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Aleklett K, Rosa D, Pickles BJ, Hart MM. Community Assembly and Stability in the Root Microbiota During Early Plant Development. Front Microbiol 2022; 13:826521. [PMID: 35531294 PMCID: PMC9069014 DOI: 10.3389/fmicb.2022.826521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
Little is known about how community composition in the plant microbiome is affected by events in the life of a plant. For example, when the plant is exposed to soil, microbial communities may be an important factor in root community assembly. We conducted two experiments asking whether the composition of the root microbiota in mature plants could be determined by either the timing of root exposure to microbial communities or priority effects by early colonizing microbes. Timing of microbial exposure was manipulated through an inoculation experiment, where plants of different ages were exposed to a common soil inoculum. Priority effects were manipulated by challenging roots with established microbiota with an exogenous microbial community. Results show that even plants with existing microbial root communities were able to acquire new microbial associates, but that timing of soil exposure affected root microbiota composition for both bacterial and fungal communities in mature plants. Plants already colonized were only receptive to colonizers at 1 week post-germination. Our study shows that the timing of soil exposure in the early life stages of a plant is important for the development of the root microbiota in mature plants.
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Affiliation(s)
- Kristin Aleklett
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Lomm, Sweden
| | - Daniel Rosa
- Department of Biology, University of British Columbia – Okanagan, Kelowna, BC, Canada
| | - Brian John Pickles
- School of Biological Sciences, University of Reading, Health & Life Sciences Building, Whiteknights, United Kingdom
| | - Miranda M. Hart
- Department of Biology, University of British Columbia – Okanagan, Kelowna, BC, Canada
- *Correspondence: Miranda M. Hart,
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2
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Martignoni MM, Garnier J, Zhang X, Rosa D, Kokkoris V, Tyson RC, Hart MM. Co-inoculation with arbuscular mycorrhizal fungi differing in carbon sink strength induces a synergistic effect in plant growth. J Theor Biol 2021; 531:110859. [PMID: 34389360 DOI: 10.1016/j.jtbi.2021.110859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022]
Abstract
Arbuscular mycorrhizal (AM) fungi play a key role in determining ecosystem functionality. Understanding how diversity in the fungal community affects plant productivity is therefore an important question in ecology. Current research has focused on understanding the role of functional complementarity in the fungal community when the host plant faces multiple stress factors. Fewer studies, however, have investigated how variation in traits affecting nutrient exchange can impact the plant growth dynamics, even in the absence of environmental stressors. Combining experimental data and a mathematical model based on ordinary differential equations, we investigate the role played by carbon sink strength on plant productivity. We simulate and measure plant growth over time when the plant is associated with two fungal isolates with different carbon sink strength, and when the plant is in pairwise association with each of the isolates alone. Overall, our theoretical as well as our experimental results show that co-inoculation with fungi with different carbon sink strength can induce positive non-additive effects (or synergistic effects) in plant productivity. Fungi with high carbon sink strength are able to quickly establish a fungal community and increase the nutrient supply to the plant, with a consequent positive impact on plant growth rate. On the other side, fungi with low carbon sink strength inflict lower carbon costs to the host plant, and support maximal plant productivity once plant biomass is large. As AM fungi are widely used as organic fertilizers worldwide, our findings have important implications for restoration ecology and agricultural management.
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Affiliation(s)
- Maria M Martignoni
- Department of Mathematics, University of British Columbia, Kelowna (BC), Canada; Department of Mathematics and Statistics, Memorial University, St. John's (NL), Canada
| | - Jimmy Garnier
- LAboratoire de MAthématiques (LAMA), CNRS, Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, Chambery, France
| | - Xinlu Zhang
- Department of Biology, University of British Columbia, Kelowna (BC), Canada
| | - Daniel Rosa
- Department of Biology, University of British Columbia, Kelowna (BC), Canada
| | - Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa (ON), Canada; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa (ON), Canada
| | - Rebecca C Tyson
- Department of Mathematics, University of British Columbia, Kelowna (BC), Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Kelowna (BC), Canada
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3
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Martignoni MM, Garnier J, Hart MM, Tyson RC. Investigating the impact of the mycorrhizal inoculum on the resident fungal community and on plant growth. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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4
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Kokkoris V, Lekberg Y, Antunes PM, Fahey C, Fordyce JA, Kivlin SN, Hart MM. Codependency between plant and arbuscular mycorrhizal fungal communities: what is the evidence? New Phytol 2020; 228:828-838. [PMID: 32452032 DOI: 10.1111/nph.16676] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/26/2020] [Indexed: 05/09/2023]
Abstract
That arbuscular mycorrhizal (AM) fungi covary with plant communities is clear, and many papers report nonrandom associations between symbiotic partners. However, these studies do not test the causal relationship, or 'codependency', whereby the composition of one guild affects the composition of the other. Here we outline underlying requirements for codependency, compare important drivers for both plant and AM fungal communities, and assess how host preference - a pre-requisite for codependency - changes across spatiotemporal scales and taxonomic resolution for both plants and AM fungi. We find few examples in the literature designed to test for codependency and those that do have been conducted within plots or mesocosms. Also, while plants and AM fungi respond similarly to coarse environmental filters, most variation remains unexplained, with host identity explaining less than 30% of the variation in AM fungal communities. These results combined question the likelihood of predictable co-occurrence, and therefore evolution of codependency, between plant and AM fungal taxa across locations. We argue that codependency is most likely to occur in homogeneous environments where specific plant - AM fungal pairings have functional consequences for the symbiosis. We end by outlining critical aspects to consider moving forward.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Ylva Lekberg
- MPG Ranch and University of Montana, Missoula, MT, 59833, USA
| | - Pedro M Antunes
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - Catherine Fahey
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6A 2G4, Canada
| | - James A Fordyce
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Stephanie N Kivlin
- Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Miranda M Hart
- Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada
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5
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Martignoni MM, Hart MM, Garnier J, Tyson RC. Parasitism within mutualist guilds explains the maintenance of diversity in multi-species mutualisms. THEOR ECOL-NETH 2020. [DOI: 10.1007/s12080-020-00472-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Martignoni MM, Hart MM, Tyson RC, Garnier J. Diversity within mutualist guilds promotes coexistence and reduces the risk of invasion from an alien mutualist. Proc Biol Sci 2020; 287:20192312. [PMID: 32208836 DOI: 10.1098/rspb.2019.2312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Biodiversity is an important component of healthy ecosystems, and thus understanding the mechanisms behind species coexistence is critical in ecology and conservation biology. In particular, few studies have focused on the dynamics resulting from the co-occurrence of mutualistic and competitive interactions within a group of species. Here we build a mathematical model to study the dynamics of a guild of competitors who are also engaged in mutualistic interactions with a common partner. We show that coexistence as well as competitive exclusion can occur depending on the competition strength and on strength of the mutualistic interactions, and we formulate concrete criteria for predicting invasion success of an alien mutualist based on propagule pressure, alien traits (such as its resource exchange ability) and composition of the recipient community. We find that intra guild diversity promotes the coexistence of species that would otherwise competitively exclude each other, and makes a guild less vulnerable to invasion. Our results can serve as a useful framework to predict the consequences of species manipulation in mutualistic communities.
