Saadony MT. Exploiting fungi in bioremediation for cleaning-up emerging pollutants in aquatic ecosystems. MARINE ENVIRONMENTAL RESEARCH 2023; 190:106068. [PMID: 37421706 DOI: 10.1016/j.marenvres.2023.106068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/04/2023] [Accepted: 06/22/2023] [Indexed: 07/10/2023]
Abstract
Aquatic pollution negatively affects water bodies, marine ecosystems, public health, and economy. Restoration of contaminated habitats has attracted global interest since protecting the health of marine ecosystems is crucial. Bioremediation is a cost-effective and eco-friendly way of transforming hazardous, resistant contaminants into environmentally benign products using diverse biological treatments. Because of their robust morphology and broad metabolic capabilities, fungi play an important role in bioremediation. This review summarizes the features employed by aquatic fungi for detoxification and subsequent bioremediation of different toxic and recalcitrant compounds in aquatic ecosystems. It also details how mycoremediation may convert chemically-suspended matters, microbial, nutritional, and oxygen-depleting aquatic contaminants into ecologically less hazardous products using multiple modes of action. Mycoremediation can also be considered in future research studies on aquatic, including marine, ecosystems as a possible tool for sustainable management, providing a foundation for selecting and utilizing fungi either independently or in microbial consortia.
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Affiliation(s)
- Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Hassan I Abd El-Fattah
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Maha M Nader
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Rashed A Zaghloul
- Department of Agricultural Microbiology, Faculty of Agriculture, Moshtohor, Benha University, Benha, 13511, Egypt
| | - Taia A Abd El-Mageed
- Department of Soils and Water, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72388, Saudi Arabia
| | - Belal A Omar
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Walid F Mosa
- Plant Production Department (Horticulture-Pomology), Faculty of Agriculture Saba Basha, Alexandria University, Alexandria, 21526, Egypt
| | - Ahmed M Saad
- Department of Biochemistry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, 15551, United Arab Emirates.
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
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28
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Hou R, Zhang S, Huang Q, Lin L, Li H, Li J, Liu S, Sun C, Xu X. Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:11476-11488. [PMID: 37462611 DOI: 10.1021/acs.est.3c03595] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.
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Affiliation(s)
- Rui Hou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Siqi Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianyi Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lang Lin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Hengxiang Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Jingxi Li
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shan Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
| | - Chengjun Sun
- Key Laboratory of Marine Eco-environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Xiangrong Xu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya 572100, China
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Hoosein S, Neuenkamp L, Trivedi P, Paschke MW. AM fungal-bacterial relationships: what can they tell us about ecosystem sustainability and soil functioning? FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1141963. [PMID: 37746131 PMCID: PMC10512368 DOI: 10.3389/ffunb.2023.1141963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/05/2023] [Indexed: 09/26/2023]
Abstract
Considering our growing population and our continuous degradation of soil environments, understanding the fundamental ecology of soil biota and plant microbiomes will be imperative to sustaining soil systems. Arbuscular mycorrhizal (AM) fungi extend their hyphae beyond plant root zones, creating microhabitats with bacterial symbionts for nutrient acquisition through a tripartite symbiotic relationship along with plants. Nonetheless, it is unclear what drives these AM fungal-bacterial relationships and how AM fungal functional traits contribute to these relationships. By delving into the literature, we look at the drivers and complexity behind AM fungal-bacterial relationships, describe the shift needed in AM fungal research towards the inclusion of interdisciplinary tools, and discuss the utilization of bacterial datasets to provide contextual evidence behind these complex relationships, bringing insights and new hypotheses to AM fungal functional traits. From this synthesis, we gather that interdependent microbial relationships are at the foundation of understanding microbiome functionality and deciphering microbial functional traits. We suggest using pattern-based inference tools along with machine learning to elucidate AM fungal-bacterial relationship trends, along with the utilization of synthetic communities, functional gene analyses, and metabolomics to understand how AM fungal and bacterial communities facilitate communication for the survival of host plant communities. These suggestions could result in improving microbial inocula and products, as well as a better understanding of complex relationships in terrestrial ecosystems that contribute to plant-soil feedbacks.
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Affiliation(s)
- Shabana Hoosein
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Lena Neuenkamp
- Institute of Landscape Ecology, Münster University, Münster, Germany
- Department of Ecology and Multidisciplinary Institute for Environment Studies “Ramon Margalef,” University of Alicante, Alicante, Spain
| | - Pankaj Trivedi
- Microbiome Network, Department of Agricultural Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
| | - Mark W. Paschke
- Department of Forest and Rangeland Stewardship/Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, United States
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Maucourt F, Doumèche B, Chapulliot D, Vallon L, Nazaret S, Fraissinet-Tachet L. Polychlorinated Biphenyl Transformation, Peroxidase and Oxidase Activities of Fungi and Bacteria Isolated from a Historically Contaminated Site. Microorganisms 2023; 11:1887. [PMID: 37630447 PMCID: PMC10457763 DOI: 10.3390/microorganisms11081887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Causing major health and ecological disturbances, polychlorinated biphenyls (PCBs) are persistent organic pollutants still recovered all over the world. Microbial PCB biotransformation is a promising technique for depollution, but the involved molecular mechanisms remain misunderstood. Ligninolytic enzymes are suspected to be involved in many PCB transformations, but their assessments remain scarce. To further inventory the capabilities of microbes to transform PCBs through their ligninolytic enzymes, we investigated the role of oxidase and peroxidase among a set of microorganisms isolated from a historically PCB-contaminated site. Among 29 isolated fungi and 17 bacteria, this work reports for the first time the PCB-transforming capabilities from fungi affiliated to Didymella, Dothiora, Ilyonectria, Naganishia, Rhodoturula, Solicoccozyma, Thelebolus and Truncatella genera and bacteria affiliated to Peribacillus frigotolerans, Peribacillus muralis, Bacillus mycoides, Bacillus cereus, Bacillus toyonensis, Pseudarthrobacter sp., Pseudomonas chlororaphis, Erwinia aphidicola and Chryseobacterium defluvii. In the same way, this is the first report of fungal isolates affiliated to the Dothiora maculans specie and Cladosporium genus that displayed oxidase (putatively laccase) and peroxidase activity, respectively, enhanced in the presence of PCBs (more than 4-fold and 20-fold, respectively, compared to controls). Based on these results, the observed activities are suspected to be involved in PCB transformation.
