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Highmore CJ, Melaugh G, Morris RJ, Parker J, Direito SOL, Romero M, Soukarieh F, Robertson SN, Bamford NC. Translational challenges and opportunities in biofilm science: a BRIEF for the future. NPJ Biofilms Microbiomes 2022; 8:68. [PMID: 36038607 PMCID: PMC9424220 DOI: 10.1038/s41522-022-00327-7] [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: 07/23/2021] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Biofilms are increasingly recognised as a critical global issue in a multitude of industries impacting health, food and water security, marine sector, and industrial processes resulting in estimated economic cost of $5 trillion USD annually. A major barrier to the translation of biofilm science is the gap between industrial practices and academic research across the biofilms field. Therefore, there is an urgent need for biofilm research to notice and react to industrially relevant issues to achieve transferable outputs. Regulatory frameworks necessarily bridge gaps between different players, but require a clear, science-driven non-biased underpinning to successfully translate research. Here we introduce a 2-dimensional framework, termed the Biofilm Research-Industrial Engagement Framework (BRIEF) for classifying existing biofilm technologies according to their level of scientific insight, including the understanding of the underlying biofilm system, and their industrial utility accounting for current industrial practices. We evidence the BRIEF with three case studies of biofilm science across healthcare, food & agriculture, and wastewater sectors highlighting the multifaceted issues around the effective translation of biofilm research. Based on these studies, we introduce some advisory guidelines to enhance the translational impact of future research.
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Affiliation(s)
- C J Highmore
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - G Melaugh
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK.,School of Engineering, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - R J Morris
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - J Parker
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - S O L Direito
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - M Romero
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
| | - F Soukarieh
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK.,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK
| | - S N Robertson
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK. .,Biodiscovery Institute, School of Life Sciences, Faculty of Health and Medical Sciences, University of Nottingham, NG7 2RD, Nottingham, UK.
| | - N C Bamford
- NBIC Interdisciplinary Research Fellows, UK National Biofilms Innovation Centre (NBIC), Southampton, UK. .,Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
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52
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Zeng Q, Man X, Lebreton A, Dai Y, Martin FM. The bacterial and fungal microbiomes of ectomycorrhizal roots from stone oaks and Yunnan pines in the subtropical forests of the Ailao Mountains of Yunnan. Front Microbiol 2022; 13:916337. [PMID: 35966686 PMCID: PMC9372452 DOI: 10.3389/fmicb.2022.916337] [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: 04/09/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Ectomycorrhizal (ECM) symbioses play an important role in tree biology and forest ecology. However, little is known on the composition of bacterial and fungal communities associated to ECM roots. In the present study, we surveyed the bacterial and fungal microbiome of ECM roots from stone oaks (Lithocarpus spp.) and Yunnan pines (Pinus yunnanensis) in the subtropical forests of the Ailao Mountains (Yunnan, China). The bacterial community was dominated by species pertaining to Rhizobiales and Acidobacteriales, whereas the fungal community was mainly composed of species belonging to the Russulales and Thelephorales. While the bacterial microbiome hosted by ECM roots from stone oaks and Yunnan pines was very similar, the mycobiome of these host trees was strikingly distinct. The microbial networks for bacterial and fungal communities showed a higher complexity in Lithocarpus ECM roots compared to Pinus ECM roots, but their modularity was higher in Pinus ECM roots. Seasonality also significantly influenced the fungal diversity and their co-occurrence network complexity. Our findings thus suggest that the community structure of fungi establishing and colonizing ECM roots can be influenced by the local soil/host tree environment and seasonality. These results expand our knowledge of the ECM root microbiome and its diversity in subtropical forest ecosystems.