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Affiliation(s)
- Maria M Martignoni
- Department of Mathematics, University of British Columbia, Kelowna, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Kelowna, Canada
| | - Rebecca C Tyson
- Department of Mathematics, University of British Columbia, Kelowna, Canada
| | - Jimmy Garnier
- Laboratoire de Mathématiques (LAMA), CNRS and Université de Savoie-Mont Blanc, Chambery, France
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7
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Kokkoris V, Pogiatzis A, Hart MM. Contrasting common measures of arbuscular mycorrhizal fungal root colonization. J Microbiol Methods 2019; 167:105727. [PMID: 31629912 DOI: 10.1016/j.mimet.2019.105727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/20/2019] [Accepted: 09/20/2019] [Indexed: 11/15/2022]
Abstract
Estimating the abundance of arbuscular mycorrhizal fungi relies entirely on indirect methods, meaning all measures are associated with some variability. The most common methods use microscopic estimates of the relative proportion of root length colonized by fungal structures. These methods typically examine root subsamples. While such methods are inexpensive and relatively simple, significant variation within single root system means there is opportunity for sampling bias. We evaluated the two most common methods of percent root length colonization for AM fungi both as a subsample and for the entire root system of flax plants. We compared these measures to a novel technique that returns projected fungal surface area (fungal coverage), by using microphotography and imaging analysis. Both microscopic methods overestimated the colonization intensity compared to image analysis. Among the microscopic methods, the method which incorporated colonization intensity (Trouvelot) was significantly more similar to imaging method results, than the method that is based on the presence/absence of the fungus (McGonigle).
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
| | - Antreas Pogiatzis
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
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8
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Abstract
We proposed a theoretical framework predicting mutualistic outcomes for the arbuscular mycorrhizal (AM) symbiosis based on host provenance (crop versus wild). To test the framework, we grew two isolates of Rhizoglomus irregulare (commercial versus an isolate locally isolated), with five crop plants and five wild plants endemic to the region that co-occur with the locally sourced fungus. While inoculation with either isolate had no effect on plant biomass, it decreased leaf P content, particularly for wild plants. All plants associating with the commercial fungus had lower leaf P. Overall, our data shows that wild plants may be more sensitive to differences in mutualistic quality among fungal isolates.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC, Canada
| | - Chantal Hamel
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec, QC, Canada
| | - Miranda M. Hart
- Department of Biology, University of British Columbia, Okanagan campus, Kelowna, BC, Canada
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9
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Affiliation(s)
- Miranda M. Hart
- Botany Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
| | - Richard J. Reader
- Botany Department, University of Guelph, Guelph, ON, Canada, N1G 2W1
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10
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Kokkoris V, Miles T, Hart MM. The role of in vitro cultivation on asymbiotic trait variation in a single species of arbuscular mycorrhizal fungus. Fungal Biol 2019; 123:307-317. [PMID: 30928039 DOI: 10.1016/j.funbio.2019.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/29/2018] [Accepted: 01/17/2019] [Indexed: 01/13/2023]
Abstract
Cultivating arbuscular mycorrhizal (AM) fungi in vitro is an efficient way to produce material for industry and research. However, such artificial growing conditions may impose selective pressure on fungi grown in vitro over many generations. We hypothesized that isolates subjected to long term propagation in vitro may develop increasingly ruderal traits. We proposed a predictive framework for the effect of in vitro cultivation on asymbiotic AM fungal traits. Using photomicrography and image processing, we analyzed morphology and growth traits for 14 isolates representing an in vitro cultivation gradient from 0 to >80 generations in vitro. We investigated the range of trait variation among asymbiotic growth of arbuscular mycorrhizal (AM) fungus isolates (Rhizoglomus irregulare). Spore dormancy was strongly associated with in vitro cultivation. We observed extremely high levels of inter-isolate variation for most fungal traits, but this was not related to time in vitro. Our results indicate that intra-specific diversity may have a strong ecological role in AM fungal communities.
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Affiliation(s)
- Vasilis Kokkoris
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada.
| | - Thea Miles
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7, Canada
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11
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Hoeksema JD, Bever JD, Chakraborty S, Chaudhary VB, Gardes M, Gehring CA, Hart MM, Housworth EA, Kaonongbua W, Klironomos JN, Lajeunesse MJ, Meadow J, Milligan BG, Piculell BJ, Pringle A, Rúa MA, Umbanhowar J, Viechtbauer W, Wang YW, Wilson GWT, Zee PC. Erratum: Author Correction: Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism. Commun Biol 2018; 1:142. [PMID: 30273421 PMCID: PMC6127152 DOI: 10.1038/s42003-018-0143-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
[This corrects the article DOI: 10.1038/s42003-018-0120-9.].
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Affiliation(s)
- Jason D Hoeksema
- Department of Biology, University of Mississippi, University, MS, 38677, USA.
| | - James D Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
| | - Sounak Chakraborty
- Department of Statistics, University of Missouri, Columbia, MO, 65201, USA
| | - V Bala Chaudhary
- Department of Environmental Science and Studies, DePaul University, Chicago, IL, 60614, USA
| | - Monique Gardes
- Laboratoire Évolution et Diversité Biologique, UMR5174 UPS - CNRS - IRD - ENSFEA, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Catherine A Gehring
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Miranda M Hart
- Department of Biology, University of British Columbia-Okanagan, Kelowna, BC, V1V 1V7, Canada
| | | | - Wittaya Kaonongbua
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - John N Klironomos
- Department of Biology, University of British Columbia-Okanagan, Kelowna, BC, V1V 1V7, Canada
| | - Marc J Lajeunesse
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - James Meadow
- Department of Land Resources and Environmental Sciences, Montana State University, 344 Leon Johnson Hall, Bozeman, MT, 59717, USA.,Institute of Ecology and Evolution, University of Oregon, 335 Pacific Hall, Eugene, OR, 97403, USA
| | - Brook G Milligan
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Bridget J Piculell
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan A Rúa
- Department of Biological Sciences, Wright State University, Dayton, OH, 45435, USA
| | - James Umbanhowar
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Neuropsychology, Maastricht University, 6200, Maastricht, Netherlands
| | - Yen-Wen Wang
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gail W T Wilson
- Natural Resource Ecology & Management, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Peter C Zee
- Department of Biology, University of Mississippi, University, MS, 38677, USA
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12
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Abstract
How men and women are portrayed in the media informs societal attitudes towards gender. Although this is true for all media, the scientific media has received little scrutiny, despite known gender biases inherent in scientific culture. We asked whether the top scientific journals, Nature and Science, represented men and women equally as authors, subjects, and objects in photographs. Overwhelmingly, women were underrepresented in these magazines, an effect that was apparent even in advertisements and stock photographs. Clearly, gender bias in science exists at many levels.
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Affiliation(s)
- Becky Loverock
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Miranda M. Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC V1V 1V7, Canada
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13
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Hoeksema JD, Bever JD, Chakraborty S, Chaudhary VB, Gardes M, Gehring CA, Hart MM, Housworth EA, Kaonongbua W, Klironomos JN, Lajeunesse MJ, Meadow J, Milligan BG, Piculell BJ, Pringle A, Rúa MA, Umbanhowar J, Viechtbauer W, Wang YW, Wilson GWT, Zee PC. Evolutionary history of plant hosts and fungal symbionts predicts the strength of mycorrhizal mutualism. Commun Biol 2018; 1:116. [PMID: 30271996 PMCID: PMC6123707 DOI: 10.1038/s42003-018-0120-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 07/24/2018] [Indexed: 11/09/2022] Open
Abstract
Most plants engage in symbioses with mycorrhizal fungi in soils and net consequences for plants vary widely from mutualism to parasitism. However, we lack a synthetic understanding of the evolutionary and ecological forces driving such variation for this or any other nutritional symbiosis. We used meta-analysis across 646 combinations of plants and fungi to show that evolutionary history explains substantially more variation in plant responses to mycorrhizal fungi than the ecological factors included in this study, such as nutrient fertilization and additional microbes. Evolutionary history also has a different influence on outcomes of ectomycorrhizal versus arbuscular mycorrhizal symbioses; the former are best explained by the multiple evolutionary origins of ectomycorrhizal lifestyle in plants, while the latter are best explained by recent diversification in plants; both are also explained by evolution of specificity between plants and fungi. These results provide the foundation for a synthetic framework to predict the outcomes of nutritional mutualisms.
