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Lekberg Y, Jansa J, McLeod M, DuPre ME, Holben WE, Johnson D, Koide RT, Shaw A, Zabinski C, Aldrich-Wolfe L. Carbon and phosphorus exchange rates in arbuscular mycorrhizas depend on environmental context and differ among co-occurring plants. New Phytol 2024; 242:1576-1588. [PMID: 38173184 DOI: 10.1111/nph.19501] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/29/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
Phosphorus (P) for carbon (C) exchange is the pivotal function of arbuscular mycorrhiza (AM), but how this exchange varies with soil P availability and among co-occurring plants in complex communities is still largely unknown. We collected intact plant communities in two regions differing c. 10-fold in labile inorganic P. After a 2-month glasshouse incubation, we measured 32P transfer from AM fungi (AMF) to shoots and 13C transfer from shoots to AMF using an AMF-specific fatty acid. AMF communities were assessed using molecular methods. AMF delivered a larger proportion of total shoot P in communities from high-P soils despite similar 13C allocation to AMF in roots and soil. Within communities, 13C concentration in AMF was consistently higher in grass than in blanketflower (Gaillardia aristata Pursh) roots, that is P appeared more costly for grasses. This coincided with differences in AMF taxa composition and a trend of more vesicles (storage structures) but fewer arbuscules (exchange structures) in grass roots. Additionally, 32P-for-13C exchange ratios increased with soil P for blanketflower but not grasses. Contrary to predictions, AMF transferred proportionally more P to plants in communities from high-P soils. However, the 32P-for-13C exchange differed among co-occurring plants, suggesting differential regulation of the AM symbiosis.
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Affiliation(s)
- Ylva Lekberg
- MPG Ranch, Missoula, MT, 59801, USA
- Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Jan Jansa
- Institute of Microbiology of the Czech Academy of Sciences, Prague, 14220, Czech Republic
| | | | | | - William E Holben
- Cellular, Molecular and Microbial Biology, University of Montana, Missoula, MT, 59812, USA
| | - David Johnson
- Department of Earth and Environmental Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Alanna Shaw
- Department of Ecosystem and Conservation Sciences, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Catherine Zabinski
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, 59717, USA
| | - Laura Aldrich-Wolfe
- Department of Biological Sciences, North Dakota State University, Fargo, ND, 58108, USA
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2
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Koide RT, Kanauchi M, Hashimoto Y. Variation Among Japanese Miso Breweries in Indoor Microbiomes is Mainly Ascribed to Variation in Type of Indoor Surface. Curr Microbiol 2024; 81:68. [PMID: 38236285 PMCID: PMC10796754 DOI: 10.1007/s00284-023-03591-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Miso is a microbially-fermented soybean food. The miso brewery indoor microbiome contributes to miso fermentation. Japanese breweries are not climate-controlled, so indoor spaces are strongly affected by the prevailing climate. Because climate influences microorganism distribution, our first hypothesis is that latitude, as a proxy for climate, is a major determinant of brewery indoor microbiome structure. Breweries vary in interior surface materials and in the way operations (steaming, processing, fermenting) are apportioned among rooms. Therefore, our second hypothesis is that more variability in indoor microbiomes exists among breweries than can be ascribed to a latitudinal gradient. Most miso produced today is inoculated with commercial microbial strains to standardize fermentation. If commercial strains outcompete indigenous microbes for membership in the indoor microbiome, this practice may homogenize indoor microbiomes among regions or breweries. Therefore, our third hypothesis is that inoculant fungal species dominate indoor fungal communities and make it impossible to distinguish communities among breweries or across their latitudinal gradient. We tested these hypotheses by sampling indoor surfaces in several breweries across a latitudinal gradient in Japan. We found that latitude had a significant but relatively small impact on indoor fungal and bacterial communities, that the effect of brewery was large relative to latitude, and that inoculant fungi made such small contributions to the indoor microbiome that distinctions among breweries and along the latitudinal gradient remained apparent. Recently, the Japanese Ministry of Agriculture, Forestry and Fisheries specified fungal inoculants to standardize miso production. However, this may not be possible so long as the indoor microbiome remains uncontrolled.