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Affiliation(s)
- Flavien Maucourt
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
- ENVISOL, 2-4 Rue Hector Berlioz, F-38110 La Tour du Pin, France
| | - Bastien Doumèche
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS 5246 ICBMS, F-69622 Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurent Vallon
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Sylvie Nazaret
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laurence Fraissinet-Tachet
- Université de Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
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31
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Maqsood Q, Sumrin A, Waseem R, Hussain M, Imtiaz M, Hussain N. Bioengineered microbial strains for detoxification of toxic environmental pollutants. ENVIRONMENTAL RESEARCH 2023; 227:115665. [PMID: 36907340 DOI: 10.1016/j.envres.2023.115665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 05/08/2023]
Abstract
Industrialization and other anthropogenic human activities pose significant environmental risks. As a result of the hazardous pollution, numerous living organisms may suffer from undesirable diseases in their separate habitats. Bioremediation, which removes hazardous compounds from the environment using microbes or their biologically active metabolites, is one of the most successful remediation approaches. According to the United Nations Environment Program (UNEP), deteriorating soil health negatively impacts food security and human health over time. Soil health restoration is critical right now. Microbes are widely known for their importance in cleaning up toxins present in the soil, such as heavy metals, pesticides, and hydrocarbons. However, the capacity of local bacteria to digest these pollutants is limited, and the process takes an extended time. Genetically modified organisms (GMOs), whose altered metabolic pathways promote the over-secretion of a variety of proteins favorable to the bioremediation process, can speed up the breakdown process. The need for remediation procedures, degrees of soil contamination, site circumstances, broad adoptions, and numerous possibilities occurring at various cleaning stages are all studied in detail. Massive efforts to restore contaminated soils have also resulted in severe issues. This review focuses on the enzymatic removal of hazardous pollutants from the environment, such as pesticides, heavy metals, dyes, and plastics. There are also in-depth assessments of present discoveries and future plans for efficient enzymatic degradation of hazardous pollutants.
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Affiliation(s)
- Quratulain Maqsood
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aleena Sumrin
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Rafia Waseem
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Maria Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mehwish Imtiaz
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nazim Hussain
- Center for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
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Sherry A, Dell’Agnese BM, Scott J. Biohybrids: Textile fibres provide scaffolds and highways for microbial translocation. Front Bioeng Biotechnol 2023; 11:1188965. [PMID: 37383521 PMCID: PMC10293675 DOI: 10.3389/fbioe.2023.1188965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: Living materials (biohybrids, textile-microbial hybrids, hybrid living materials) have gained much attention in recent years with enormous potential for applications in biomedical science, the built environment, construction and architecture, drug delivery and as environmental biosensors. Living materials contain matrices which incorporate microorganisms or biomolecules as the bioactive components. A cross-disciplinary approach, operating at the intersection of creative practice and scientific research, incorporated textile technology and microbiology to demonstrate textile fibres providing microbial scaffolds and highways during this study. Methods: The study evolved from previous research which showed bacteria utilising the water layer surrounding fungal mycelium for motility, termed the 'fungal highway', which led to the investigation of the directional dispersal of microbes across a range of fibre types (natural and synthetic). The application of the study centred around the potential for biohybrids to be used as a biotechnology to improve oil bioremediation through seeding of hydrocarbon-degrading microbes into polluted environments via fungal or fibre highways, therefore treatments in the presence of crude oil were tested. Furthermore, from a design perspective, textiles have huge potential to act as a conduit for water and nutrients, essential to sustain microorganisms within living materials. Using the moisture absorption properties of natural fibres, the research explored how to engineer variable liquid absorption rates using cellulosics and wool to produce shape-changing knitted fabrics suitable for adaptation to oil spill capture. Results: At a cellular scale, confocal microscopy provided evidence to show that bacteria were able to utilise a water layer surrounding the fibres, supporting the hypothesis that fibres can aid bacterial translocation through their use as 'fibre highways'. A motile bacterial culture, Pseudomonas putida, was shown to translocate around a liquid layer surrounding polyester, nylon, and linen fibres, yet no evidence of translocation was apparent on silk or wool fibres, suggesting microbes elicit different responses to specific fibre types. Findings showed that translocation activity around highways did not diminish in the presence of crude oil, known to contain an abundance of toxic compounds, in comparison to oil-free controls. A design series demonstrated the growth of fungal mycelium (Pleurotus ostreatus) through knitted structures, highlighting the ability for natural fabrics to provide a scaffold to support microbial communities whilst retaining the ability to undergo environmentally responsive shape-change. A final prototype, Ebb&Flow, demonstrated the potential to scale up the responsive capacities of the material system using locally produced UK wool. The prototype conceptualised both the uptake of a hydrocarbon pollutant by fibres, and the translocation of microbes along fibre highways. Discussion: The research works towards facilitating the translation of fundamental science and design into biotechnological solutions that can be used in real world applications.