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Affiliation(s)
- Jason D Hoeksema
- Department of Biology, University of Mississippi, University, MS, 38677, USA.
| | - James D Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
| | - Sounak Chakraborty
- Department of Statistics, University of Missouri, Columbia, MO, 65201, USA
| | - V Bala Chaudhary
- Department of Environmental Science and Studies, DePaul University, Chicago, IL, 60614, USA
| | - Monique Gardes
- Laboratoire Évolution et Diversité Biologique, UMR5174 UPS - CNRS - IRD - ENSFEA, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Catherine A Gehring
- Department of Biological Sciences and Merriam-Powell Center for Environmental Research, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Miranda M Hart
- Department of Biology, University of British Columbia-Okanagan, Kelowna, BC, V1V 1V7, Canada
| | | | - Wittaya Kaonongbua
- Department of Microbiology, Faculty of Science, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - John N Klironomos
- Department of Biology, University of British Columbia-Okanagan, Kelowna, BC, V1V 1V7, Canada
| | - Marc J Lajeunesse
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - James Meadow
- Department of Land Resources and Environmental Sciences, Montana State University, 344 Leon Johnson Hall, Bozeman, MT, 59717, USA
- Institute of Ecology and Evolution, University of Oregon, 335 Pacific Hall, Eugene, OR, 97403, USA
| | - Brook G Milligan
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Bridget J Piculell
- Department of Biology, College of Charleston, Charleston, SC, 29424, USA
| | - Anne Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Megan A Rúa
- Department of Biological Sciences, Wright State University, Dayton, OH, 45435, USA
| | - James Umbanhowar
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Neuropsychology, Maastricht University, 6200, MD, Maastricht, Netherlands
| | - Yen-Wen Wang
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gail W T Wilson
- Natural Resource Ecology & Management, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Peter C Zee
- Department of Biology, University of Mississippi, University, MS, 38677, USA
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14
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Lekberg Y, Bever JD, Bunn RA, Callaway RM, Hart MM, Kivlin SN, Klironomos J, Larkin BG, Maron JL, Reinhart KO, Remke M, van der Putten WH. Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence. Ecol Lett 2018; 21:1268-1281. [PMID: 29896848 DOI: 10.1111/ele.13093] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Revised: 12/28/2017] [Accepted: 05/03/2018] [Indexed: 01/22/2023]
Abstract
Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant-soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low-resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure.
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Affiliation(s)
- Ylva Lekberg
- MPG Ranch Missoula, MT, 59801, USA.,Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, 59812, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, and Kansas Biological Survey, University of Kansas, Lawrence, KS, 66047, USA
| | - Rebecca A Bunn
- Department of Environmental Sciences, Western Washington University, Bellingham, WA, 98225, USA
| | - Ragan M Callaway
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812.,Wildlife Biology and the Institute on Ecosystems, University of Montana, Missoula, MT
| | - Miranda M Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada
| | - Stephanie N Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - John Klironomos
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada
| | | | - John L Maron
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812
| | - Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Michael Remke
- School of Forestry, College of Engineering Forestry and Natural Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Wim H van der Putten
- Department of Terrestrial Ecology (NIOO-KNAW), Netherlands Institute of Ecology, 6708 PB, Wageningen, the Netherlands.,Department of Plant Sciences, Laboratory of Nematology, Wageningen University (WUR), 6700 ES, Wageningen, the Netherlands
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15
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16
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Tasnim N, Abulizi N, Pither J, Hart MM, Gibson DL. Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live? Front Microbiol 2017; 8:1935. [PMID: 29056933 PMCID: PMC5635058 DOI: 10.3389/fmicb.2017.01935] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022] Open
Abstract
Global comparisons reveal a decrease in gut microbiota diversity attributed to Western diets, lifestyle practices such as caesarian section, antibiotic use and formula-feeding of infants, and sanitation of the living environment. While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernized societies. Since the immune system development is influenced by microbial components, early microbial colonization may be a key factor in determining disease susceptibility patterns later in life. Evidence indicates that the gut microbiota is vertically transmitted from the mother and this affects offspring immunity. However, the role of the external environment in gut microbiome and immune development is poorly understood. Studies show that growing up in microbe-rich environments, such as traditional farms, can have protective health effects on children. These health-effects may be ablated due to changes in the human lifestyle, diet, living environment and environmental biodiversity as a result of urbanization. Importantly, if early-life exposure to environmental microbes increases gut microbiota diversity by influencing patterns of gut microbial assembly, then soil biodiversity loss due to land-use changes such as urbanization could be a public health threat. Here, we summarize key questions in environmental health research and discuss some of the challenges that have hindered progress toward a better understanding of the role of the environment on gut microbiome development.
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Affiliation(s)
- Nishat Tasnim
- Department of Biology, The Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Nijiati Abulizi
- Department of Biology, The Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Jason Pither
- Department of Biology, The Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Miranda M Hart
- Department of Biology, The Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC, Canada
| | - Deanna L Gibson
- Department of Biology, The Irving K. Barber School of Arts and Sciences, University of British Columbia, Kelowna, BC, Canada
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Eisenhauer N, Antunes PM, Bennett AE, Birkhofer K, Bissett A, Bowker MA, Caruso T, Chen B, Coleman DC, de Boer W, de Ruiter P, DeLuca TH, Frati F, Griffiths BS, Hart MM, Hättenschwiler S, Haimi J, Heethoff M, Kaneko N, Kelly LC, Leinaas HP, Lindo Z, Macdonald C, Rillig MC, Ruess L, Scheu S, Schmidt O, Seastedt TR, van Straalen NM, Tiunov AV, Zimmer M, Powell JR. Priorities for research in soil ecology. Pedobiologia (Jena) 2017; 63:1-7. [PMID: 29129942 PMCID: PMC5675051 DOI: 10.1016/j.pedobi.2017.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ecological interactions that occur in and with soil are of consequence in many ecosystems on the planet. These interactions provide numerous essential ecosystem services, and the sustainable management of soils has attracted increasing scientific and public attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In this perspectives paper, we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia - Journal of Soil Ecology. These editors work at universities and research centers in Europe, North America, Asia, and Australia.The questions were categorized into four themes: (1) soil biodiversity and biogeography, (2) interactions and the functioning of ecosystems, (3) global change and soil management, and (4) new directions. The respondents identified priorities that may be achievable in the near future, as well as several that are currently achievable but remain open. While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise.
