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Berrios L, Yeam J, Holm L, Robinson W, Pellitier PT, Chin ML, Henkel TW, Peay KG. Positive interactions between mycorrhizal fungi and bacteria are widespread and benefit plant growth. Curr Biol 2023:S0960-9822(23)00760-1. [PMID: 37369208 DOI: 10.1016/j.cub.2023.06.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023]
Abstract
Bacteria, ectomycorrhizal (EcM) fungi, and land plants have been coevolving for nearly 200 million years, and their interactions presumably contribute to the function of terrestrial ecosystems. The direction, stability, and strength of bacteria-EcM fungi interactions across landscapes and across a single plant host, however, remains unclear. Moreover, the genetic mechanisms that govern them have not been addressed. To these ends, we collected soil samples from Bishop pine forests across a climate-latitude gradient spanning coastal California, fractionated the soil samples based on their proximity to EcM-colonized roots, characterized the microbial communities using amplicon sequencing, and generated linear regression models showing the impact that select bacterial taxa have on EcM fungal abundance. In addition, we paired greenhouse experiments with transcriptomic analyses to determine the directionality of these relationships and identify which genes EcM-synergist bacteria express during tripartite symbioses. Our data reveal that ectomycorrhizas (i.e., EcM-colonized roots) enrich conserved bacterial taxa across climatically heterogeneous regions. We also show that phylogenetically diverse EcM synergists are positively associated with plant and fungal growth and have unique gene expression profiles compared with EcM-antagonist bacteria. In sum, we identify common mechanisms that facilitate widespread and diverse multipartite symbioses, which inform our understanding of how plants develop in complex environments.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Jay Yeam
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wallis Robinson
- Forestry and Forest Health Program, University of California Cooperative Extension Humboldt and Del Norte Counties, Eureka, CA 95503, USA
| | | | - Mei Lin Chin
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Terry W Henkel
- Department of Biological Sciences, California State Polytechnic University, Humboldt, Arcata, CA 95521, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Earth System Science, Stanford University, Stanford, CA 94305, USA
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Hao X, Zhu YG, Nybroe O, Nicolaisen MH. The Composition and Phosphorus Cycling Potential of Bacterial Communities Associated With Hyphae of Penicillium in Soil Are Strongly Affected by Soil Origin. Front Microbiol 2020; 10:2951. [PMID: 31969866 PMCID: PMC6960115 DOI: 10.3389/fmicb.2019.02951] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 12/09/2019] [Indexed: 02/05/2023] Open
Abstract
Intimate fungal-bacterial interactions are widespread in nature. However the main drivers for the selection of hyphae-associated bacterial communities and their functional traits in soil systems remain elusive. In the present study, baiting microcosms were used to recover hyphae-associated bacteria from two Penicillium species with different phosphorus-solubilizing capacities in five types of soils. Based on amplicon sequencing of 16S rRNA genes, the composition of bacterial communities associated with Penicillium hyphae differed significantly from the soil communities, showing a lower diversity and less variation in taxonomic structure. Furthermore, soil origin had a significant effect on hyphae-associated community composition, whereas the two fungal species used in this study had no significant overall impact on bacterial community structure, despite their different capacities to solubilize phosphorus. However, discriminative taxa and specific OTUs were enriched in hyphae-associated communities of individual Penicillium species indicating that each hyphosphere represented a unique niche for bacterial colonization. Additionally, an increased potential of phosphorus cycling was found in hyphae-associated communities, especially for the gene phnK involved in phosphonate degradation. Altogether, it was established that the two Penicillium hyphae represent unique niches in which microbiome assemblage and phosphorus cycling potential are mainly driven by soil origin, with less impact made by fungal identity with a divergent capacity to utilize phosphorus.