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Affiliation(s)
- Angela Sherry
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Bruna Martins Dell’Agnese
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Jane Scott
- Hub for Biotechnology in the Built Environment, School of Architecture Planning and Landscape, Newcastle University, Newcastle upon Tyne, United Kingdom
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Richter I, Wein P, Uzum Z, Stanley CE, Krabbe J, Molloy EM, Moebius N, Ferling I, Hillmann F, Hertweck C. Transcription activator-like effector protects bacterial endosymbionts from entrapment within fungal hyphae. Curr Biol 2023:S0960-9822(23)00623-1. [PMID: 37301202 DOI: 10.1016/j.cub.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/12/2023]
Abstract
As an endosymbiont of the ecologically and medically relevant fungus Rhizopus microsporus, the toxin-producing bacterium Mycetohabitans rhizoxinica faces myriad challenges, such as evading the host's defense mechanisms. However, the bacterial effector(s) that facilitate the remarkable ability of M. rhizoxinica to freely migrate within fungal hyphae have thus far remained unknown. Here, we show that a transcription activator-like (TAL) effector released by endobacteria is an essential symbiosis factor. By combining microfluidics with fluorescence microscopy, we observed enrichment of TAL-deficient M. rhizoxinica in side hyphae. High-resolution live imaging showed the formation of septa at the base of infected hyphae, leading to the entrapment of endobacteria. Using a LIVE/DEAD stain, we demonstrate that the intracellular survival of trapped TAL-deficient bacteria is significantly reduced compared with wild-type M. rhizoxinica, indicative of a protective host response in the absence of TAL proteins. Subversion of host defense in TAL-competent endobacteria represents an unprecedented function of TAL effectors. Our data illustrate an unusual survival strategy of endosymbionts in the host and provide deeper insights into the dynamic interactions between bacteria and eukaryotes.
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Affiliation(s)
- Ingrid Richter
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Wein
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zerrin Uzum
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Claire E Stanley
- Department of Bioengineering, Imperial College, South Kensington, London SW7 2AZ, UK
| | - Jana Krabbe
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Evelyn M Molloy
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Nadine Moebius
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Iuliia Ferling
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Falk Hillmann
- Junior Research Group Evolution of Microbial Interactions, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745 Jena, Germany; Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany.
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Chiba de Castro WA, Vaz GCDO, da Silva Matos DM, Vale AH, Bueno ACP, Fagundes LFG, da Costa L, Bonugli Santos RC. The Invasive Tradescantia zebrina Affects Litter Decomposition, but It Does Not Change the Lignocellulolytic Fungal Community in the Atlantic Forest, Brazil. PLANTS (BASEL, SWITZERLAND) 2023; 12:2162. [PMID: 37299140 PMCID: PMC10255722 DOI: 10.3390/plants12112162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Invasive plants affect ecosystems across various scales. In particular, they affect the quality and quantity of litter, which influences the composition of decomposing (lignocellulolytic) fungal communities. However, the relationship among the quality of invasive litter, lignocellulolytic cultivated fungal community composition, and litter decomposition rates under invasive conditions is still unknown. We evaluated whether the invasive herbaceous Tradescantia zebrina affects the litter decomposition in the Atlantic Forest and the lignocellulolytic cultivated fungal community composition. We placed litter bags with litter from the invader and native plants in invaded and non-invaded areas, as well as under controlled conditions. We evaluated the lignocellulolytic fungal communities by culture method and molecular identification. Litter from T. zebrina decomposed faster than litter from native species. However, the invasion of T. zebrina did not alter decomposition rates of either litter type. Although the lignocellulolytic fungal community composition changed over decomposition time, neither the invasion of T. zebrina nor litter type influenced lignocellulolytic fungal communities. We believe that the high plant richness in the Atlantic Forest enables a highly diversified and stable decomposing biota formed in conditions of high plant diversity. This diversified fungal community is capable of interacting with different litter types under different environmental conditions.