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Affiliation(s)
- Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
- Institute of Biology, Leipzig University, Johannisallee 21, 04103 Leipzig, Germany
- Corresponding author:
| | - Pedro M. Antunes
- Department of Biology, Algoma University, 1520 Queen Street East, Sault Ste. Marie, ON, P6A 2G4 Canada
| | - Alison E. Bennett
- Ecological Sciences, James Hutton Institute, Errol Road, Invergowrie, Dundee DD2 5DA United Kingdom
| | - Klaus Birkhofer
- Chair of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046 Cottbus, Germany
| | - Andrew Bissett
- CSIRO Oceans and Atmosphere, Hobart, TAS 7000, Australia
| | - Matthew A. Bowker
- School of Forestry, Northern Arizona University, 200 East Pine Knoll Drive, Flagstaff, Arizona 86011, USA
| | - Tancredi Caruso
- School of Biological Sciences and Institute for Global Food Security, Queen's University of Belfast, 97 Lisburn Road, Belfast, BT9 7BL, Northern Ireland
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 18 Shuangqinglu, Haidian District, Beijing 100085, China
- University of Chinese Academy of Sciences, 19 Yuquanlu, Shijingshan District, Beijing 100049, China
| | - David C. Coleman
- Odum School of Ecology, University of Georgia, Athens, Georgia 30602, USA
| | - Wietse de Boer
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, 6708 PB, The Netherlands
- Department of Soil Quality, Wageningen University, Wageningen, 6708 PB, the Netherlands
| | - Peter de Ruiter
- Institute for Biodiversity and Ecosystem Dynamics (IBED), Faculty of Science, Universiteit van Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Thomas H. DeLuca
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA 98195-2100, USA
| | - Francesco Frati
- Department of Life Sciences, University of Siena, via Aldo Moro 2, 53100, Siena, Italy
| | - Bryan S. Griffiths
- Crop and Soil Systems Research Group, Scotland’s Rural College, West Mains Road, Edinburgh, EH9 3JG, United Kingdom
| | - Miranda M. Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna, BC, Canada
| | - Stephan Hättenschwiler
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE) UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHE, 1919 Route de Mende, 34293 Montpellier, France
| | - Jari Haimi
- Department of Biological and Environmental Science, University of Jyväskylä, P.O.Box 35, FI-40014, Finland
| | - Michael Heethoff
- Ecological Networks, TU Darmstadt, Schnittspahnstr. 3, 64287 Darmstadt
| | - Nobuhiro Kaneko
- Soil Ecology Research Group, Yokohama National University ,79-7 Tokiwadai, Hodogaya, Yokohama 240-8501, Japan
| | - Laura C. Kelly
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Oxford Road, M1 5GD, United Kingdom
| | - Hans Petter Leinaas
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Zoë Lindo
- Department of Biology, The University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Catriona Macdonald
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
| | - Matthias C. Rillig
- Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195 Berlin, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), 14195 Berlin, Germany
| | - Liliane Ruess
- Institute of Biology, Ecology Group, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Stefan Scheu
- JFB Institute of Zoology and Anthropology, University of Göttingen, Berliner Str. 28, 37073 Göttingen, Germany
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Timothy R. Seastedt
- Department of Ecology and Evolutionary Biology, Institute of Arctic and Alpine Research, University of Colorado, Boulder, UCB 450, CO 80309, USA
| | - Nico M. van Straalen
- Department of Ecological Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution RAS, Leninsky Prospect 33, 119071 Moscow, Russia
| | - Martin Zimmer
- Leibniz-Centre for Tropical Marine Research, Fahrenheitstr. 6, 28359 Bremen
| | - Jeff R. Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith NSW 2751, Australia
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Ohsowski BM, Dunfield K, Klironomos JN, Hart MM. Plant response to biochar, compost, and mycorrhizal fungal amendments in post-mine sandpits. Restor Ecol 2017. [DOI: 10.1111/rec.12528] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brian M. Ohsowski
- Institute of Environmental Sustainability; Loyola University Chicago - Lakeshore Campus; Chicago IL 60660 U.S.A
| | - Kari Dunfield
- School of Environmental Sciences; University of Guelph; Guelph ON N1G 2W1 Canada
| | - John N. Klironomos
- Department of Biology; University of British Columbia; Okanagan Campus Kelowna BC V1V 1V7 Canada
| | - Miranda M. Hart
- Department of Biology; University of British Columbia; Okanagan Campus Kelowna BC V1V 1V7 Canada
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Koch AM, Antunes PM, Maherali H, Hart MM, Klironomos JN. Evolutionary asymmetry in the arbuscular mycorrhizal symbiosis: conservatism in fungal morphology does not predict host plant growth. New Phytol 2017; 214:1330-1337. [PMID: 28186629 DOI: 10.1111/nph.14465] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/24/2016] [Indexed: 05/19/2023]
Abstract
Although arbuscular mycorrhizal (AM) fungi are obligate symbionts that can influence plant growth, the magnitude and direction of these effects are highly variable within fungal genera and even among isolates within species, as well as among plant taxa. To determine whether variability in AM fungal morphology and growth is correlated with AM fungal effects on plant growth, we established a common garden experiment with 56 AM fungal isolates comprising 17 genera and six families growing with three plant host species. Arbuscular mycorrhizal fungal morphology and growth was highly conserved among isolates of the same species and among species within a family. By contrast, plant growth response to fungal inoculation was highly variable, with the majority of variation occurring among different isolates of the same AM fungal species. Our findings show that host performance cannot be predicted from AM fungal morphology and growth traits. Divergent effects on plant growth among isolates within an AM fungal species may be caused by coevolution between co-occurring fungal and plant populations.
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Affiliation(s)
- Alexander M Koch
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - Pedro M Antunes
- Department of Biology, Algoma University, Sault Ste. Marie, ON, P6B 2G4, Canada
| | - Hafiz Maherali
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
| | - John N Klironomos
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, V1V 1V7, Canada
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Egan CP, Callaway RM, Hart MM, Pither J, Klironomos J. Phylogenetic structure of arbuscular mycorrhizal fungal communities along an elevation gradient. Mycorrhiza 2017; 27:273-282. [PMID: 27909817 DOI: 10.1007/s00572-016-0752-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Despite the importance of arbuscular mycorrhizal (AM) fungi within terrestrial ecosystems, we know little about how natural AM fungal communities are structured. To date, the majority of studies examining AM fungal community diversity have focused on single habitats with similar environmental conditions, with relatively few studies having assessed the diversity of AM fungi over large-scale environmental gradients. In this study, we characterized AM fungal communities in the soil along a high-elevation gradient in the North American Rocky Mountains. We focused on phylogenetic patterns of AM fungal communities to gain insight into how AM fungal communities are naturally assembled. We found that alpine AM fungal communities had lower phylogenetic diversity relative to lower elevation communities, as well as being more heterogeneous in composition than either treeline or subalpine communities. AM fungal communities were phylogenetically clustered at all elevations sampled, suggesting that environmental filtering, either selection by host plants or fungal niches, is the primary ecological process structuring communities along the gradient.
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Affiliation(s)
- Cameron P Egan
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada.
| | - Ragan M Callaway
- Division of Biological Sciences and the Institute on Ecosystems, University of Montana, Missoula, MT, 59812, USA
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - Jason Pither
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
| | - John Klironomos
- Department of Biology, University of British Columbia, Okanagan campus, 3333 University Way, Kelowna, BC, V1V 1V7, Canada
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Gorzelak MA, Pickles BJ, Hart MM. Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts. Mol Ecol 2017; 26:1586-1597. [PMID: 28099772 DOI: 10.1111/mec.14023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/26/2016] [Accepted: 01/03/2017] [Indexed: 11/28/2022]
Abstract
Arbuscular mycorrhizal fungi (AMF) are globally distributed, monophyletic root symbionts with ancient origins. Their contribution to carbon cycling and nutrient dynamics is ecologically important, given their obligate association with over 70% of vascular plant species. Current understanding of AMF species richness and community structure is based primarily on studies of grasses, herbs and agricultural crops, typically in disturbed environments. Few studies have considered AMF interactions with long-lived woody perennial species in undisturbed ecosystems. Here we examined AMF communities associated with roots and soils of young, mature and old western redcedar (Thuja plicata) at two sites in the old-growth temperate rainforests of British Columbia. Due to the unique biology of AMF, community richness and structure were assessed using a conservative, clade-based approach. We found 91 AMF OTUs across all samples, with significantly greater AMF richness in the southern site, but no differences in richness along the host chronosequence at either site. All host age classes harboured AMF communities that were overdispersed (more different to each other than expected by chance), with young tree communities most resembling old tree communities. A comparison with similar clade richness data obtained from the literature indicates that western redcedar AMF communities are as rich as those of grasses, tropical trees and palms. Our examination of undisturbed temperate old-growth rainforests suggests that priority effects, rather than succession, are an important aspect of AMF community assembly in this ecosystem.
