Bacterial–fungal interactions: ecology, mechanisms and challenges
Abstract
Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial–fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial–fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.
- Authors:
-
[8];
[9];
[11];
- Univ. de Lorraine, Champenoux (France)
- Michigan State Univ., East Lansing, MI (United States)
- Duke Univ., Durham, NC (United States); Univ. of California, Berkeley, CA (United States)
- Institut de Biologie et Genetique Cellulaire, Bordeaux cedex (France)
- Leibniz-Institute of Vegetable and Ornamental Crops, GroBbeeren (Germany)
- Univ. of Neuchatel, Neuchatel (Switzerland)
- Max Planck Institute for Plant Breeding Research, Cologne (Germany)
- Univ. of Neuchatel, Neuchatel (Switzerland); Univ. of Lausanne, Lausanne (Switzerland)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
- Cornell Univ., Ithaca, NY (United States)
- Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Eotvos Lorand Univ., Budapest (Hungary)
- Univ. of Torino, Torino (Italy)
- Academic Centre for Dentistry, Amsterdam (The Netherlands)
- Fujian Agriculture and Forestry Univ. (FAFU), Fuzhou (China)
- Univ. of Groningen, Groningen (The Netherlands)
- Helmholtz Centre for Environmental Research—UFZ, Leipzig (Germany)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1468277
- Alternate Identifier(s):
- OSTI ID: 1471883
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- FEMS Microbiology Reviews
- Additional Journal Information:
- Journal Volume: 42; Journal Issue: 3; Journal ID: ISSN 1574-6976
- Publisher:
- Federation of European Microbiological Societies
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; bacterial–fungal interactions; metaorganisms; microbiome; mechanism; microbial logistics
Citation Formats
Deveau, Aurélie, Bonito, Gregory, Uehling, Jessie, Paoletti, Mathieu, Becker, Matthias, Bindschedler, Saskia, Hacquard, Stéphane, Hervé, Vincent, Labbé, Jessy, Lastovetsky, Olga A., Mieszkin, Sophie, Millet, Larry J., Vajna, Balázs, Junier, Pilar, Bonfante, Paola, Krom, Bastiaan P., Olsson, Stefan, van Elsas, Jan Dirk, and Wick, Lukas Y. Bacterial–fungal interactions: ecology, mechanisms and challenges. United States: N. p., 2018.
Web. doi:10.1093/femsre/fuy008.
Deveau, Aurélie, Bonito, Gregory, Uehling, Jessie, Paoletti, Mathieu, Becker, Matthias, Bindschedler, Saskia, Hacquard, Stéphane, Hervé, Vincent, Labbé, Jessy, Lastovetsky, Olga A., Mieszkin, Sophie, Millet, Larry J., Vajna, Balázs, Junier, Pilar, Bonfante, Paola, Krom, Bastiaan P., Olsson, Stefan, van Elsas, Jan Dirk, & Wick, Lukas Y. Bacterial–fungal interactions: ecology, mechanisms and challenges. United States. https://doi.org/10.1093/femsre/fuy008
Deveau, Aurélie, Bonito, Gregory, Uehling, Jessie, Paoletti, Mathieu, Becker, Matthias, Bindschedler, Saskia, Hacquard, Stéphane, Hervé, Vincent, Labbé, Jessy, Lastovetsky, Olga A., Mieszkin, Sophie, Millet, Larry J., Vajna, Balázs, Junier, Pilar, Bonfante, Paola, Krom, Bastiaan P., Olsson, Stefan, van Elsas, Jan Dirk, and Wick, Lukas Y. Mon .
"Bacterial–fungal interactions: ecology, mechanisms and challenges". United States. https://doi.org/10.1093/femsre/fuy008. https://www.osti.gov/servlets/purl/1468277.