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Affiliation(s)
- Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, USA.
| | - Makoto Kanauchi
- Department of Food Management, Miyagi University, Sendai, Japan
| | - Yasushi Hashimoto
- Section of Ecology and Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
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3
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Xu C, Zhang N, Zhang K, Li S, Xia Q, Xiao J, Liang M, Lei W, He J, Chen G, Ge C, Zheng X, Zhu J, Hu S, Koide RT, Firestone MK, Cheng L. Coupled anaerobic methane oxidation and metal reduction in soil under elevated CO 2. Glob Chang Biol 2023. [PMID: 37221551 DOI: 10.1111/gcb.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/01/2023] [Indexed: 05/25/2023]
Abstract
Continued current emissions of carbon dioxide (CO2 ) and methane (CH4 ) by human activities will increase global atmospheric CO2 and CH4 concentrations and surface temperature significantly. Fields of paddy rice, the most important form of anthropogenic wetlands, account for about 9% of anthropogenic sources of CH4 . Elevated atmospheric CO2 may enhance CH4 production in rice paddies, potentially reinforcing the increase in atmospheric CH4 . However, what is not known is whether and how elevated CO2 influences CH4 consumption under anoxic soil conditions in rice paddies, as the net emission of CH4 is a balance of methanogenesis and methanotrophy. In this study, we used a long-term free-air CO2 enrichment experiment to examine the impact of elevated CO2 on the transformation of CH4 in a paddy rice agroecosystem. We demonstrate that elevated CO2 substantially increased anaerobic oxidation of methane (AOM) coupled to manganese and/or iron oxides reduction in the calcareous paddy soil. We further show that elevated CO2 may stimulate the growth and metabolism of Candidatus Methanoperedens nitroreducens, which is actively involved in catalyzing AOM when coupled to metal reduction, mainly through enhancing the availability of soil CH4 . These findings suggest that a thorough evaluation of climate-carbon cycle feedbacks may need to consider the coupling of methane and metal cycles in natural and agricultural wetlands under future climate change scenarios.
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Affiliation(s)
- Chenchao Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Naifang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kaihang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuyao Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qing Xia
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jing Xiao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Maojun Liang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weilei Lei
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Junpan He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Gaiping Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengjun Ge
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Xunhua Zheng
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Shuijin Hu
- Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, Utah, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Lei Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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Koide RT. On Holobionts, Holospecies, and Holoniches: the Role of Microbial Symbioses in Ecology and Evolution. Microb Ecol 2023; 85:1143-1149. [PMID: 35396623 PMCID: PMC10167095 DOI: 10.1007/s00248-022-02005-9] [Citation(s) in RCA: 1] [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: 11/19/2021] [Accepted: 03/29/2022] [Indexed: 05/10/2023]
Abstract
My goal in writing this is to increase awareness of the roles played by microbial symbionts in eukaryote ecology and evolution. Most eukaryotes host one or more species of symbiotic microorganisms, including prokaryotes and fungi. Many of these have profound impacts on the biology of their hosts. For example, microbial symbionts may expand the niches of their hosts, cause rapid adaptation of the host to the environment and re-adaptation to novel conditions via symbiont swapping, facilitate speciation, and fundamentally alter our concept of the species. In some cases, microbial symbionts and multicellular eukaryote hosts have a mutual dependency, which has obvious conservation implications. Hopefully, this contribution will stimulate a reevaluation of important ecological and evolutionary concepts including niche, adaptation, the species, speciation, and conservation of multicellular eukaryotes.