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Affiliation(s)
- Monika A Gorzelak
- Department of Forest and Conservation Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Brian J Pickles
- School of Biological Sciences, University of Reading, Harborne Building, Whiteknights, Reading, RG6 8AS, UK
| | - Miranda M Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, V1V 1V7, Canada
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Bennett JA, Maherali H, Reinhart KO, Lekberg Y, Hart MM, Klironomos J. Plant-soil feedbacks and mycorrhizal type influence temperate forest population dynamics. Science 2017; 355:181-184. [DOI: 10.1126/science.aai8212] [Citation(s) in RCA: 340] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/25/2016] [Indexed: 01/25/2023]
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Liu L, Hart MM, Zhang J, Cai X, Gai J, Christie P, Li X, Klironomos JN. Altitudinal distribution patterns of AM fungal assemblages in a Tibetan alpine grassland. FEMS Microbiol Ecol 2015; 91:fiv078. [PMID: 26142427 DOI: 10.1093/femsec/fiv078] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2015] [Indexed: 11/13/2022] Open
Abstract
A better understanding of biogeography of Glomeromycota is essential for the conservation of arbuscular mycorrhizal (AM) fungal species and the ecosystem services that they provide worldwide. We examined the spatial dynamics of AM fungi along two slopes (4149 m a.s.l. to the summit at 5033 m a.s.l.) of Mount Mila on the Tibetan Plateau. Our hypothesis was that AM fungal communities at higher elevation would show distinct assemblages with lower diversity in conditions of increasing environmental harshness. A total of 52 operational taxonomic units (OTUs) spanning all four orders were detected and some OTUs were habitat specific. Nearly 30% of the OTUs were new phylotypes, including two family-like clades. Distinct communities of AM fungi were found at the higher elevation, demonstrating potential niche differentiation along the elevation gradient. Elevation patterns of taxon richness/diversity differed between the two transects, decreasing with increasing elevation on the eastern slope and being unimodal (or lacking a pattern) on the western slope. Taken together, our findings provide evidence of a significant spatial structure of AM fungi across the elevation gradient, with the distribution patterns of these fungi regulated simultaneously by the plant communities, soil properties and climatic conditions in this plateau montane ecosystem.
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Affiliation(s)
- Lei Liu
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC, Canada
| | - Junling Zhang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaobu Cai
- Tibet Agricultural and Animal Husbandry College, Tibet University, Linzhi 860000, Tibet
| | - Jingping Gai
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Peter Christie
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaolin Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - John N Klironomos
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC, Canada
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Hart MM, Aleklett K, Chagnon PL, Egan C, Ghignone S, Helgason T, Lekberg Y, Öpik M, Pickles BJ, Waller L. Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi. New Phytol 2015; 207:235-247. [PMID: 25737096 DOI: 10.1111/nph.13340] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/18/2015] [Indexed: 05/02/2023]
Abstract
Data generated from next generation sequencing (NGS) will soon comprise the majority of information about arbuscular mycorrhizal fungal (AMF) communities. Although these approaches give deeper insight, analysing NGS data involves decisions that can significantly affect results and conclusions. This is particularly true for AMF community studies, because much remains to be known about their basic biology and genetics. During a workshop in 2013, representatives from seven research groups using NGS for AMF community ecology gathered to discuss common challenges and directions for future research. Our goal was to improve the quality and accessibility of NGS data for the AMF research community. Discussions spanned sampling design, sample preservation, sequencing, bioinformatics and data archiving. With concrete examples we demonstrated how different approaches can significantly alter analysis outcomes. Failure to consider the consequences of these decisions may compound bias introduced at each step along the workflow. The products of these discussions have been summarized in this paper in order to serve as a guide for any researcher undertaking NGS sequencing of AMF communities.
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Affiliation(s)
- Miranda M Hart
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Kristin Aleklett
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Pierre-Luc Chagnon
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'université, Sherbrooke, QC, Canada
| | - Cameron Egan
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Stefano Ghignone
- Istituto per la Protezione Sostenibile delle Piante (UOS Torino), C.N.R., Torino, Italy
| | - Thorunn Helgason
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ylva Lekberg
- MPG Ranch and Department for Ecosystem and Conservation Sciences, University of Montana, Missoula, MT, USA
| | - Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Brian J Pickles
- Biology University of British Columbia Okanagan, Kelowna, BC, Canada
| | - Lauren Waller
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
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Aguilar-Trigueros CA, Hempel S, Powell JR, Anderson IC, Antonovics J, Bergmann J, Cavagnaro TR, Chen B, Hart MM, Klironomos J, Petermann JS, Verbruggen E, Veresoglou SD, Rillig MC. Branching out: Towards a trait-based understanding of fungal ecology. FUNGAL BIOL REV 2015. [DOI: 10.1016/j.fbr.2015.03.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Xing X, Gai X, Liu Q, Hart MM, Guo S. Mycorrhizal fungal diversity and community composition in a lithophytic and epiphytic orchid. Mycorrhiza 2015; 25:289-96. [PMID: 25319065 DOI: 10.1007/s00572-014-0612-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/07/2014] [Indexed: 05/20/2023]
Abstract
Some orchid species are present as epiphytes and lithophytes in the same habitat, but little is known about the differences of their mycorrhizal fungal communities. We used Coelogyne viscosa, which occurs both as an epiphyte and a lithophyte, as a study system to investigate orchid mycorrhizal fungal communities in lithophytes and epiphytes in Xishuangbanna National Nature Reserve (Yunnan Province, China). Twenty-three fungal operational taxonomic units (OTUs) from 18 sampling sites were identified. Results indicated that mycorrhizal fungal community composition was different between epi- and lithophytes. When we analyzed the Tulasnellaceae and Sebacinales communities separately, we found that the Sebacinales fungal communities were significantly different in the two growth habitats, but the Tulasnellaceae fungal communities were not. Our results provide evidence for distinct orchid mycorrhiza fungal communities depending on the growth habitat of the orchid. Consistent with some recent investigations of mycorrhizal fungus community composition, this study suggests that for one orchid, growth habitat affects mycorrhizal symbioses.
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Affiliation(s)
- Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China,
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Ohsowski BM, Zaitsoff PD, Öpik M, Hart MM. Where the wild things are: looking for uncultured Glomeromycota. New Phytol 2014; 204:171-179. [PMID: 24946898 DOI: 10.1111/nph.12894] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/13/2014] [Indexed: 06/03/2023]
Abstract
Our knowledge of Glomeromycotan fungi rests largely on studies of cultured isolates. However, these isolates probably comprise one life-history strategy - ruderal. Consequently, our knowledge of arbuscular mycorrhizal (AM) fungi may be biased towards fungi that occur primarily in disturbed habitats and associate with disturbance-tolerant host plants. We can expect to see a signal for this in DNA-based community surveys: human-impacted habitats and cultivated plants should yield a higher proportion of AM fungal species that have been cultured compared with natural habitats and wild plants. Using the MaarjAM database (a curated open-access database of Glomeromycotan sequences), we performed a meta-analysis on studies that described AM fungal communities from a variety of habitats and host plants. We found a greater proportion of cultured AM fungal taxa in human-impacted habitats. In particular, undisturbed forests and grasslands/savannahs contained significantly fewer cultured taxa than human-impacted sites. We also found that wild plants hosted fewer cultured fungal taxa than cultivated plants. Our data show that natural communities of AM fungi are composed largely of uncultured taxa, and this is particularly pronounced in natural habitats and wild plants. We are better poised to understand the functioning of AM symbioses associated with cultivated plants and human-impacted habitats.