@article{osti_1468277,
title = {Bacterial–fungal interactions: ecology, mechanisms and challenges},
author = {Deveau, Aurélie and Bonito, Gregory and Uehling, Jessie and Paoletti, Mathieu and Becker, Matthias and Bindschedler, Saskia and Hacquard, Stéphane and Hervé, Vincent and Labbé, Jessy and Lastovetsky, Olga A. and Mieszkin, Sophie and Millet, Larry J. and Vajna, Balázs and Junier, Pilar and Bonfante, Paola and Krom, Bastiaan P. and Olsson, Stefan and van Elsas, Jan Dirk and Wick, Lukas Y.},
abstractNote = {Fungi and bacteria are found living together in a wide variety of environments. Their interactions are significant drivers of many ecosystem functions and are important for the health of plants and animals. A large number of fungal and bacterial families engage in complex interactions that lead to critical behavioural shifts of the microorganisms ranging from mutualism to antagonism. The importance of bacterial–fungal interactions (BFI) in environmental science, medicine and biotechnology has led to the emergence of a dynamic and multidisciplinary research field that combines highly diverse approaches including molecular biology, genomics, geochemistry, chemical and microbial ecology, biophysics and ecological modelling. In this review, we discuss recent advances that underscore the roles of BFI across relevant habitats and ecosystems. A particular focus is placed on the understanding of BFI within complex microbial communities and in regard of the metaorganism concept. We also discuss recent discoveries that clarify the (molecular) mechanisms involved in bacterial–fungal relationships, and the contribution of new technologies to decipher generic principles of BFI in terms of physical associations and molecular dialogues. Finally, we discuss future directions for research in order to stimulate synergy within the BFI research area and to resolve outstanding questions.},
doi = {10.1093/femsre/fuy008},
journal = {FEMS Microbiology Reviews},
number = 3,
volume = 42,
place = {United States},
year = {Mon Feb 19 00:00:00 EST 2018},
month = {Mon Feb 19 00:00:00 EST 2018}
}
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Figure 1: Relevance, applications and drivers of BFI. Biotic and abiotic environments filter microbial communities selecting for specific consortia and conversely interactions between microorganisms influence the biotic and abiotic environment. Bacterial–fungal phenotypes emerge from physical and molecular interactions between members of the microbial community and are highly dependent on timemore »
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- Pathogens, Vol. 8, Issue 4
Deciphering bacterial and fungal endophyte communities in leaves of two maple trees with green islands
journal, October 2019
- Wemheuer, Franziska; Wemheuer, Bernd; Daniel, Rolf
- Scientific Reports, Vol. 9, Issue 1
Necrobiome framework for bridging decomposition ecology of autotrophically and heterotrophically derived organic matter
journal, September 2018
- Benbow, M. Eric; Barton, Philip S.; Ulyshen, Michael D.
- Ecological Monographs, Vol. 89, Issue 1
Gene mobility in microbiomes of the mycosphere and mycorrhizosphere –role of plasmids and bacteriophages
journal, April 2019
- Pratama, Akbar Adjie; van Elsas, Jan Dirk
- FEMS Microbiology Ecology, Vol. 95, Issue 5
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
journal, October 2019
- Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran
- Nature Communications, Vol. 10, Issue 1
Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
journal, January 2019
- Krüger, U. S.; Dechesne, A.; Bak, F.
- Applied and Environmental Microbiology, Vol. 85, Issue 6
Mycelial network-mediated rhizobial dispersal enhances legume nodulation
journal, January 2020
- Zhang, Wei; Li, Xiao-Gang; Sun, Kai
- The ISME Journal, Vol. 14, Issue 4
Volatile‐mediated antagonism of soil bacterial communities against fungi
journal, August 2019
- Li, Xiaogang; Garbeva, Paolina; Liu, Xiaojiao
- Environmental Microbiology, Vol. 22, Issue 3
Increasing access to microfluidics for studying fungi and other branched biological structures
journal, June 2019
- Millet, Larry J.; Aufrecht, Jayde; Labbé, Jessy
- Fungal Biology and Biotechnology, Vol. 6, Issue 1
Interaction with Soil Bacteria Affects the Growth and Amino Acid Content of Piriformospora indica
journal, January 2020
- Leyva-Rojas, Jorge A.; Coy-Barrera, Ericsson; Hampp, Rüdiger
- Molecules, Vol. 25, Issue 3
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
journal, October 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- The ISME Journal, Vol. 13, Issue 3
The Host Immune System Facilitates Disseminated Staphylococcus aureus Disease Due to Phagocytic Attraction to Candida albicans during Coinfection: a Case of Bait and Switch
journal, August 2019
- Allison, Devon L.; Scheres, Nina; Willems, Hubertine M. E.