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Affiliation(s)
- Wagner Antonio Chiba de Castro
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Giselle Cristina de Oliveira Vaz
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Dalva Maria da Silva Matos
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Department of Hydrobiology, Federal University of São Carlos, São Carlos 13600-970, SP, Brazil
| | - Alvaro Herrera Vale
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Any Caroline Pantaleão Bueno
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Luiz Fernando Grandi Fagundes
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Letícia da Costa
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
| | - Rafaella Costa Bonugli Santos
- Neotropical Biodiversity Graduate Program, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
- Latin American Institute of Life and Nature Sciences, Federal University of Latin American Integration, Foz do Iguaçu 85866-000, PR, Brazil
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Álvarez-Barragán J, Cravo-Laureau C, Xiong B, Wick LY, Duran R. Marine Fungi Select and Transport Aerobic and Anaerobic Bacterial Populations from Polycyclic Aromatic Hydrocarbon-Contaminated Sediments. mBio 2023; 14:e0276122. [PMID: 36786561 PMCID: PMC10127579 DOI: 10.1128/mbio.02761-22] [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: 10/01/2022] [Accepted: 01/23/2023] [Indexed: 02/15/2023] Open
Abstract
The organization of microbial communities in marine sediment relies on complex biotic and abiotic interactions. Among them, the interaction between fungi and bacteria plays a crucial role building specific microbial assemblages, resulting in metabolic networks adapted to environmental conditions. The fungal-bacterial interaction (FBI) includes bacterial translocation via fungal mycelia, allowing bacterial dispersion, and ecological niche colonization. In order to demonstrate that the translocation of bacteria through fungal mycelia involves bacterial selection, the mycelia of two fungi isolated from marine coastal sediment, Alternaria destruens F10.81 and Fusarium pseudonygamai F5.76, showing different strategies for uptake of polycyclic aromatic hydrocarbon (PAH), homogenous internalization and vacuole forming respectively, were used to translocate bacteria through hydrophobic hydrocarbon contaminated sediments. A. destruens F10.81 selected four specific bacteria, while bacterial selection by F. pseudonygamai F5.76 was not evident. Among the bacteria selected by A. destruens F10.81, Spirochaeta litoralis, known as strictly anaerobic bacterium, was identified, indicating that A. destruens F10.81 selects and transports both aerobic and anaerobic bacteria. Such a result is consistent with the observed formation of anoxic micro-niches in areas surrounding and affected by fungal hyphae. Our findings provide new insights on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. IMPORTANCE The study provides advances for understanding fungal-bacterial relationships, particularly on the selection and dispersion of bacterial communities by fungi, which are crucial for the organization of microbial communities and their functioning in coastal PAH-contaminated sediments. The transportation of bacteria via fungal hyphae (fungal highway) results in bacterial selection; in particular, fungal hyphae offer adequate conditions for the transport of both aerobic and anaerobic bacteria through hydrophobic patches for the colonization of novel niches.
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Affiliation(s)
| | | | - Bijing Xiong
- Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - Lukas Y. Wick
- Helmholtz Centre for Environmental Research–UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - Robert Duran
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau, France
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Khan N, Muge E, Mulaa FJ, Wamalwa B, von Bergen M, Jehmlich N, Wick LY. Mycelial nutrient transfer promotes bacterial co-metabolic organochlorine pesticide degradation in nutrient-deprived environments. THE ISME JOURNAL 2023; 17:570-578. [PMID: 36707614 PMCID: PMC10030463 DOI: 10.1038/s41396-023-01371-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/28/2023]
Abstract
Biotransformation of soil organochlorine pesticides (OCP) is often impeded by a lack of nutrients relevant for bacterial growth and/or co-metabolic OCP biotransformation. By providing space-filling mycelia, fungi promote contaminant biodegradation by facilitating bacterial dispersal and the mobilization and release of nutrients in the mycosphere. We here tested whether mycelial nutrient transfer from nutrient-rich to nutrient-deprived areas facilitates bacterial OCP degradation in a nutrient-deficient habitat. The legacy pesticide hexachlorocyclohexane (HCH), a non-HCH-degrading fungus (Fusarium equiseti K3), and a co-metabolically HCH-degrading bacterium (Sphingobium sp. S8) isolated from the same HCH-contaminated soil were used in spatially structured model ecosystems. Using 13C-labeled fungal biomass and protein-based stable isotope probing (protein-SIP), we traced the incorporation of 13C fungal metabolites into bacterial proteins while simultaneously determining the biotransformation of the HCH isomers. The relative isotope abundance (RIA, 7.1-14.2%), labeling ratio (LR, 0.13-0.35), and the shape of isotopic mass distribution profiles of bacterial peptides indicated the transfer of 13C-labeled fungal metabolites into bacterial proteins. Distinct 13C incorporation into the haloalkane dehalogenase (linB) and 2,5-dichloro-2,5-cyclohexadiene-1,4-diol dehydrogenase (LinC), as key enzymes in metabolic HCH degradation, underpin the role of mycelial nutrient transport and fungal-bacterial interactions for co-metabolic bacterial HCH degradation in heterogeneous habitats. Nutrient uptake from mycelia increased HCH removal by twofold as compared to bacterial monocultures. Fungal-bacterial interactions hence may play an important role in the co-metabolic biotransformation of OCP or recalcitrant micropollutants (MPs).
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Affiliation(s)
- Nelson Khan
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
- Helmholtz Centre for Environmental Research UFZ, Department of Environmental Microbiology, 04318, Leipzig, Germany
| | - Edward Muge
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
| | - Francis J Mulaa
- University of Nairobi, Department of Biochemistry, 00200-30197, Nairobi, Kenya
| | - Benson Wamalwa
- University of Nairobi, Department of Chemistry, 00200-30197, Nairobi, Kenya
| | - Martin von Bergen
- Helmholtz Centre for Environmental Research UFZ, Department of Molecular Systems Biology, 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research, (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103, Leipzig, Germany
- University of Leipzig, Faculty of Life Sciences, Institute of Biochemistry, Brüderstraße 34, 04103, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz Centre for Environmental Research UFZ, Department of Molecular Systems Biology, 04318, Leipzig, Germany
| | - Lukas Y Wick
- Helmholtz Centre for Environmental Research UFZ, Department of Environmental Microbiology, 04318, Leipzig, Germany.