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Affiliation(s)
- Brian M Ohsowski
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC, Canada
| | - P Dylan Zaitsoff
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC, Canada
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Miranda M Hart
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC, Canada
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Xing X, Ma X, Hart MM, Wang A, Guo S. Genetic diversity and evolution of Chinese traditional medicinal fungus Polyporus umbellatus (Polyporales, Basidiomycota). PLoS One 2013; 8:e58807. [PMID: 23554929 PMCID: PMC3598919 DOI: 10.1371/journal.pone.0058807] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 02/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polyporus umbellatus is an important medicinal fungus distributed throughout most area of China. Its wide distribution may have resulted in substantial intraspecific genetic diversity for the fungus, potentially creating variation in its medical value. To date, we know little about the intraspecific genetic diversity of P. umbellatus. METHODOLOGY/PRINCIPAL FINDINGS The objective of this research was to assess genetic differences of P. umbellatus from geographically diverse regions of China based on nrDNA ITS and 28S rRNA (LSU, large subunit) sequences. Significant sequence variations in the ITS and LSU sequences were detected. All sclerotial samples were clustered into four clades based on phylogenetic analysis of ITS, LSU and a combined data set of both regions. Heterogeneity of ITS and LSU sequences was detected in 5 and 7 samples respectively. All clone sequences clustered into the same clade except for one LSU clone sequences (from Henan province) which clustered into two clades (Clade I and Clade II). Significant genetic divergence in P. umbellatus was observed and the genetic diversification was greater among sclerotial samples from Shaanxi, Henan and Gansu provinces than among other provinces. Polymorphism of ITS and LSU sequences indicated that in China, P. umbellatus may spread from a center (Shaanxi, Henan and Gansu province) to other regions. CONCLUSIONS/SIGNIFICANCE We found sclerotial samples of P. umbellatus contained levels of intraspecific genetic diversity. These findings suggested that P. umbellatus populations in Shaanxi, Henan and Gansu are important resources of genetic diversity and should be conserved accordingly.
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Affiliation(s)
- Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xueting Ma
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Miranda M. Hart
- Biology, University of British Columbia Okanagan, Kelowna, Canada
| | - Airong Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shunxing Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Hart MM, Forsythe J, Oshowski B, Bücking H, Jansa J, Kiers ET. Hiding in a crowd—does diversity facilitate persistence of a low-quality fungal partner in the mycorrhizal symbiosis? Symbiosis 2012. [DOI: 10.1007/s13199-012-0197-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xing X, Koch AM, Jones AMP, Ragone D, Murch S, Hart MM. Mutualism breakdown in breadfruit domestication. Proc Biol Sci 2012; 279:1122-30. [PMID: 21920983 PMCID: PMC3267145 DOI: 10.1098/rspb.2011.1550] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 08/25/2011] [Indexed: 11/12/2022] Open
Abstract
During the process of plant domestication, below-ground communities are rarely considered. Some studies have attempted to understand the changes in root symbionts owing to domestication, but little is known about how it influences mycorrhizal response in domesticated crops. We hypothesized that selection for above-ground traits may also result in decreased mycorrhizal abundance in roots. Breadfruit (Artocarpus sp.) has a long domestication history, with a strong geographical movement of cultivars from west to east across the Melanesian and Polynesian islands. Our results clearly show a decrease in arbuscular mycorrhizas (AMs) along a domestication gradient from wild to recently derived cultivars. We showed that the vesicular and arbuscular colonization rate decreased significantly in more recently derived breadfruit cultivars. In addition, molecular analyses of breadfruit roots indicated that AM fungal species richness also responded along the domestication gradient. These results suggest that human-driven selection for plant cultivars can have unintended effects on below-ground mutualists, with potential impacts on the stress tolerance of crops and long-term food security.
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Affiliation(s)
- Xiaoke Xing
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Alexander M. Koch
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, CanadaV1V 1V7
| | - A. Maxwell P. Jones
- Department of Plant Agriculture, University of Guelph, Guelph, ON, CanadaN1G 2W1
| | - Diane Ragone
- Breadfruit Institute, National Tropical Botanical Garden, Kalaheo, HI 96741, USA
| | - Susan Murch
- Department of Chemistry, University of British Columbia Okanagan, Kelowna, BC, CanadaV1V 1V7
| | - Miranda M. Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna, BC, CanadaV1V 1V7
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Courtney KC, Bainard LD, Sikes BA, Koch AM, Maherali H, Klironomos JN, Hart MM. Determining a minimum detection threshold in terminal restriction fragment length polymorphism analysis. J Microbiol Methods 2011; 88:14-8. [PMID: 22015816 DOI: 10.1016/j.mimet.2011.09.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 09/30/2011] [Indexed: 12/21/2022]
Abstract
Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common technique used to characterize soil microbial diversity. The fidelity of this technique in accurately reporting diversity has not been thoroughly evaluated. Here we determine if rare fungal species can be reliably detected by T-RFLP analysis. Spores from three arbuscular mycorrhizal fungal species were each mixed at a range of concentrations (1%, 10%, 50%, and 100%) with Glomus irregulare to establish a minimum detection threshold. T-RFLP analysis was capable of detecting diagnostic peaks of rare taxa at concentrations as low as 1%. The relative proportion of the target taxa in the sample and DNA concentration influenced peak detection reliability. However, low concentrations produced small, inconsistent electropherogram peaks contributing to difficulty in differentiating true peaks from signal noise. The results of this experiment suggest T-RFLP is a reproducible and high fidelity procedure, which requires careful data interpretation in order to accurately characterize sample diversity.
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Affiliation(s)
- Kevin C Courtney
- Department of Integrative Biology, University of Guelph, 50 Stone Road East, Guelph, ON, Canada N1G 2 W1
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Kiers ET, Duhamel M, Beesetty Y, Mensah JA, Franken O, Verbruggen E, Fellbaum CR, Kowalchuk GA, Hart MM, Bago A, Palmer TM, West SA, Vandenkoornhuyse P, Jansa J, Bücking H. Reciprocal rewards stabilize cooperation in the mycorrhizal symbiosis. Science 2011; 333:880-2. [PMID: 21836016 DOI: 10.1126/science.1208473] [Citation(s) in RCA: 821] [Impact Index Per Article: 63.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Plants and their arbuscular mycorrhizal fungal symbionts interact in complex underground networks involving multiple partners. This increases the potential for exploitation and defection by individuals, raising the question of how partners maintain a fair, two-way transfer of resources. We manipulated cooperation in plants and fungal partners to show that plants can detect, discriminate, and reward the best fungal partners with more carbohydrates. In turn, their fungal partners enforce cooperation by increasing nutrient transfer only to those roots providing more carbohydrates. On the basis of these observations we conclude that, unlike many other mutualisms, the symbiont cannot be "enslaved." Rather, the mutualism is evolutionarily stable because control is bidirectional, and partners offering the best rate of exchange are rewarded.