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Affiliation(s)
- Qingchao Zeng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | - Xiaowu Man
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Forestry, Beijing Forestry University, Beijing, China
| | - Annie Lebreton
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
| | - Yucheng Dai
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Ecology and Nature Conservation, Institute of Microbiology, Beijing Forestry University, Beijing, China
- *Correspondence: Yucheng Dai,
| | - Francis M. Martin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Université de Lorraine, INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE, Grand Est-Nancy, Champenoux, France
- Francis M. Martin,
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53
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Agricultural management and pesticide use reduce the functioning of beneficial plant symbionts. Nat Ecol Evol 2022; 6:1145-1154. [PMID: 35798840 PMCID: PMC7613230 DOI: 10.1038/s41559-022-01799-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/11/2022] [Indexed: 01/04/2023]
Abstract
Phosphorus (P) acquisition is key for plant growth. Arbuscular mycorrhizal fungi (AMF) help plants acquire P from soil. Understanding which factors drive AMF-supported nutrient uptake is essential to develop more sustainable agroecosystems. Here we collected soils from 150 cereal fields and 60 non-cropped grassland sites across a 3,000 km trans-European gradient. In a greenhouse experiment, we tested the ability of AMF in these soils to forage for the radioisotope 33P from a hyphal compartment. AMF communities in grassland soils were much more efficient in acquiring 33P and transferred 64% more 33P to plants compared with AMF in cropland soils. Fungicide application best explained hyphal 33P transfer in cropland soils. The use of fungicides and subsequent decline in AMF richness in croplands reduced 33P uptake by 43%. Our results suggest that land-use intensity and fungicide use are major deterrents to the functioning and natural nutrient uptake capacity of AMF in agroecosystems.
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54
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Plett JM, Plett KL. Leveraging genomics to understand the broader role of fungal small secreted proteins in niche colonization and nutrition. ISME COMMUNICATIONS 2022; 2:49. [PMID: 37938664 PMCID: PMC9723739 DOI: 10.1038/s43705-022-00139-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/24/2022] [Accepted: 06/08/2022] [Indexed: 08/09/2023]
Abstract
The last few years have seen significant advances in the breadth of fungi for which we have genomic resources and our understanding of the biological mechanisms evolved to enable fungi to interact with their environment and other organisms. One field of research that has seen a paradigm shift in our understanding concerns the role of fungal small secreted proteins (SSPs) classified as effectors. Classically thought to be a class of proteins utilized by pathogenic microbes to manipulate host physiology in support of colonization, comparative genomic studies have demonstrated that mutualistic fungi and fungi not associated with a living host (i.e., saprotrophic fungi) also encode inducible effector and candidate effector gene sequences. In this review, we discuss the latest advances in understanding how fungi utilize these secreted proteins to colonize a particular niche and affect nutrition and nutrient cycles. Recent studies show that candidate effector SSPs in fungi may have just as significant a role in modulating hyphosphere microbiomes and in orchestrating fungal growth as they do in supporting colonization of a living host. We conclude with suggestions on how comparative genomics may direct future studies seeking to characterize and differentiate effector from other more generalized functions of these enigmatic secreted proteins across all fungal lifestyles.
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Affiliation(s)
- Jonathan M Plett
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia.
| | - Krista L Plett
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, 2568, Australia
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55
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Recreating in vitro tripartite mycorrhizal associations through functional bacterial biofilms. Appl Microbiol Biotechnol 2022; 106:4237-4250. [DOI: 10.1007/s00253-022-11996-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 05/14/2022] [Accepted: 05/16/2022] [Indexed: 12/19/2022]
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56
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Bonfante P. Microbe Profile: Gigaspora margarita, a multifaceted arbuscular mycorrhizal fungus. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35737726 DOI: 10.1099/mic.0.001202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gigaspora margarita is a cosmopolitan arbuscular mycorrhizal fungus, which - as an obligate symbiont- requires being associated to a host plant to accomplish its life cycle. It is characterized by huge white spores, the development of extraradical auxiliary cells, and the lack of intraradical vesicles. Its genome is dominated by transposable elements and is one of the largest fungal genomes so far sequenced. G. margarita has the peculiar feature to host taxonomically different endobacteria in its cytoplasm. The development of a cured line has allowed us to demonstrate how the endobacteria have a positive impact on the fungal physiology and -with a cascade effect- on the mycorrhizal plant.
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Affiliation(s)
- Paola Bonfante
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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57
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Sadiq FA, Hansen MF, Burmølle M, Heyndrickx M, Flint S, Lu W, Chen W, Zhang H. Towards understanding mechanisms and functional consequences of bacterial interactions with members of various kingdoms in complex biofilms that abound in nature. FEMS Microbiol Rev 2022; 46:6595875. [PMID: 35640890 DOI: 10.1093/femsre/fuac024] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 11/12/2022] Open
Abstract
The microbial world represents a phenomenal diversity of microorganisms from different kingdoms of life which occupy an impressive set of ecological niches. Most, if not all, microorganisms once colonise a surface develop architecturally complex surface-adhered communities which we refer to as biofilms. They are embedded in polymeric structural scaffolds serve as a dynamic milieu for intercellular communication through physical and chemical signalling. Deciphering microbial ecology of biofilms in various natural or engineered settings has revealed co-existence of microorganisms from all domains of life, including Bacteria, Archaea and Eukarya. The coexistence of these dynamic microbes is not arbitrary, as a highly coordinated architectural setup and physiological complexity show ecological interdependence and myriads of underlying interactions. In this review, we describe how species from different kingdoms interact in biofilms and discuss the functional consequences of such interactions. We highlight metabolic advances of collaboration among species from different kingdoms, and advocate that these interactions are of great importance and need to be addressed in future research. Since trans-kingdom biofilms impact diverse contexts, ranging from complicated infections to efficient growth of plants, future knowledge within this field will be beneficial for medical microbiology, biotechnology, and our general understanding of microbial life in nature.