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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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Arellano-Caicedo C, Ohlsson P, Bengtsson M, Beech JP, Hammer EC. Habitat complexity affects microbial growth in fractal maze. Curr Biol 2023; 33:1448-1458.e4. [PMID: 36933553 DOI: 10.1016/j.cub.2023.02.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/09/2023] [Accepted: 02/21/2023] [Indexed: 03/19/2023]
Abstract
The great variety of earth's microorganisms and their functions are attributed to the heterogeneity of their habitats, but our understanding of the impact of this heterogeneity on microbes is limited at the microscale. In this study, we tested how a gradient of spatial habitat complexity in the form of fractal mazes influenced the growth, substrate degradation, and interactions of the bacterial strain Pseudomonas putida and the fungal strain Coprinopsis cinerea. These strains responded in opposite ways: complex habitats strongly reduced fungal growth but, in contrast, increased the abundance of bacteria. Fungal hyphae did not reach far into the mazes and forced bacteria to grow in deeper regions. Bacterial substrate degradation strongly increased with habitat complexity, even more than bacterial biomass, up to an optimal depth, while the most remote parts of the mazes showed both decreased biomass and substrate degradation. These results suggest an increase in enzymatic activity in confined spaces, where areas may experience enhanced microbial activity and resource use efficiency. Very remote spaces showing a slower turnover of substrates illustrate a mechanism which may contribute to the long-term storage of organic matter in soils. We demonstrate here that the sole effect of spatial microstructures affects microbial growth and substrate degradation, leading to differences in local microscale spatial availability. These differences might add up to considerable changes in nutrient cycling at the macroscale, such as contributing to soil organic carbon storage.
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Affiliation(s)
| | - Pelle Ohlsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Martin Bengtsson
- Department of Biomedical Engineering, Lund University, Ole Römers väg 3, 223 63 Lund, Sweden
| | - Jason P Beech
- Division of Solid State Physics, Lund University, Sölvegatan 16, 223 63 Lund, Sweden
| | - Edith C Hammer
- Department of Biology, Lund University, Sölvegatan 35, 223 62 Lund, Sweden; Centre for Environmental and Climate Science, CEC, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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Hussain M, Zahra N, Lang T, Zain M, Raza M, Shakoor N, Adeel M, Zhou H. Integrating nanotechnology with plant microbiome for next-generation crop health. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:703-711. [PMID: 36809731 DOI: 10.1016/j.plaphy.2023.02.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/02/2023] [Accepted: 02/12/2023] [Indexed: 06/18/2023]
Abstract
Nanotechnology has enormous potential for sustainable agriculture, such as improving nutrient use efficiency, plant health, and food production. Nanoscale modulation of the plant-associated microbiota offers an additional valuable opportunity to increase global crop production and ensure future food and nutrient security. Nanomaterials (NMs) applied to agricultural crops can impact plant and soil microbiota, which offers valuable services to host plants, including the acquisition of nutrients, abiotic stress tolerance, and disease suppression. Dissecting the complex interactions between NMs and plants by integrating multi-omic approaches is providing new insights into how NMs can activate host responses and functionality as well as influence native microbial communities. Such nexus and moving beyond descriptive microbiome studies to hypothesis-driven research will foster microbiome engineering and open up opportunities for the development of synthetic microbial communities to provide agronomic solutions. Herein, we first summarize the significant role of NMs and the plant microbiome in crop productivity and then focus on NMs effects on plant-associated microbiota. We outline three urgent priority research areas and call for a transdisciplinary collaborative approach, involving plant scientists, soil scientists, environmental scientists, ecologists, microbiologists, taxonomists, chemists, physicists, and stakeholders, to advance nano-microbiome research. Detailed understanding of the nanomaterial-plant-microbiome interactions and the mechanisms underlying NMs-mediated shifts in the microbiome assembly and functions may help to exploit the services of both nano-objects and microbiota for next-generation crop health.
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Affiliation(s)
- Muzammil Hussain
- MNR Key Laboratory for Geo-Environmental Monitoring of Great Bay Area & Shenzhen Key Laboratory of Marine Bio-resource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China; College of Physics and Optoelectronic Engineering, Shenzhen University, 518060, Shenzhen, China.
| | - Nosheen Zahra
- Inservice Agricultural Training Institute, Sargodha, 40100, Punjab, Pakistan
| | - Tao Lang
- MNR Key Laboratory for Geo-Environmental Monitoring of Great Bay Area & Shenzhen Key Laboratory of Marine Bio-resource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China; College of Physics and Optoelectronic Engineering, Shenzhen University, 518060, Shenzhen, China
| | - Muhammad Zain
- Department of Botany, University of LakkiMarwat, LakkiMarwat, Khyber Pakhtunkhwa, 28420, Pakistan
| | - Mubashar Raza
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Noman Shakoor
- Beijing Key Laboratory of Farmland Soil Pollution Prevention and Remediation and College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Muhammad Adeel
- BNU-HKUST Laboratory of Green Innovation, Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, Guangdong, China.
| | - Haichao Zhou
- MNR Key Laboratory for Geo-Environmental Monitoring of Great Bay Area & Shenzhen Key Laboratory of Marine Bio-resource and Eco-environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518071, China.