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Affiliation(s)
- Xiuli Hao
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ole Nybroe
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette H. Nicolaisen
- Section for Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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Kranabetter JM, Harman-Denhoed R, Hawkins BJ. Saprotrophic and ectomycorrhizal fungal sporocarp stoichiometry (C : N : P) across temperate rainforests as evidence of shared nutrient constraints among symbionts. THE NEW PHYTOLOGIST 2019; 221:482-492. [PMID: 30084239 DOI: 10.1111/nph.15380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/07/2018] [Indexed: 06/08/2023]
Abstract
Quantifying nutritional dynamics of free-living saprotrophs and symbiotic ectomycorrhizal fungi in the field is challenging, but the stoichiometry of fruiting bodies (sporocarps) may be an effective methodology for this purpose. Carbon (C), nitrogen (N) and phosphorus (P) concentrations of soils, foliage and 146 sporocarp collections were analyzed from 14 Pseudotsuga menziesii var. menziesii stands across a podzolization gradient on Vancouver Island (Canada). N and P concentrations were considerably higher in saprotrophic fungi. Fungal N% increased with soil N content at a greater rate for saprotrophs than ectomycorrhizal fungi, while fungal P% of saprotrophs was more constrained. Fungal N : P was more responsive to soil N : P for ectomycorrhizal fungi (homeostatic regulation coefficient 'H' = 2.9) than saprotrophs (H = 5.9), while N : P of ectomycorrhizal fungi and host tree foliage scaled almost identically. Results underscore the role of ectomycorrhizal fungi as nutrient conduits, supporting host trees, whereas saprotrophs maintain a greater degree of nutritional homeostasis. Site nutrient constraints were shared in equal measure between ectomycorrhizal fungi and host trees, particularly for P, suggesting neither partner benefits from enhanced nutrition at the expense of the other. Sporocarp stoichiometry provides new insights into mycorrhizal relationships and illustrates pervasive P deficiencies across temperate rainforests of the Pacific Northwest.
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Affiliation(s)
- J Marty Kranabetter
- British Columbia Ministry of Forests, Lands and Natural Resource Operations, PO Box 9536, Stn Prov Govt, Victoria, BC, V8W 9C4, Canada
| | - Rachael Harman-Denhoed
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, Victoria, BC, V8W 3N5, Canada
| | - Barbara J Hawkins
- Centre for Forest Biology, University of Victoria, PO Box 3020, STN CSC, Victoria, BC, V8W 3N5, Canada
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Zeng W, Zhang J, Wang W. Strong root respiration response to nitrogen and phosphorus addition in nitrogen-limited temperate forests. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 642:646-655. [PMID: 29909332 DOI: 10.1016/j.scitotenv.2018.06.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 06/08/2023]
Abstract
Nutrient availability is one of the key regulator of the global forest carbon balance. The use of fossil fuels and fertilizers has increased the amount of biologically reactive nitrogen (N) in recent decades and N fertilization also changes the availability of other nutrients such as phosphorous (P) and potassium (K). The increased soil nutrient availability is known to stimulate forest growth, but we currently lack comprehensive understanding of the response of soil respiration and its three components (roots, microbes, and ectomycorrhizal (ECM) fungi) to the increased soil N, P and K availability. We conducted a 4-year field fertilization experiment with N, P and K addition in an N-limited temperate forest and separated ECM fungi respiration (Rm), root respiration (Rr) and heterotrophic microbial respiration (Rh) from total soil respiration. Our results showed that Rr increased with N and P addition while Rh and Rm did not respond to nutrient addition. Rm, Rr and Rh varied substantially from year to year, but their responses to nutrient addition did not fluctuate in different years. Our results indicate that in N-limited forest ecosystems, Rh and Rm may not respond substantially to future changes in nutrient addition and that inter-annual variation in climate may be the determinant of soil CO2 efflux in response to global changes.
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Affiliation(s)
- Wenjing Zeng
- Department of Ecology, College of Urban and Environmental Sciences, the Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
| | - Jiangyong Zhang
- Department of Ecology, College of Urban and Environmental Sciences, the Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China; Key Laboratory for Urban Habitat Environmental Science and Technology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Wei Wang
- Department of Ecology, College of Urban and Environmental Sciences, the Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China.