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Affiliation(s)
- Faizan Ahmed Sadiq
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium
| | - Mads Frederik Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Denmark
| | - Marc Heyndrickx
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology & Food Sciences Unit, Melle, Belgium.,Department of Pathology, Bacteriology and Poultry Diseases, Ghent University, Merelbeke, Belgium
| | - Steve Flint
- School of Food and Advanced Technology, Massey University, Private Bag, 11222, Palmerston North, New Zealand
| | - Wenwei Lu
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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58
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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; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [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 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, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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59
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Bennett AE, Groten K. The Costs and Benefits of Plant-Arbuscular Mycorrhizal Fungal Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:649-672. [PMID: 35216519 DOI: 10.1146/annurev-arplant-102820-124504] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The symbiotic interaction between plants and arbuscular mycorrhizal (AM) fungi is often perceived as beneficial for both partners, though a large ecological literature highlights the context dependency of this interaction. Changes in abiotic variables, such as nutrient availability, can drive the interaction along the mutualism-parasitism continuum with variable outcomes for plant growth and fitness. However, AM fungi can benefit plants in more ways than improved phosphorus nutrition and plant growth. For example, AM fungi can promote abiotic and biotic stress tolerance even when considered parasitic from a nutrient provision perspective. Other than being obligate biotrophs, very little is known about the benefits AM fungi gain from plants. In this review, we utilize both molecular biology and ecological approaches to expand our understanding of the plant-AM fungal interaction across disciplines.
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Affiliation(s)
- Alison E Bennett
- Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, Ohio, USA;
| | - Karin Groten
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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60
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Zhang L, Zhou J, George TS, Limpens E, Feng G. Arbuscular mycorrhizal fungi conducting the hyphosphere bacterial orchestra. TRENDS IN PLANT SCIENCE 2022; 27:402-411. [PMID: 34782247 DOI: 10.1016/j.tplants.2021.10.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 05/22/2023]
Abstract
More than two-thirds of terrestrial plants acquire nutrients by forming a symbiosis with arbuscular mycorrhizal (AM) fungi. AM fungal hyphae recruit distinct microbes into their hyphosphere, the narrow region of soil influenced by hyphal exudates. They thereby shape this so-called second genome of AM fungi, which significantly contributes to nutrient mobilization and turnover. We summarize current insights into characteristics of the hyphosphere microbiome and the role of hyphal exudates on orchestrating its composition. The hyphal exudates not only contain carbon-rich compounds but also promote bacterial growth and activity and influence the microbial community structure. These effects lead to shifts in function and cause changes in organic nutrient cycling, making the hyphosphere a unique and largely overlooked functional zone in ecosystems.
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Affiliation(s)
- Lin Zhang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | - Jiachao Zhou
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China
| | | | - Erik Limpens
- Laboratory of Molecular Biology, Wageningen University & Research, Wageningen 6708, PB, The Netherlands
| | - Gu Feng
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing 100193, China.