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Microbiome engineering for bioremediation of emerging pollutants. Bioprocess Biosyst Eng 2023; 46:323-339. [PMID: 36029349 DOI: 10.1007/s00449-022-02777-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/12/2022] [Indexed: 11/02/2022]
Abstract
Axenic microbial applications in the open environment are unrealistic and may not be always practically viable. Therefore, it is important to use mixed microbial cultures and their interactions with the microbiome in the targeted ecosystem to perform robust functions towards their sustainability in harsh environmental conditions. Emerging pollutants like phthalates and hydrocarbons that are toxic to several aquatic and terrestrial life forms in the water bodies and lands are an alarming situation. The present review explores the possibility of devising an inclusive eco-friendly strategy like microbiome engineering which proves to be a unique and crucial technology involving the power of microbial communication through quorum sensing. This review discusses the interspecies and intra-species communications between different microbial groups with their respective environments. Moreover, this review also envisages the efforts for designing the next level of microbiome-host engineering concept (MHEC). The focus of the review also extended toward using omics and metabolic network analysis-based tools for effective microbiome engineering. These approaches might be quite helpful in the future to understand such microbial interactions but it will be challenging to implement in the real environment to get the desired functions. Finally, the review also discusses multiple approaches for the bioremediation of toxic chemicals from the soil environment.
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Probst M, Telagathoti A, Siewert B, Khomenko I, Betta E, Biasioli F, Peintner U. Co-cultivation of Mortierellaceae with Pseudomonas helmanticensis affects both their growth and volatilome. Sci Rep 2023; 13:2213. [PMID: 36750680 PMCID: PMC9905594 DOI: 10.1038/s41598-023-29134-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Volatile organic compounds (VOCs) might mediate microbial interactions, especially in spatially structured environments, such as soil. However, the variety and specificity of VOC production are poorly understood. Here, we studied 25 Mortierellaceae strains belonging to the genera Linnemannia and Entomortierella in both pure and co-culture with Pseudomonas helmanticensis under laboratory conditions. We analysed both the fungal growth depending on co-cultivation and the cultures' volatilomes applying proton-transfer-reaction time-of-flight and gas chromatography-mass spectrometry (PTR-ToF-MS and GC-MS). In a strain-specific manner, we found the fungi's radial growth rate and colony morphology affected by the presence of P. helmanticensis. The fungus seemed to generally reduce the bacterial growth. The volatilomes of the fungal and bacterial pure and co-cultures were diverse. While the fungi frequently consumed VOCs, P. helmanticensis produced a higher diversity and amount of VOCs than any fungal strain. Our results support that both the pure and co-culture volatilomes are taxonomically conserved. Taken together, our data supports the relevance of VOCs in Mortierellaceae-P. helmanticensis interaction. We also discuss individual VOCs that appear relevant in the interaction.
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Affiliation(s)
- Maraike Probst
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Anusha Telagathoti
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Bianka Siewert
- Institute of Pharmacy, Center for Chemistry and Biomedicine, Center for Molecular Biosciences Innsbruck (CMBI), Universität Innsbruck, Innrain 80 - 82/IV, 6020, Innsbruck, Austria
| | - Iuliia Khomenko
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Emanuela Betta
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Franco Biasioli
- Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38010, San Michele all'Adige, Italy
| | - Ursula Peintner
- Department of Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Keuschnig C, Martins JMF, Navel A, Simonet P, Larose C. Micro-fractionation shows microbial community changes in soil particles below 20 μm. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1091773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
IntroductionMicro-scale analysis of microbes in soil is essential to the overall understanding of microbial organization, interactions, and ecosystem functioning. Soil fractionation according to its aggregated structure has been used to access microbial habitats. While bacterial communities have been extensively described, little is known about the fungal communities at scales relevant to microbial interactions.MethodsWe applied a gentle soil fractionation method to preserve stable aggregated structures within the range of micro-aggregates and studied fungal and bacterial communities as well as nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size fractions (PSFs; >250 μm, 250–63 μm, 63–20 μm, 20–2 μm, <2 μm, and supernatant).ResultsOverall bacterial and fungal community structures changed in PSFs below 20 μm. The relative abundance of Basidiomycota decreased with decreasing particle size over the entire measure range, while Ascomycota showed an increase and Mucoromycota became more prominent in particles below 20 μm. Bacterial diversity was found highest in the < 2 μm fraction, but only a few taxa were washed-off during the procedure and found in supernatant samples. These taxa have been associated with exopolysaccharide production and biofilm formation (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium, and Variovorax). The potential for nitrogen reduction was found elevated in bigger aggregates.DiscussionThe observed changes below 20 μm particle are in line with scales where microbes operate and interact, highlighting the potential to focus on little researched sub-fractions of micro-aggregates. The applied method shows potential for use in studies focusing on the role of microbial biofilms in soil and might also be adapted to research various other soil microbial functions. Technical advances in combination with micro-sampling methods in soil promise valuable output in soil studies when particles below 20 μm are included.
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Ruan C, Ramoneda J, Gogia G, Wang G, Johnson DR. Fungal hyphae regulate bacterial diversity and plasmid-mediated functional novelty during range expansion. Curr Biol 2022; 32:5285-5294.e4. [PMID: 36455559 DOI: 10.1016/j.cub.2022.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/20/2022] [Accepted: 11/03/2022] [Indexed: 12/05/2022]
Abstract
The amount of bacterial diversity present on many surfaces is enormous; however, how these levels of diversity persist in the face of the purifying processes that occur as bacterial communities expand across space (referred to here as range expansion) remains enigmatic. We shed light on this apparent paradox by providing mechanistic evidence for a strong role of fungal hyphae-mediated dispersal on regulating bacterial diversity during range expansion. Using pairs of fluorescently labeled bacterial strains and a hyphae-forming fungal strain that expand together across a nutrient-amended surface, we show that a hyphal network increases the spatial intermixing and extent of range expansion of the bacterial strains. This is true regardless of the type of interaction (competition or resource cross-feeding) imposed between the bacterial strains. We further show that the underlying cause is that flagellar motility drives bacterial dispersal along the hyphal network, which counteracts the purifying effects of ecological drift at the expansion frontier. We finally demonstrate that hyphae-mediated spatial intermixing increases the conjugation-mediated spread of plasmid-encoded antibiotic resistance. In conclusion, fungal hyphae are important regulators of bacterial diversity and promote plasmid-mediated functional novelty during range expansion in an interaction-independent manner.