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Affiliation(s)
- Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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Davis EL, Weatherhead E, Koide RT. The potential saprotrophic capacity of foliar endophytic fungi from Quercus gambelii. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Weatherhead E, Davis EL, Koide RT. Many foliar endophytic fungi of Quercus gambelii are capable of psychrotolerant saprotrophic growth. PLoS One 2022; 17:e0275845. [PMID: 36223398 PMCID: PMC9555652 DOI: 10.1371/journal.pone.0275845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/25/2022] [Indexed: 11/30/2022] Open
Abstract
Many endophytic fungi have the potential to function as saprotrophs when living host tissues senesce and enter the litter pool. The consumption of plant litter by fungi obviously requires moisture but, in the arid, western USA, the native range of Quercus gambelii Nutt., most of the precipitation occurs during the coldest months of the year. Therefore, we hypothesized that the endophytic fungi of Q. gambelii have the potential to function as psychrotolerant saprotrophs, which we defined in this study as an organism capable of significant growth on leaf litter at 5°C. We further hypothesized that a tradeoff exists between growth of endophytic fungi at 5°C and at 17°C such that fungal isolates are either cold- or warm-temperature specialists. Consistent with our first hypothesis, we found that 36 of our 40 isolates consumed leaf litter at 5°C, but there was a surprisingly high degree of variability among isolates in this ability, even among isolates of a given species. Contrary to our second hypothesis, there was no tradeoff between saprotrophic growth at 5°C and saprotrophic growth at 17°C. Indeed, the isolates that grew poorly as saprotrophs at 5°C were generally those that grew poorly as saprotrophs at 17°C. By virtue of being endophytic, endophytic fungi have priority in litter over decomposer fungi that colonize plant tissues only after they enter the litter pool. Moreover, by virtue of being psychrotolerant, some endophytic fungi may function as saprotrophs during the cold months of the year when moisture is temporarily available. Therefore, we suggest that some endophytic fungi of Q. gambelii could play significant ecosystem roles in litter decomposition and nutrient cycling.
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Affiliation(s)
- Emily Weatherhead
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Emily Lorine Davis
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States of America
- * E-mail:
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7
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Koide RT, Garlick J, Klatt S, Boekweg N, Tambe A, Jensen K, Weatherhead E. Predicting the Topographic Zonation of Vegetation in a Salt Playa in Utah, USA. WEST N AM NATURALIST 2022. [DOI: 10.3398/064.082.0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Jakob Garlick
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Spencer Klatt
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Noah Boekweg
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Augustine Tambe
- Department of Biology, Brigham Young University, Provo, UT 84602
| | - Katherine Jensen
- Department of Biology, Brigham Young University, Provo, UT 84602
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8
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Zhang Q, Tang J, Angel R, Wang D, Hu X, Gao S, Zhang L, Tang Y, Zhang X, Koide RT, Yang H, Sun Q. Soil Properties Interacting With Microbial Metagenome in Decreasing CH 4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation. Front Microbiol 2022; 13:830019. [PMID: 35283824 PMCID: PMC8905362 DOI: 10.3389/fmicb.2022.830019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Wetlands are the largest natural source of terrestrial CH4 emissions. Afforestation can enhance soil CH4 oxidation and decrease methanogenesis, yet the driving mechanisms leading to these effects remain unclear. We analyzed the structures of communities of methanogenic and methanotrophic microbes, quantification of mcrA and pmoA genes, the soil microbial metagenome, soil properties and CH4 fluxes in afforested and non-afforested areas in the marshland of the Yangtze River. Compared to the non-afforested land use types, net CH4 emission decreased from bare land, natural vegetation and 5-year forest plantation and transitioned to net CH4 sinks in the 10- and 20-year forest plantations. Both abundances of mcrA and pmoA genes decreased significantly with increasing plantation age. By combining random forest analysis and structural equation modeling, our results provide evidence for an important role of the abundance of functional genes related to methane production in explaining the net CH4 flux in this ecosystem. The structures of methanogenic and methanotrophic microbial communities were of lower importance as explanatory factors than functional genes in terms of in situ CH4 flux. We also found a substantial interaction between functional genes and soil properties in the control of CH4 flux, particularly soil particle size. Our study provides empirical evidence that microbial community function has more explanatory power than taxonomic microbial community structure with respect to in situ CH4 fluxes. This suggests that focusing on gene abundances obtained, e.g., through metagenomics or quantitative/digital PCR could be more effective than community profiling in predicting CH4 fluxes, and such data should be considered for ecosystem modeling.