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61
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See CR, Keller AB, Hobbie SE, Kennedy PG, Weber PK, Pett-Ridge J. Hyphae move matter and microbes to mineral microsites: Integrating the hyphosphere into conceptual models of soil organic matter stabilization. GLOBAL CHANGE BIOLOGY 2022; 28:2527-2540. [PMID: 34989058 DOI: 10.1111/gcb.16073] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Associations between soil minerals and microbially derived organic matter (often referred to as mineral-associated organic matter or MAOM) form a large pool of slowly cycling carbon (C). The rhizosphere, soil immediately adjacent to roots, is thought to control the spatial extent of MAOM formation because it is the dominant entry point of new C inputs to soil. However, emphasis on the rhizosphere implicitly assumes that microbial redistribution of C into bulk (non-rhizosphere) soils is minimal. We question this assumption, arguing that because of extensive fungal exploration and rapid hyphal turnover, fungal redistribution of soil C from the rhizosphere to bulk soil minerals is common, and encourages MAOM formation. First, we summarize published estimates of fungal hyphal length density and turnover rates and demonstrate that fungal C inputs are high throughout the rhizosphere-bulk soil continuum. Second, because colonization of hyphal surfaces is a common dispersal mechanism for soil bacteria, we argue that hyphal exploration allows for the non-random colonization of mineral surfaces by hyphae-associated taxa. Third, these bacterial communities and their fungal hosts determine the chemical form of organic matter deposited on colonized mineral surfaces. Collectively, our analysis demonstrates that omission of the hyphosphere from conceptual models of soil C flow overlooks key mechanisms for MAOM formation in bulk soils. Moving forward, there is a clear need for spatially explicit, quantitative research characterizing the environmental drivers of hyphal exploration and hyphosphere community composition across systems, as these are important controls over the rate and organic chemistry of C deposited on minerals.
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Affiliation(s)
- Craig R See
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Adrienne B Keller
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Sarah E Hobbie
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter G Kennedy
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter K Weber
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
| | - Jennifer Pett-Ridge
- Physical and Life Science Directorate, Lawrence Livermore National Lab, Livermore, California, USA
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62
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Organic nitrogen utilisation by an arbuscular mycorrhizal fungus is mediated by specific soil bacteria and a protist. THE ISME JOURNAL 2022; 16:676-685. [PMID: 34545172 PMCID: PMC8857242 DOI: 10.1038/s41396-021-01112-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/24/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi lack efficient exoenzymes to access organic nutrients directly. Nevertheless, the fungi often obtain and further channel to their host plants a significant share of nitrogen (N) and/or phosphorus from such resources, presumably via cooperation with other soil microorganisms. Because it is challenging to disentangle individual microbial players and processes in complex soil, we took a synthetic approach here to study 15N-labelled chitin (an organic N source) recycling via microbial loop in AM fungal hyphosphere. To this end, we employed a compartmented in vitro cultivation system and monoxenic culture of Rhizophagus irregularis associated with Cichorium intybus roots, various soil bacteria, and the protist Polysphondylium pallidum. We showed that upon presence of Paenibacillus sp. in its hyphosphere, the AM fungus (and associated plant roots) obtained several-fold larger quantities of N from the chitin than it did with any other bacteria, whether chitinolytic or not. Moreover, we demonstrated that adding P. pallidum to the hyphosphere with Paenibacillus sp. further increased by at least 65% the gain of N from the chitin by the AM fungus compared to the hyphosphere without protists. We thus directly demonstrate microbial interplay possibly involved in efficient organic N utilisation by AM fungal hyphae.
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63
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Wen Z, White PJ, Shen J, Lambers H. Linking root exudation to belowground economic traits for resource acquisition. THE NEW PHYTOLOGIST 2022; 233:1620-1635. [PMID: 34761404 DOI: 10.1111/nph.17854] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
The concept of a root economics space (RES) is increasingly adopted to explore root trait variation and belowground resource-acquisition strategies. Much progress has been made on interactions of root morphology and mycorrhizal symbioses. However, root exudation, with a significant carbon (C) cost (c. 5-21% of total photosynthetically fixed C) to enhance resource acquisition, remains a missing link in this RES. Here, we argue that incorporating root exudation into the structure of RES is key to a holistic understanding of soil nutrient acquisition. We highlight the different functional roles of root exudates in soil phosphorus (P) and nitrogen (N) acquisition. Thereafter, we synthesize emerging evidence that illustrates how root exudation interacts with root morphology and mycorrhizal symbioses at the level of species and individual plant and argue contrasting patterns in species evolved in P-impoverished vs N-limited environments. Finally, we propose a new conceptual framework, integrating three groups of root functional traits to better capture the complexity of belowground resource-acquisition strategies. Such a deeper understanding of the integrated and dynamic interactions of root morphology, root exudation, and mycorrhizal symbioses will provide valuable insights into the mechanisms underlying species coexistence and how to explore belowground interactions for sustainable managed systems.