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Affiliation(s)
- Chujin Ruan
- College of Land Science and Technology, China Agricultural University, 100193 Beijing, China; Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Josep Ramoneda
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
| | - Guram Gogia
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Department of Environmental Systems Science, Swiss Federal Institute of Technology, 8092 Zürich, Switzerland
| | - Gang Wang
- College of Land Science and Technology, China Agricultural University, 100193 Beijing, China; National Black Soil & Agriculture Research, China Agricultural University, 100193 Beijing, China.
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland; Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.
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Kuhn T, Mamin M, Bindschedler S, Bshary R, Estoppey A, Gonzalez D, Palmieri F, Junier P, Richter XYL. Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211592. [PMID: 36483758 PMCID: PMC9727664 DOI: 10.1098/rsos.211592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.
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Affiliation(s)
- Thierry Kuhn
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Marine Mamin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Redouan Bshary
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Diego Gonzalez
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Xiang-Yi Li Richter
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
- Laboratory of Eco-Ethology, Institute of Biology, University of Neuchâtel, Rue Émile-Argand 11, CH-2000 Neuchâtel, Switzerland
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Balseiro-Romero M, Prieto-Fernández Á, Shor LM, Ghoshal S, Baveye PC, Ortega-Calvo JJ. Chemotactic Bacteria Facilitate the Dispersion of Nonmotile Bacteria through Micrometer-Sized Pores in Engineered Porous Media. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:13975-13984. [PMID: 36103595 PMCID: PMC9535858 DOI: 10.1021/acs.est.2c03149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/09/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Recent research has demonstrated that chemotactic bacteria can disperse inside microsized pores while traveling toward favorable conditions. Microbe-microbe cotransport might enable nonmotile bacteria to be carried with motile partners to enhance their dispersion and reduce their deposition in porous systems. The aim of this study was to demonstrate the enhancement in the dispersion of nonmotile bacteria (Mycobacterium gilvum VM552, a polycyclic aromatic hydrocarbon-degrader, and Sphingobium sp. D4, a hexachlorocyclohexane-degrader, through micrometer-sized pores near the exclusion-cell-size limit, in the presence of motile Pseudomonas putida G7 cells. For this purpose, we used bioreactors equipped with two chambers that were separated with membrane filters with 3, 5, and 12 μm pore sizes and capillary polydimethylsiloxane (PDMS) microarrays (20 μm × 35 μm × 2.2 mm). The cotransport of nonmotile bacteria occurred exclusively in the presence of a chemoattractant concentration gradient, and therefore, a directed flow of motile cells. This cotransport was more intense in the presence of larger pores (12 μm) and strong chemoeffectors (γ-aminobutyric acid). The mechanism that governed cotransport at the cell scale involved mechanical pushing and hydrodynamic interactions. Chemotaxis-mediated cotransport of bacterial degraders and its implications in pore accessibility opens new avenues for the enhancement of bacterial dispersion in porous media and the biodegradation of heterogeneously contaminated scenarios.
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Affiliation(s)
- María Balseiro-Romero
- Instituto
de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Ángeles Prieto-Fernández
- Instituto
de Investigaciones Agrobiológicas de Galicia (IIAG), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. de Vigo s/n, 15705 Santiago de Compostela, Spain
| | - Leslie M. Shor
- Department
of Chemical and Biomolecular Engineering, University of Connecticut, Castleman Building Rm. 224, Connecticut 06269-3237 Storrs, United States
| | - Subhasis Ghoshal
- Department
of Civil Engineering, McGill University, 817 Sherbrooke Street West, Montreal, Quebec H3A 0C3, Canada
| | | | - José Julio Ortega-Calvo
- Instituto
de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas
(CSIC), Avda. Reina Mercedes 10, 41012 Sevilla, Spain
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The Wheat Head Blight Pathogen Fusarium graminearum Can Recruit Collaborating Bacteria from Soil. Cells 2022; 11:cells11193004. [PMID: 36230966 PMCID: PMC9563980 DOI: 10.3390/cells11193004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
In nature, fungal endophytes often have facultative endohyphal bacteria (FEB). Can a model plant pathogenic fungus have them, and does it affect their phenotype? We constructed a growth system/microcosm to allow an F. graminearum isolate to grow through natural soil and then re-isolated it on a gentamicin-containing medium, allowing endohyphal growth of bacteria while killing other bacteria. F. graminearum PH-1 labelled with a His1mCherry gene staining the fungal nuclei fluorescent red was used to confirm the re-isolation of the fungus. Most new re-isolates contained about 10 16SrRNA genes per fungal mCherry gene determined by qPCR. The F. graminearum + FEB holobiont isolates containing the bacteria were sub-cultured several times, and their bacterial contents were stable. Sequencing the bacterial 16SrRNA gene from several Fg-FEB holobiont isolates revealed endophytic bacteria known to be capable of nitrogen fixation. We tested the pathogenicity of one common Fg-FEB holobiont association, F. graminearum + Stenatrophomonas maltophilia, and found increased pathogenicity. The 16SrRNA gene load per fungal His1mCherry gene inside the wheat stayed the same as previously found in vitro. Finally, strong evidence was found for Fg-S. maltophilia symbiotic nitrogen fixation benefitting the fungus.