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Affiliation(s)
- Qian Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jie Tang
- Hunan Academy of Forestry, Changsha, China
| | - Roey Angel
- Soil and Water Research Infrastructure and Institute of Soil Biology, Biology Centre, Czech Academy of Sciences (CAS), České Budějovice, Czechia
| | - Dong Wang
- Institute of Forest Ecology, Environment and Nature Conservation, Chinese Academy of Forestry, Beijing, China
| | - Xingyi Hu
- Hubei Academy of Forestry, Wuhan, China
| | - Shenghua Gao
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Lei Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuxi Tang
- Hunan Academy of Forestry, Changsha, China
| | - Xudong Zhang
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States
| | - Haishui Yang
- College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Qixiang Sun
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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9
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Jensen K, Koide RT. The protection of Salicornia rubra from ultraviolet radiation by betacyanins and phenolic compounds. Plant Environ Interact 2021; 2:229-234. [PMID: 37284514 PMCID: PMC10168037 DOI: 10.1002/pei3.10061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 06/08/2023]
Abstract
Salicornia rubra is a commonly occurring annual species of the salt playas of the Great Basin Desert of the western United States. In such habitats, plants experience high levels of ultraviolet radiation, which could potentially damage DNA. As a member of the Amaranthaceae (Caryophyllales), S. rubra shoots typically contain high concentrations of the red-violet pigments called betacyanins, which are ultraviolet-absorbing compounds. Nevertheless, some specimens of S. rubra are green even when growing with full exposure to the sun. We, therefore, tested several hypotheses regarding the causes of variation among S. rubra plants in betacyanin concentration and the role of betacyanins in the absorption of ultraviolet radiation. We measured ultraviolet radiation absorption and the concentrations of betacyanins and phenolic compounds of the cell sap expressed from red and green plants growing in full sun, as well as plants grown under various levels of shade. We found that while betacyanin concentrations were predictable from plant color (red plants contained more betacyanins than green plants), the ability to absorb ultraviolet radiation was determined primarily by the concentration of phenolic compounds, which was determined by the level of exposure to the sun. Therefore, the DNA of green plants growing in full sun appears to be at no greater risk than the DNA of red plants.
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Affiliation(s)
| | - Roger T. Koide
- Department of BiologyBrigham Young UniversityProvoUtahUSA
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10
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Chen W, Koide RT, Eissenstat DM. Topographic and Host Effects on Arbuscular Mycorrhizal and Ectomycorrhizal Fungal Communities in a Forested Watershed. Ecosystems 2020. [DOI: 10.1007/s10021-020-00486-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Martin FM, Dickie I, Lindahl BD, Lennon S, Öpik M, Polle A, Requena N, Selosse MA, Koide RT, Jakobsen I, Watts-Williams SJ, Cavagnaro TR. A tribute to Sally E. Smith. New Phytol 2020; 228:397-402. [PMID: 33460160 DOI: 10.1111/nph.16895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Francis M Martin
- Lab of Excellence ARBRE, UMR 1136 INRA-Université de Lorraine 'Interactions Arbres/Micro-organismes', INRAE, 54280, Champenoux, France
| | - Ian Dickie
- College of Science, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Box 7014, 750 07, Uppsala, Sweden
| | - Sarah Lennon
- New Phytologist Central Office, Bailrigg House, Lancaster University, Lancaster, LA1 4YE, UK
| | - Maarja Öpik
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005, Tartu, Estonia
| | - Andrea Polle
- Department of Forest Botany and Tree Physiology, Buesgen-Institute and Göttingen Center for Molecular Biosciences (GZMB), University of Göttingen, Göttingen, 37077, Germany
| | - Natalia Requena
- Molecular Phytopathology Department, Karlsruhe Institute of Technology, Fritz Haber-Weg 4, Geb. 30.43, 2. OG, D-76131, Karlsruhe, Germany
| | - Marc-André Selosse
- Département Systématique et Evolution, UMR 7205 ISYEB CP 50, Muséum national d'Histoire naturelle, 45 rue Buffon, Paris, 75005, France
- Faculty of Biology, University of Gdansk, ul. Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Iver Jakobsen
- Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Stephanie J Watts-Williams
- School of Agriculture, Food & Wine and the Waite Research Institute, The University of Adelaide, Urrbrae, SA, 5064, Australia
| | - Timothy R Cavagnaro
- School of Agriculture, Food & Wine and the Waite Research Institute, The University of Adelaide, Urrbrae, SA, 5064, Australia
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12