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Affiliation(s)
- Zhihui Wen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193, Beijing, China
| | - Philip J White
- Ecological Science Group, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jianbo Shen
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193, Beijing, China
| | - Hans Lambers
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193, Beijing, China
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA, 6009, Australia
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64
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Custódio V, Gonin M, Stabl G, Bakhoum N, Oliveira MM, Gutjahr C, Castrillo G. Sculpting the soil microbiota. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:508-522. [PMID: 34743401 DOI: 10.1111/tpj.15568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/20/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Soil is a living ecosystem, the health of which depends on fine interactions among its abiotic and biotic components. These form a delicate equilibrium maintained through a multilayer network that absorbs certain perturbations and guarantees soil functioning. Deciphering the principles governing the interactions within soils is of critical importance for their management and conservation. Here, we focus on soil microbiota and discuss the complexity of interactions that impact the composition and function of soil microbiota and their interaction with plants. We discuss how physical aspects of soils influence microbiota composition and how microbiota-plant interactions support plant growth and responses to nutrient deficiencies. We predict that understanding the principles determining the configuration and functioning of soil microbiota will contribute to the design of microbiota-based strategies to preserve natural resources and develop more environmentally friendly agricultural practices.
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Affiliation(s)
- Valéria Custódio
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Mathieu Gonin
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Georg Stabl
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Niokhor Bakhoum
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich (TUM), Emil Ramann Str. 4, Freising, 85354, Germany
| | - Gabriel Castrillo
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, Nottingham, UK
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Duan S, Declerck S, Zhang L, Feng G. Two-component system in Rahnella aquatilis is impacted by the hyphosphere of the arbuscular mycorrhizal fungus Rhizophagus irregularis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:119-129. [PMID: 34951128 DOI: 10.1111/1758-2229.13039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Two-component systems (TCS) are ubiquitous among bacteria, playing key roles in signalling events. However, to what extent the TCS of Rahnella aquatilis (a Phosphate solubilizing bacteria) is influenced by the hyphosphere of the arbuscular mycorrhizal (AM) fungus Rhizophagus irregularis is totally unknown. Here, the expression of 16 genes encoding the TCS of R. aquatilis (i.e. involved in carbon-sensing and nutrient-sensing) and of eight genes regulated by the PhoR TCS (i.e. involved in inorganic and organic phosphorus mobilization) were analysed at regular intervals in presence of hyphae of R. irregularis. The study was conducted under in vitro culture conditions with phytate as the unique source of phosphorus. In presence of the AM fungus, the expression of TCS genes involved in carbon-sensing and nutrient-sensing were stimulated. Only, BaeS at 30 and 120 min, and BaeR at 60 min were inhibited. In addition, the PhoR TCS stimulated the expression of genes encoding phosphatase but inhibited the expression of genes involved in gluconic acid production. As the mechanism of coupling environmental changes with cellular physiological changes, TCS plays a pivotal role in regulating specific gene expression in R. aquatilis, recognizing environmental signals. More importantly, TCS genes may regulate bacteria response to hyphal carbon to mobilize phosphorus efficiently in the hyphosphere.
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Affiliation(s)
- Shilong Duan
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
| | - Stéphane Declerck
- Université Catholique de Louvain, Earth and Life Institute, Applied Microbiology, Mycology, Croix du Sud 2, bte L7.05.06, Louvain-la-Neuve, B-1348, Belgium
| | - Lin Zhang
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
| | - Gu Feng
- College of Resources and Environmental Sciences, MOE Key Laboratory of Plant-Soil Interactions, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 10093, China
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Ujvári G, Turrini A, Avio L, Agnolucci M. Possible role of arbuscular mycorrhizal fungi and associated bacteria in the recruitment of endophytic bacterial communities by plant roots. MYCORRHIZA 2021; 31:527-544. [PMID: 34286366 PMCID: PMC8484141 DOI: 10.1007/s00572-021-01040-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/17/2021] [Indexed: 05/12/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) represent an important group of root symbionts, given the key role they play in the enhancement of plant nutrition, health, and product quality. The services provided by AMF often are facilitated by large and diverse beneficial bacterial communities, closely associated with spores, sporocarps, and extraradical mycelium, showing different functional activities, such as N2 fixation, nutrient mobilization, and plant hormone, antibiotic, and siderophore production and also mycorrhizal establishment promotion, leading to the enhancement of host plant performance. The potential functional complementarity of AMF and associated microbiota poses a key question as to whether members of AMF-associated bacterial communities can colonize the root system after establishment of mycorrhizas, thereby becoming endophytic. Root endophytic bacterial communities are currently studied for the benefits provided to host plants in the form of growth promotion, stress reduction, inhibition of plant pathogens, and plant hormone release. Their quantitative and qualitative composition is influenced by many factors, such as geographical location, soil type, host genotype, and cultivation practices. Recent data suggest that an additional factor affecting bacterial endophyte recruitment could be AMF and their associated bacteria, even though the mechanisms allowing members of AMF-associated bacterial communities to actually establish in the root system, becoming endophytic, remain to be determined. Given the diverse plant growth-promoting properties shown by AMF-associated bacteria, further studies are needed to understand whether AMF may represent suitable tools to introduce beneficial root endophytes in sustainable and organic agriculture where the functioning of such multipartite association may be crucial for crop production.