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Kuhn T, Buffi M, Bindschedler S, Chain PS, Gonzalez D, Stanley CE, Wick LY, Junier P, Richter XYL. Design and construction of 3D printed devices to investigate active and passive bacterial dispersal on hydrated surfaces. BMC Biol 2022; 20:203. [PMID: 36104696 PMCID: PMC9476585 DOI: 10.1186/s12915-022-01406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/12/2022] Open
Abstract
Background To disperse in water-unsaturated environments, such as the soil, bacteria rely on the availability and structure of water films forming on biotic and abiotic surfaces, and, especially, along fungal mycelia. Dispersal along such “fungal highways” may be driven both by mycelial physical properties and by interactions between bacteria and fungi. However, we still do not have a way to disentangle the biotic and abiotic elements. Results We designed and 3D printed two devices establishing stable liquid films that support bacteria dispersal in the absence of biotic interactions. The thickness of the liquid film determined the presence of hydraulic flow capable of transporting non-motile cells. In the absence of flow, only motile cells can disperse in the presence of an energy source. Non-motile cells could not disperse autonomously without flow but dispersed as “hitchhikers” when co-inoculated with motile cells. Conclusions The 3D printed devices can be used as an abiotic control to study bacterial dispersal on hydrated surfaces, such as plant roots and fungal hyphae networks in the soil. By teasing apart the abiotic and biotic dimensions, these 3D printed devices will stimulate further research on microbial dispersal in soil and other water-unsaturated environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01406-z.
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:fuac022. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on Earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review, we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals but also beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, D-50674 Cologne, Germany
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Richter F, Bindschedler S, Calonne-Salmon M, Declerck S, Junier P, Stanley CE. Fungi-on-a-Chip: microfluidic platforms for single-cell studies on fungi. FEMS Microbiol Rev 2022; 46:6674677. [PMID: 36001464 PMCID: PMC9779915 DOI: 10.1093/femsre/fuac039] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 01/07/2023] Open
Abstract
This review highlights new advances in the emerging field of 'Fungi-on-a-Chip' microfluidics for single-cell studies on fungi and discusses several future frontiers, where we envisage microfluidic technology development to be instrumental in aiding our understanding of fungal biology. Fungi, with their enormous diversity, bear essential roles both in nature and our everyday lives. They inhabit a range of ecosystems, such as soil, where they are involved in organic matter degradation and bioremediation processes. More recently, fungi have been recognized as key components of the microbiome in other eukaryotes, such as humans, where they play a fundamental role not only in human pathogenesis, but also likely as commensals. In the food sector, fungi are used either directly or as fermenting agents and are often key players in the biotechnological industry, where they are responsible for the production of both bulk chemicals and antibiotics. Although the macroscopic fruiting bodies are immediately recognizable by most observers, the structure, function, and interactions of fungi with other microbes at the microscopic scale still remain largely hidden. Herein, we shed light on new advances in the emerging field of Fungi-on-a-Chip microfluidic technologies for single-cell studies on fungi. We discuss the development and application of microfluidic tools in the fields of medicine and biotechnology, as well as in-depth biological studies having significance for ecology and general natural processes. Finally, a future perspective is provided, highlighting new frontiers in which microfluidic technology can benefit this field.
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Affiliation(s)
- Felix Richter
- Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Saskia Bindschedler
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Maryline Calonne-Salmon
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Stéphane Declerck
- Laboratory of Mycology, Université catholique de Louvain, Place Croix du Sud 2, B-1348 Louvain-la-Neuve, Belgium
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Claire E Stanley
- Corresponding author: Department of Bioengineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, United Kingdom. E-mail:
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Lee KK, Kim H, Lee YH. Cross-kingdom co-occurrence networks in the plant microbiome: Importance and ecological interpretations. Front Microbiol 2022; 13:953300. [PMID: 35958158 PMCID: PMC9358436 DOI: 10.3389/fmicb.2022.953300] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 12/04/2022] Open
Abstract
Microbial co-occurrence network analysis is being widely used for data exploration in plant microbiome research. Still, challenges lie in how well these microbial networks represent natural microbial communities and how well we can interpret and extract eco-evolutionary insights from the networks. Although many technical solutions have been proposed, in this perspective, we touch on the grave problem of kingdom-level bias in network representation and interpretation. We underscore the eco-evolutionary significance of using cross-kingdom (bacterial-fungal) co-occurrence networks to increase the network's representability of natural communities. To do so, we demonstrate how ecosystem-level interpretation of plant microbiome evolution changes with and without multi-kingdom analysis. Then, to overcome oversimplified interpretation of the networks stemming from the stereotypical dichotomy between bacteria and fungi, we recommend three avenues for ecological interpretation: (1) understanding dynamics and mechanisms of co-occurrence networks through generalized Lotka-Volterra and consumer-resource models, (2) finding alternative ecological explanations for individual negative and positive fungal-bacterial edges, and (3) connecting cross-kingdom networks to abiotic and biotic (host) environments.
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Affiliation(s)
- Kiseok Keith Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, South Korea
- Plant Immunity Research Center, Seoul National University, Seoul, South Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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