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Xu C, Zhang K, Zhu W, Xiao J, Zhu C, Zhang N, Yu F, Li S, Zhu C, Tu Q, Chen X, Zhu J, Hu S, Koide RT, Firestone MK, Cheng L. Large losses of ammonium-nitrogen from a rice ecosystem under elevated CO 2. Sci Adv 2020; 6:eabb7433. [PMID: 33067230 PMCID: PMC10764100 DOI: 10.1126/sciadv.abb7433] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
Inputs of nitrogen into terrestrial ecosystems, mainly via the use of ammonium-based fertilizers in agroecosystems, are enormous, but the fate of this nitrogen under elevated atmospheric carbon dioxide (CO2) is not well understood. We have taken advantage of a 15-year free-air CO2 enrichment study to investigate the influence of elevated CO2 on the transformation of ammonium-nitrogen in a rice ecosystem in which ammonium is usually assumed to be stable under anaerobic conditions. We demonstrate that elevated CO2 causes substantial losses of ammonium-nitrogen that result from anaerobic oxidation of ammonium coupled to reduction of iron. We identify a new autotrophic member of the bacterial order Burkholderiales that may use soil CO2 as a carbon source to couple anaerobic ammonium oxidation and iron reduction. These findings offer insight into the coupled cycles of nitrogen and iron in terrestrial ecosystems and raise questions about the loss of ammonium-nitrogen from arable soils under future climate-change scenarios.
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Affiliation(s)
- Chenchao Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kaihang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanying Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jing Xiao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chen Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Naifang Zhang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Fangjian Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuyao Li
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chunwu Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Jinan 250100, China
| | - Xin Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianguo Zhu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shuijin Hu
- Department of Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lei Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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13
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Nettles R, Ricks KD, Koide RT. The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics. Microb Ecol 2020; 80:573-592. [PMID: 32451559 DOI: 10.1007/s00248-020-01525-6] [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: 01/21/2020] [Accepted: 05/05/2020] [Indexed: 05/25/2023]
Abstract
We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.
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Affiliation(s)
- Rachel Nettles
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Currently: Kintai Therapeutics, 26 Landsdowne Street, Boston, MA, 02139, USA
| | - Kevin D Ricks
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Currently: Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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14
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Abstract
Naturally occurring, mixed litter decomposes at unpredictable rates when individual components do not decompose in mixtures as they do individually. Consequently, nutrient, carbon and energy fluxes associated with decomposition may be difficult to predict. However, predictability is improved when we understand the mechanisms responsible for such non-additive decomposition. In this study, we explored mechanisms to explain our previous observation that an approximately 30% increase in oat straw decomposition due to the presence of clover litter is associated with a significant increase in the activity of cellobiohydrolase, an enzyme involved in litter decomposition. We hypothesized that resources limiting decomposer microbe enzyme activity in oat straw can be supplied by clover litter. Amendment of oat straw with water, NH4Cl, glucose, or NH4Cl combined with glucose did not account for the significant, positive effect of clover litter on oat straw decomposition and cellobiohydrolase activity. However, amendment of oat straw with a complete set of mineral nutrients for plant growth did account for the entire effect of clover litter, and the addition of the complete set of mineral nutrients without N accounted for the majority of the clover effect. In our system, therefore, the majority of the positive effect of clover litter on oat straw decomposition and cellobiohydrolase activity was unexpectedly not attributable to the transfer from clover to oat straw of labile N. We found that mineral soil could substitute for the mineral nutrients other than N. This highlights the role of soil as a potential source of limiting resources for microbes decomposing litter. It may also explain why positive, non-additive decomposition has been observed in some previous studies but not in others depending on whether the soil supplied a resource that limited decomposer activity.