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Affiliation(s)
- E Toby Kiers
- Institute of Ecological Science, Vrije Universiteit, 1081 HV Amsterdam, Netherlands.
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Sigel MM, Hart MM, Hobbs G, Guthner B. DEMONSTRATION OF INFLUENZA VIRUS, TYPE B, IN A RECENT OUTBREAK OF UPPER RESPIRATORY INFECTION. Science 2010; 102:646. [PMID: 17788251 DOI: 10.1126/science.102.2660.646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Powell JR, Parrent JL, Hart MM, Klironomos JN, Rillig MC, Maherali H. Phylogenetic trait conservatism and the evolution of functional trade-offs in arbuscular mycorrhizal fungi. Proc Biol Sci 2009; 276:4237-45. [PMID: 19740877 PMCID: PMC2821337 DOI: 10.1098/rspb.2009.1015] [Citation(s) in RCA: 169] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 08/17/2009] [Indexed: 11/12/2022] Open
Abstract
The diversity of functional and life-history traits of organisms depends on adaptation as well as the legacy of shared ancestry. Although the evolution of traits in macro-organisms is well studied, relatively little is known about character evolution in micro-organisms. Here, we surveyed an ancient and ecologically important group of microbial plant symbionts, the arbuscular mycorrhizal (AM) fungi, and tested hypotheses about the evolution of functional and life-history traits. Variation in the extent of root and soil colonization by AM fungi is constrained to a few nodes basal to the most diverse groups within the phylum, with relatively little variation associated with recent divergences. We found no evidence for a trade-off in biomass allocated to root versus soil colonization in three published glasshouse experiments; rather these traits were positively correlated. Partial support was observed for correlated evolution between fungal colonization strategies and functional benefits of the symbiosis to host plants. The evolution of increased soil colonization was positively correlated with total plant biomass and shoot phosphorus content. Although the effect of AM fungi on infection by root pathogens was phylogenetically conserved, there was no evidence for correlated evolution between the extent of AM fungal root colonization and pathogen infection. Variability in colonization strategies evolved early in the diversification of AM fungi, and we propose that these strategies were influenced by functional interactions with host plants, resulting in an evolutionary stasis resembling trait conservatism.
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Affiliation(s)
- Jeff R Powell
- Freie Universität Berlin, Institut für Biologie, Okologie der Pflanzen, Altensteinstrasse 6, 14195 Berlin, Germany.
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Powell JR, Levy-Booth DJ, Gulden RH, Asbil WL, Campbell RG, Dunfield KE, Hamill AS, Hart MM, Lerat S, Nurse RE, Pauls KP, Sikkema PH, Swanton CJ, Trevors JT, Klironomos JN. Effects of genetically modified, herbicide-tolerant crops and their management on soil food web properties and crop litter decomposition. J Appl Ecol 2009. [DOI: 10.1111/j.1365-2664.2009.01617.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Levy-Booth DJ, Campbell RG, Gulden RH, Hart MM, Powell JR, Klironomos JN, Pauls KP, Swanton CJ, Trevors JT, Dunfield KE. Real-time polymerase chain reaction monitoring of recombinant DNA entry into soil from decomposing roundup ready leaf biomass. J Agric Food Chem 2008; 56:6339-47. [PMID: 18570434 DOI: 10.1021/jf800767g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Glyphosate-tolerant, Roundup Ready (RR) soybeans account for about 57% of all genetically modified (GM) crops grown worldwide. The entry of recombinant DNA into soil from GM crops has been identified as an environmental concern due to the possibility of their horizontal transfer to soil microorganisms. RR soybeans contain recombinant gene sequences that can be differentiated from wild-type plant and microbial genes in soil by using a sequence-specific molecular beacon and real-time polymerase chain reaction (PCR). A molecular beacon-based real-time PCR system to quantify a wild-type soybean lectin ( le1) gene was designed to compare amounts of endogenous soybean genes to recombinant DNA in soil. Microcosm studies were carried out to develop methodologies for the detection of recombinant DNA from RR soybeans in soil. RR soybean leaf litterbags were imbedded in the soil under controlled environmental conditions (60% water holding capacity, 10/15 degrees C, and 8/16 h day/night) for 30 days. The soybean biomass decomposition was described using a single-phase exponential equation, and the DNA concentration in planta and in soil was quantified using real-time PCR using sequence-specific molecular beacons for the recombinant cp4 epsps and endogenous soybean lectin ( le1) genes. The biomass of RR soybean leaves was 8.6% less than nontransgenic (NT) soybean leaves after 30 days. The pooled half-disappearance time for cp4 epsps and le1 in RR and of le1 in NT soybean leaves was 1.4 days. All genes from leaves were detected in soil after 30 days. This study provides a methodology for monitoring the entry of RR and NT soybean DNA into soil from decomposing plant residues.
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Affiliation(s)
- David J Levy-Booth
- Departments of Environmental Biology, Plant Agriculture, Integrative Biology, and Land Resource Science, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Lerat S, Gulden RH, Hart MM, Powell JR, England LS, Pauls KP, Swanton CJ, Klironomos JN, Trevors JT. Quantification and persistence of recombinant DNA of Roundup Ready corn and soybean in rotation. J Agric Food Chem 2007; 55:10226-31. [PMID: 17997522 DOI: 10.1021/jf072457z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The presence of the recombinant cp4 epsps gene from Roundup Ready (RR) corn and RR soybean was quantified using real-time PCR in soil samples from a field experiment growing RR and conventional corn and soybean in rotation. RR corn and RR soybean cp4 epsps persisted in soil for up to 1 year after seeding. The concentration of recombinant DNA in soil peaked in July and August in RR corn and RR soybean plots, respectively. A small fraction of soil samples from plots seeded with conventional crops contained recombinant DNA, suggesting transgene dispersal by means of natural process or agricultural practices. This research will aid in the understanding of the persistence of recombinant DNA in agricultural cropping systems.
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Affiliation(s)
- Sylvain Lerat
- Departments of Environmental Biology, Plant Agriculture, and Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Powell JR, Gulden RH, Hart MM, Campbell RG, Levy-Booth DJ, Dunfield KE, Pauls KP, Swanton CJ, Trevors JT, Klironomos JN. Mycorrhizal and rhizobial colonization of genetically modified and conventional soybeans. Appl Environ Microbiol 2007; 73:4365-7. [PMID: 17483262 PMCID: PMC1932798 DOI: 10.1128/aem.00594-07] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Accepted: 05/01/2007] [Indexed: 11/20/2022] Open
Abstract
We grew plants of nine soybean varieties, six of which were genetically modified to express transgenic cp4-epsps, in the presence of Bradyrhizobium japonicum and arbuscular mycorrhizal fungi. Mycorrhizal colonization and nodule abundance and mass differed among soybean varieties; however, in no case was variation significantly associated with the genetic modification.
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Affiliation(s)
- Jeff R Powell
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada.
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Saleh-Lakha S, Miller M, Campbell RG, Schneider K, Elahimanesh P, Hart MM, Trevors JT. Microbial gene expression in soil: methods, applications and challenges. J Microbiol Methods 2005; 63:1-19. [PMID: 15939495 DOI: 10.1016/j.mimet.2005.03.007] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Accepted: 03/11/2005] [Indexed: 11/29/2022]
Abstract
About 99% of soil microorganisms are unculturable. However, advances in molecular biology techniques allow for the analysis of living microorganisms. With the advent of new technologies and the optimization of previous methods, various approaches to studying gene expression are expanding the field of microbiology and molecular biology. Methods used for RNA extraction, DNA microarrays, real-time PCR, competitive RT-PCR, stable isotope probing and the use of reporter genes provide methods for detecting and quantifying gene expression. Through the use of these methods, researchers can study the influence of soil environmental factors such as nutrients, oxygen status, pH, pollutants, agro-chemicals, moisture and temperature on gene expression and some of the mechanisms involved in the responses of cells to their environment. This review will also address information gaps in bacterial gene expression in soil and possible future research to develop an understanding of microbial activities in soil environments.