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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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Procter AC, Ellis JC, Fay PA, Polley HW, Jackson RB. Fungal Community Responses to Past and Future Atmospheric CO2 Differ by Soil Type. Appl Environ Microbiol 2014; 80:7364-77. [PMID: 25239904 PMCID: PMC4249185 DOI: 10.1128/aem.02083-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/16/2014] [Indexed: 11/20/2022] Open
Abstract
Soils sequester and release substantial atmospheric carbon, but the contribution of fungal communities to soil carbon balance under rising CO2 is not well understood. Soil properties likely mediate these fungal responses but are rarely explored in CO2 experiments. We studied soil fungal communities in a grassland ecosystem exposed to a preindustrial-to-future CO2 gradient (250 to 500 ppm) in a black clay soil and a sandy loam soil. Sanger sequencing and pyrosequencing of the rRNA gene cluster revealed that fungal community composition and its response to CO2 differed significantly between soils. Fungal species richness and relative abundance of Chytridiomycota (chytrids) increased linearly with CO2 in the black clay (P < 0.04, R(2) > 0.7), whereas the relative abundance of Glomeromycota (arbuscular mycorrhizal fungi) increased linearly with elevated CO2 in the sandy loam (P = 0.02, R(2) = 0.63). Across both soils, decomposition rate was positively correlated with chytrid relative abundance (r = 0.57) and, in the black clay soil, fungal species richness. Decomposition rate was more strongly correlated with microbial biomass (r = 0.88) than with fungal variables. Increased labile carbon availability with elevated CO2 may explain the greater fungal species richness and Chytridiomycota abundance in the black clay soil, whereas increased phosphorus limitation may explain the increase in Glomeromycota at elevated CO2 in the sandy loam. Our results demonstrate that soil type plays a key role in soil fungal responses to rising atmospheric CO2.
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Affiliation(s)
- Andrew C Procter
- Department of Biology, Duke University, Durham, North Carolina, USA
| | | | - Philip A Fay
- Grassland, Soil and Water Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Temple, Texas, USA
| | - H Wayne Polley
- Grassland, Soil and Water Research Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Temple, Texas, USA
| | - Robert B Jackson
- Department of Biology, Duke University, Durham, North Carolina, USA Nicholas School of the Environment, Duke University, Durham, North Carolina, USA School of Earth Sciences, Stanford University, Stanford, California, USA
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Uroz S, Courty PE, Pierrat JC, Peter M, Buée M, Turpault MP, Garbaye J, Frey-Klett P. Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum. MICROBIAL ECOLOGY 2013; 66:404-15. [PMID: 23455431 DOI: 10.1007/s00248-013-0199-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 02/08/2013] [Indexed: 05/09/2023]
Abstract
An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.
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Affiliation(s)
- S Uroz
- INRA, UMR1136 INRA-Nancy Université Interactions Arbres-Microorganismes, Centre INRA de Nancy, 54280, Champenoux, France.
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Ofek M, Hadar Y, Minz D. Ecology of root colonizing Massilia (Oxalobacteraceae). PLoS One 2012; 7:e40117. [PMID: 22808103 PMCID: PMC3394795 DOI: 10.1371/journal.pone.0040117] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 06/01/2012] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Ecologically meaningful classification of bacterial populations is essential for understanding the structure and function of bacterial communities. As in soils, the ecological strategy of the majority of root-colonizing bacteria is mostly unknown. Among those are Massilia (Oxalobacteraceae), a major group of rhizosphere and root colonizing bacteria of many plant species. METHODOLOGY/PRINCIPAL FINDINGS The ecology of Massilia was explored in cucumber root and seed, and compared to that of Agrobacterium population, using culture-independent tools, including DNA-based pyrosequencing, fluorescence in situ hybridization and quantitative real-time PCR. Seed- and root-colonizing Massilia were primarily affiliated with other members of the genus described in soil and rhizosphere. Massilia colonized and proliferated on the seed coat, radicle, roots, and also on hyphae of phytopathogenic Pythium aphanidermatum infecting seeds. High variation in Massilia abundance was found in relation to plant developmental stage, along with sensitivity to plant growth medium modification (amendment with organic matter) and potential competitors. Massilia absolute abundance and relative abundance (dominance) were positively related, and peaked (up to 85%) at early stages of succession of the root microbiome. In comparison, variation in abundance of Agrobacterium was moderate and their dominance increased at later stages of succession. CONCLUSIONS In accordance with contemporary models for microbial ecology classification, copiotrophic and competition-sensitive root colonization by Massilia is suggested. These bacteria exploit, in a transient way, a window of opportunity within the succession of communities within this niche.
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Affiliation(s)
- Maya Ofek
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Bet Dagan, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yitzhak Hadar
- The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dror Minz
- Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Bet Dagan, Israel
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