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Affiliation(s)
- Gergely Ujvári
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Alessandra Turrini
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Luciano Avio
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy
| | - Monica Agnolucci
- Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.
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Bread Wheat ( Triticum aestivum) Responses to Arbuscular Mycorrhizae Inoculation under Drought Stress Conditions. PLANTS 2021; 10:plants10091756. [PMID: 34579289 PMCID: PMC8466081 DOI: 10.3390/plants10091756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 11/17/2022]
Abstract
Abiotic constraints such as water deficit reduce cereal production. Plants have different strategies against these stresses to improve plant growth, physiological metabolism and crop production. For example, arbuscular mycorrhiza (AM)—bread wheat association has been shown to improve tolerance to drought stress conditions. The objective of this study was to determine the effect of AM inoculation on plant characteristics, lipid peroxidation, solute accumulation, water deficit saturation, photosynthetic activity, total phenol secretion and enzymatic activities including peroxidise (PO) and polyphenol oxidase (PPO) in two bread wheat cultivars (PAN3497 and SST806) under well-watered and drought-stressed conditions in plants grown under greenhouse conditions, to determine whether AM can enhance drought tolerance in wheat. AM inoculation improved morphological and physiological parameters in plants under stress. The leaf number increased by 35% and 5%, tiller number by 25% and 23%, chlorophyll content by 7% and 10%, accumulation of soluble sugars by 33% and 14%, electrolyte leakage by 26% and 32%, PPO by 44% and 47% and PO by 30% and 37% respectively, in PAN3497 and SST806, respectively. However, drought stress decreased proline content by 20% and 24%, oxidative damage to lipids measured as malondialdehyde by 34% and 60%, and total phenol content by 55% and 40% respectively, in AM treated plants of PAN3497 and SST806. PAN3497 was generally more drought-sensitive than SST806. This study showed that AM can contribute to protect plants against drought stress by alleviating water deficit induced oxidative stress.
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Sharma S, Compant S, Franken P, Ruppel S, Ballhausen MB. It Takes Two to Tango: A Bacterial Biofilm Provides Protection against a Fungus-Feeding Bacterial Predator. Microorganisms 2021; 9:microorganisms9081566. [PMID: 34442645 PMCID: PMC8398733 DOI: 10.3390/microorganisms9081566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/17/2021] [Indexed: 11/23/2022] Open
Abstract
Fungus-bacterium interactions are widespread, encompass multiple interaction types from mutualism to parasitism, and have been frequent targets for microbial inoculant development. In this study, using in vitro systems combined with confocal laser scanning microscopy and real-time quantitative PCR, we test whether the nitrogen-fixing bacterium Kosakonia radicincitans can provide protection to the plant-beneficial fungus Serendipita indica, which inhabits the rhizosphere and colonizes plants as an endophyte, from the fungus-feeding bacterium Collimonas fungivorans. We show that K. radicincitans can protect fungal hyphae from bacterial feeding on solid agar medium, with probable mechanisms being quick hyphal colonization and biofilm formation. We furthermore find evidence for different feeding modes of K. radicincitans and C. fungivorans, namely “metabolite” and “hyphal feeding”, respectively. Overall, we demonstrate, to our knowledge, the first evidence for a bacterial, biofilm-based protection of fungal hyphae against attack by a fungus-feeding, bacterial predator on solid agar medium. Besides highlighting the importance of tripartite microbial interactions, we discuss implications of our results for the development and application of microbial consortium-based bioprotectants and biostimulants.
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Affiliation(s)
- Shubhangi Sharma
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Stéphane Compant
- AIT Austrian Institute of Technology, Center for Health and Bioresources, Konrad Lorenz Strasse 24, 3430 Tulln, Austria;
| | - Philipp Franken
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Institute of Microbiology, Friedrich Schiller University Jena, Neugasse 24, 07743 Jena, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
| | - Max-Bernhard Ballhausen
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany; (S.S.); (P.F.); (S.R.)
- Correspondence:
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