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Affiliation(s)
- Na Yin
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, Utah, United States of America
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15
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Ricks KD, Koide RT. The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities. PLoS One 2019; 14:e0219832. [PMID: 31310633 PMCID: PMC6640817 DOI: 10.1371/journal.pone.0219832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 01/15/2023] Open
Abstract
Because of disturbance and plant species loss at the local level, many arid ecosystems in the western USA benefit from revegetation. There is a growing interest in improving revegetation success by purposefully inoculating revegetation plants with mutualistic endophytic fungi that increase plant stress tolerance. However, inoculant fungi must compete against fungi that indigenous to the habitat, many of which may not be mutualistic. Our overall goal, therefore, is to learn how to efficiently colonize revegetation plants using endophytic fungal inoculum. The goal will be facilitated by understanding the factors that limit colonization of plants by endophytic fungi, including inoculum dispersal and host compatibility. We analyzed endophytic fungal communities in leaves of Bromus tectorum and Elymus elymoides (Poaceae), Chrysothamnus depressus and Artemisia tridentata (Asteraceae), Alyssum alyssoides (Brassicaceae) and Atriplex canescens (Amaranthaceae), each occurring in each of 18 field plots. We found that dispersal limitation was significant for endophytic fungal communities of Atriplex canescens and Bromus tectorum, accounting for 9 and 17%, respectively, of the variation in endophytic fungal community structure, even though the maximum distance between plots was only 350 m. Plant species identity accounted for 33% of the variation in endophytic fungal community structure. These results indicate that the communities of endophytic fungi assembling in these plant species depend significantly on proximity to inoculum source as well as the identity of the plant species. Therefore, if endophytic fungi are to be used to facilitate revegetation by these plant species, land managers may find it profitable to consider both the proximity of inoculum to revegetation plants and the suitability of the inoculum to targeted host plant species.
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Affiliation(s)
- Kevin D. Ricks
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States of America
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16
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Zak DR, Pellitier PT, Argiroff W, Castillo B, James TY, Nave LE, Averill C, Beidler KV, Bhatnagar J, Blesh J, Classen AT, Craig M, Fernandez CW, Gundersen P, Johansen R, Koide RT, Lilleskov EA, Lindahl BD, Nadelhoffer KJ, Phillips RP, Tunlid A. Exploring the role of ectomycorrhizal fungi in soil carbon dynamics. New Phytol 2019; 223:33-39. [PMID: 30636276 DOI: 10.1111/nph.15679] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [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: 11/02/2018] [Accepted: 01/07/2019] [Indexed: 05/26/2023]
Abstract
The extent to which ectomycorrhizal (ECM) fungi enable plants to access organic nitrogen (N) bound in soil organic matter (SOM) and transfer this growth-limiting nutrient to their plant host, has important implications for our understanding of plant-fungal interactions, and the cycling and storage of carbon (C) and N in terrestrial ecosystems. Empirical evidence currently supports a range of perspectives, suggesting that ECM vary in their ability to provide their host with N bound in SOM, and that this capacity can both positively and negatively influence soil C storage. To help resolve the multiplicity of observations, we gathered a group of researchers to explore the role of ECM fungi in soil C dynamics, and propose new directions that hold promise to resolve competing hypotheses and contrasting observations. In this Viewpoint, we summarize these deliberations and identify areas of inquiry that hold promise for increasing our understanding of these fundamental and widespread plant symbionts and their role in ecosystem-level biogeochemistry.