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Affiliation(s)
- Saleema Saleh-Lakha
- Department of Environmental Biology, University of Guelph, Guelph, ON, Canada N1G 2W1
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Gulden RH, Lerat S, Hart MM, Powell JR, Trevors JT, Pauls KP, Klironomos JN, Swanton CJ. Quantitation of transgenic plant DNA in leachate water: real-time polymerase chain reaction analysis. J Agric Food Chem 2005; 53:5858-65. [PMID: 16028966 DOI: 10.1021/jf0504667] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Roundup Ready (RR) genetically modified (GM) corn and soybean comprise a large portion of the annual planted acreage of GM crops. Plant growth and subsequent plant decomposition introduce the recombinant DNA (rDNA) into the soil environment, where its fate has not been completely researched. Little is known of the temporal and spatial distribution of plant-derived rDNA in the soil environment and in situ transport of plant DNA by leachate water has not been studied before. The objectives of this study were to determine whether sufficient quantities of plant rDNA were released by roots during growth and early decomposition to be detected in water collected after percolating through a soil profile and to determine the influence of temperature on DNA persistence in the leachate water. Individual plants of RR corn and RR soybean were grown in modified cylinders in a growth room, and the cylinders were flushed with rain water weekly. Immediately after collection, the leachate was subjected to DNA purification followed by rDNA quantification using real-time Polymerase Chain Reaction (PCR) analysis. To test the effects of temperature on plant DNA persistence in leachate water, water samples were spiked with known quantities of RR soybean or RR corn genomic DNA and DNA persistence was examined at 5, 15, and 25 degrees C. Differences in the amounts and temporal distributions of root-derived rDNA were observed between corn and soybean plants. The results suggest that rainfall events may distribute plant DNA throughout the soil and into leachate water. Half-lives of plant DNA in leachate water ranged from 1.2 to 26.7 h, and persistence was greater at colder temperatures (5 and 15 degrees C).
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Affiliation(s)
- Robert H Gulden
- Department of Plant Agriculture, Environmental Biology, and Integrative Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Waliszewski SM, Carvajal O, Infanzon RM, Trujillo P, Hart MM. Copartition ratios of persistent organochlorine pesticides between human adipose tissue and blood serum lipids. Bull Environ Contam Toxicol 2004; 73:732-738. [PMID: 15389340 DOI: 10.1007/s00128-004-0487-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- S M Waliszewski
- Institute of Forensic Medicine, University of Veracruz, SS Juan Pablo II s/n, Boca del Río, Veracruz C.P. 94290, Mexico
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Waliszewski SM, Infanzon RM, Hart MM. Differences in persistent organochlorine pesticides concentration between breast adipose tissue and blood serum. Bull Environ Contam Toxicol 2003; 70:920-926. [PMID: 12719816 DOI: 10.1007/s00128-003-0070-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Affiliation(s)
- S M Waliszewski
- Institute of Forensic Medicine, University of Veracruz, SS Juan Pablo II s/n, Boca del Río, Veracruz C.P. 94290, Mexico
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Hart MM, Reader RJ. Does percent root length colonization and soil hyphal length reflect the extent of colonization for all AMF? Mycorrhiza 2002; 12:297-301. [PMID: 12466917 DOI: 10.1007/s00572-002-0186-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2002] [Accepted: 06/07/2002] [Indexed: 05/24/2023]
Abstract
Percent root length colonization may not be an appropriate measure of root colonization by arbuscular mycorrhizal fungi (AMF) in all cases. We suggest that AMF will differ in how well percent root length colonization measures the amount of AMF colonization in the root due to differences among AMF in hyphal structure and hyphal aggregation. Although soil hyphal length accounts for hyphal density, we suggest that it does not consider differences in hyphal structure in measurements of external colonization and thus might also misrepresent the true amount of AMF in the soil. To test these suggestions, we measured and compared percent root length colonization and soil hyphal length with root ergosterol and soil ergosterol, respectively, for 21 different species of AMF from three families in a greenhouse experiment. Percent root length colonization predicted intra-radical colonization best for Glomaceae and Acaulosporaceae isolates, while soil hyphal length best represented soil ergosterol for Gigasporaceae isolates. The results show that conventional methods for estimating AMF colonization are not universal for all AMF. Caution is advised when drawing inferences for different groups of AMF.
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Affiliation(s)
- Miranda M Hart
- Department of Botany, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Klironomos JN, Hart MM. Colonization of roots by arbuscular mycorrhizal fungi using different sources of inoculum. Mycorrhiza 2002; 12:181-184. [PMID: 12189472 DOI: 10.1007/s00572-002-0169-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2001] [Accepted: 03/08/2002] [Indexed: 05/23/2023]
Abstract
Arbuscular mycorrhizal fungi (AMF) form a number of different infective propagules that are used to form new mycorrhizal associations. These are spores, extraradical hyphae and infected roots. However, not all fungi are equally capable of colonizing roots with all of the above-mentioned propagules and there is conflicting evidence of major differences in colonization strategy between members of the Glomineae and Gigasporineae. In this study, we tested the abilities of eight fungal species from four different genera to colonize roots using three different types of inoculum. Glomus and Acaulospora isolates colonized from all inoculum types, whereas Gigaspora and Scutellospora isolates colonized mainly from spores and to a limited degree from root fragments. Extraradical hyphae were not suitable propagules for the species of Gigaspora and Scutellospora tested. This indicates that AMF have different colonization strategies and that this is largely differentiated at the suborder level. It is unclear why there is such a difference among the fungi in inoculum types. Future research should examine differences in the anatomy and physiology to discern a mechanism for such differences in life-history strategies.
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Affiliation(s)
- John N Klironomos
- Department of Botany, University of Guelph, Guelph, Ontario, Canada N1G 2W1.
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Hart MM, Reader RJ, Klironomos JN. Life-History Strategies of Arbuscular Mycorrhizal Fungi in Relation to Their Successional Dynamics. Mycologia 2001. [DOI: 10.2307/3761678] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Klironomos JN, Hart MM, Gurney JE, Moutoglis P. Interspecific differences in the tolerance of arbuscular mycorrhizal fungi to freezing and drying. ACTA ACUST UNITED AC 2001. [DOI: 10.1139/b01-099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Arbuscular mycorrhizal fungal communities in northern temperate ecosystems must function during extremes in environmental conditions. However, it is not known if arbuscular mycorrhizal fungi that co-exist in soil communities have similar tolerances to stresses such as drought and freezing. The phenology of arbuscular mycorrhizal fungi was determined over one year in a community in southern Ontario, Canada. Five fungal species from the same community were then used to inoculate five plant species, in all possible combinations, and were subjected to either a freezing treatment or a drought treatment after which new seedlings were transplanted into the treated pots. The percent colonization of roots of each plant species was measured as the difference in mean colonization from the control. Freezing reduced percent colonization in almost every case, whereas drought resulted in both increased and decreased percent colonization. Fungal species responded differently to the treatments, and there was a pronounced plant × fungus effect. These results support the hypothesis that distinct functional groups of arbuscular mycorrhizal fungi exist, and these may determine plant community structure.Key words: arbuscular mycorrhizal fungi, freezing, drying, functional diversity.
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