- Infection and Immunity, Vol. 87, Issue 11
Necrobiome Framework for Bridging Decomposition Ecology of Autotrophically and Heterotrophically Derived Organic Matter
journal, January 2019
- Benbow, Mark Eric; Barton, Philip S.; Ulyshen, Michael D.
- The Bulletin of the Ecological Society of America, Vol. 100, Issue 1
Fungal hyphae colonization by Bacillus subtilis relies on biofilm matrix components
journal, December 2019
- Kjeldgaard, Bodil; Listian, Stevanus A.; Ramaswamhi, Valliyammai
- Biofilm, Vol. 1
Compost Fungi Allow for Effective Dispersal of Putative PGP Bacteria
journal, August 2021
- González-González, Susett; Astorga-Eló, Marcia; Campos, Marco
- Agronomy, Vol. 11, Issue 8
Volatile‐mediated antagonism of soil bacterial communities against fungi
journal, August 2019
- Li, Xiaogang; Garbeva, Paolina; Liu, Xiaojiao
- Environmental Microbiology, Vol. 22, Issue 3
Who is eating fructose within the Aedes albopictus gut microbiota?
journal, April 2020
- Guégan, Morgane; Tran Van, Van; Martin, Edwige
- Environmental Microbiology, Vol. 22, Issue 4
Terpene Synthase Genes Originated from Bacteria through Horizontal Gene Transfer Contribute to Terpenoid Diversity in Fungi
journal, June 2019
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- Scientific Reports, Vol. 9, Issue 1
Multidisciplinarity in Microbiome Research: A Challenge and Opportunity to Rethink Causation, Variability, and Scale
journal, May 2019
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- BioEssays, Vol. 41, Issue 10
Influences of a Prolific Gut Fungus ( Zancudomyces culisetae ) on Larval and Adult Mosquito ( Aedes aegypti )-Associated Microbiota
journal, November 2019
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- Applied and Environmental Microbiology, Vol. 86, Issue 3
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
text, January 2019
- Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran
- Nature Publishing Group
Assessment of functional and structural changes of soil fungal and oomycete communities in holm oak declined dehesas through metabarcoding analysis
journal, March 2019
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- Scientific Reports, Vol. 9, Issue 1
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
text, January 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- ETH Zurich
Orchard Conditions and Fruiting Body Characteristics Drive the Microbiome of the Black Truffle Tuber aestivum
journal, June 2019
- Splivallo, Richard; Vahdatzadeh, Maryam; Maciá-Vicente, Jose G.
- Frontiers in Microbiology, Vol. 10
Growing edible mushrooms: a conversation between bacteria and fungi
journal, August 2019
- Carrasco, Jaime; Preston, Gail M.
- Environmental Microbiology, Vol. 22, Issue 3
Induction of antibacterial proteins and peptides in the coprophilous mushroom Coprinopsis cinerea in response to bacteria
journal, October 2018
- Kombrink, Anja; Tayyrov, Annageldi; Essig, Andreas
- The ISME Journal, Vol. 13, Issue 3
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
text, January 2019
- Wagg, Cameron; Schlaeppi, Klaus; Banerjee, Samiran
- Nature Publishing Group
Effects of Quorum Quenching on Biofilm Metacommunity in a Membrane Bioreactor
journal, June 2019
- Jeong, So-Yeon; Lee, Chung-Hak; Yi, Taewoo
- Microbial Ecology, Vol. 79, Issue 1
Fungi in aquatic ecosystems
journal, March 2019
- Grossart, Hans-Peter; Van den Wyngaert, Silke; Kagami, Maiko
- Nature Reviews Microbiology, Vol. 17, Issue 6
Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile
journal, January 2019
- Krüger, U. S.; Dechesne, A.; Bak, F.
- Applied and Environmental Microbiology, Vol. 85, Issue 6
Increasing access to microfluidics for studying fungi and other branched biological structures
journal, June 2019
- Millet, Larry J.; Aufrecht, Jayde; Labbé, Jessy
- Fungal Biology and Biotechnology, Vol. 6, Issue 1
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