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Affiliation(s)
- Donald R Zak
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter T Pellitier
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - WilliamA Argiroff
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Buck Castillo
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Timothy Y James
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lucas E Nave
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Colin Averill
- Department of Earth and Environment, Boston University, Boston, MA, 02215, USA
| | - Kaitlyn V Beidler
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | | | - Jennifer Blesh
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Aimée T Classen
- The Rubenstein School of Environment & Natural Resources, University of Vermont, Burlington, VT, 05405, USA
- The Gund Institute for Environment, University of Vermont, Burlington, VT, 05405, USA
| | - Matthew Craig
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | | | - Per Gundersen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, DK-1711, Denmark
| | - Renee Johansen
- Los Alamos National Laboratory, Santa Fe, NM, 87545, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Erik A Lilleskov
- US Forest Service, Northern Research Station, 410 Mac Innes Dr., Houghton, MI, 49931, USA
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Knute J Nadelhoffer
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | | | - Anders Tunlid
- Department of Biology, Microbial Ecology Group, Lund University, Lund, SE-221 00, Sweden
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17
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Abstract
The assembly of horizontally transmitted endophytic fungi within plant tissues may be affected by "biotic filtering". In other words, only particular endophytic fungal taxa from the available inoculum pool may be able to colonize a given plant species. We tested that hypothesis in Bromus tectorum, an important invasive species in the arid, western United States. We collected seed from Bromus tectorum and sources of inoculum for endophytic fungi including soil and various kinds of plant litter at a field site in central Utah. We characterized, using Illumina sequencing, the endophytic fungal communities in the various inoculum sources, inoculated Bromus tectorum seedlings under gnotobiotic conditions with the various sources, and then characterized the communities of endophytic fungi that assembled in their roots and leaves. Different inoculum sources containing significantly different endophytic fungal communities produced complex communities of endophytic fungi in leaves and roots of Bromus tectorum. In leaves, the communities assembling from the various inoculum sources were not significantly different from each other and, in roots, they were only slightly different from each other, mainly due to variation in a single fungal OTU, Coprinopsis brunneofibrillosa. Consequently, there was significantly more variation in the structure of the communities of endophytic fungi among the inoculum sources than in the resultant endophytic fungal communities in the leaves and roots of Bromus tectorum. These results are consistent with biotic filtering playing a significant role in endophytic fungal community assembly.
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Affiliation(s)
- Kevin D Ricks
- Department of Biology, Brigham Young University, Provo, UT, 84663, USA. .,Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84663, USA
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18
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Awaydul A, Zhu W, Yuan Y, Xiao J, Hu H, Chen X, Koide RT, Cheng L. Common mycorrhizal networks influence the distribution of mineral nutrients between an invasive plant, Solidago canadensis, and a native plant, Kummerowa striata. Mycorrhiza 2019; 29:29-38. [PMID: 30421153 DOI: 10.1007/s00572-018-0873-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 04/21/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Invasive species often reduce ecosystem services and lead to a serious threat to native biodiversity. Roots of invasive plants are often linked to roots of native plants by common mycorrhizal networks (CMNs) of arbuscular mycorrhizal (AM) fungi, but whether and how CMNs mediate interactions between invasive and native plant species remains largely uninvestigated. We conducted two microcosm experiments, one in which we amended the soil with mineral N and another in which we amended the soil with mineral P. In each experiment, we grew a pair of test plants consisting of Kummerowia striata (native to our research site) and Solidago canadensis (an invasive species). CMNs were established between the plants, and these were either left intact or severed. Intact CMNs increased growth and nutrient acquisition by S. canadensis while they decreased nutrient acquisition by K. striata in comparison with severed CMNs. 15N and P analyses indicated that compared to severed CMNs, intact CMNs preferentially transferred mineral nutrients to S. canadensis. CMNs produced by different species of AM fungi had slightly different effects on the interaction between these two plant species. These results highlight the role of CMNs in the understanding of interactions between the invasive species S. canadensis and its native neighbor.
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Affiliation(s)
- Awagul Awaydul
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wanying Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yongge Yuan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- School of Life Science, Taizhou University, Taizhou, 318000, China
| | - Jing Xiao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hao Hu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xin Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Lei Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
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19
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Koide RT, Fernandez CW. The continuing relevance of "older" mycorrhiza literature: insights from the work of John Laker Harley (1911-1990). Mycorrhiza 2018; 28:577-586. [PMID: 30014212 DOI: 10.1007/s00572-018-0854-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 05/09/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
To new generations of scientists beginning their careers in research, we strongly recommend the practice of reading older literature. To illustrate the value of doing so, we highlight six insights of one of the most influential mycorrhiza researchers of the twentieth century, Jack Harley. These insights concerning mycotrophy, the new niche, the sheath, C cycling, N cycling, and mutualism were published prior to 1975 and so may have escaped the notice of many, but they laid the groundwork for some of the most important research of today.
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Affiliation(s)
- Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA.
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20
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Williams A, Jordan NR, Smith RG, Hunter MC, Kammerer M, Kane DA, Koide RT, Davis AS. A regionally-adapted implementation of conservation agriculture delivers rapid improvements to soil properties associated with crop yield stability. Sci Rep 2018; 8:8467. [PMID: 29855528 PMCID: PMC5981580 DOI: 10.1038/s41598-018-26896-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [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: 12/06/2017] [Accepted: 05/21/2018] [Indexed: 11/13/2022] Open
Abstract
Climate models predict increasing weather variability, with negative consequences for crop production. Conservation agriculture (CA) may enhance climate resilience by generating certain soil improvements. However, the rate at which these improvements accrue is unclear, and some evidence suggests CA can lower yields relative to conventional systems unless all three CA elements are implemented: reduced tillage, sustained soil cover, and crop rotational diversity. These cost-benefit issues are important considerations for potential adopters of CA. Given that CA can be implemented across a wide variety of regions and cropping systems, more detailed and mechanistic understanding is required on whether and how regionally-adapted CA can improve soil properties while minimizing potential negative crop yield impacts. Across four US states, we assessed short-term impacts of regionally-adapted CA systems on soil properties and explored linkages with maize and soybean yield stability. Structural equation modeling revealed increases in soil organic matter generated by cover cropping increased soil cation exchange capacity, which improved soybean yield stability. Cover cropping also enhanced maize minimum yield potential. Our results demonstrate individual CA elements can deliver rapid improvements in soil properties associated with crop yield stability, suggesting that regionally-adapted CA may play an important role in developing high-yielding, climate-resilient agricultural systems.
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Affiliation(s)
- Alwyn Williams
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA.
- School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD, Australia.
| | - Nicholas R Jordan
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN, USA
| | - Richard G Smith
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Mitchell C Hunter
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Kammerer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Daniel A Kane
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, USA
| | - Adam S Davis
- USDA-ARS, Global Change and Photosynthesis Research Unit, Urbana, IL, USA
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21
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Affiliation(s)
- Weile Chen
- Intercollege Graduate Degree Program in Ecology The Pennsylvania State University University Park PA USA
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
| | - Roger T. Koide
- Intercollege Graduate Degree Program in Ecology The Pennsylvania State University University Park PA USA
- Department of Biology Brigham Young University Provo UT USA
| | - David M. Eissenstat
- Intercollege Graduate Degree Program in Ecology The Pennsylvania State University University Park PA USA
- Department of Ecosystem Science and Management The Pennsylvania State University University Park PA USA
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22
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Cheng L, Chen W, Adams TS, Wei X, Li L, McCormack ML, DeForest JL, Koide RT, Eissenstat DM. Mycorrhizal fungi and roots are complementary in foraging within nutrient patches. Ecology 2016; 97:2815-2823. [DOI: 10.1002/ecy.1514] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/13/2016] [Accepted: 06/13/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Lei Cheng
- College of Life Sciences Zhejiang University Hangzhou 310058 China
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Weile Chen
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Thomas S. Adams
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Xing Wei
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Le Li
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Michael Luke McCormack
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
| | - Jared L. DeForest
- Department of Environmental and Plant Biology Ohio University Athens Ohio 45701 USA
| | - Roger T. Koide
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
- Department of Biology Brigham Young University Provo Utah 84602 USA
| | - David M. Eissenstat
- Department of Ecosystem Science and Management The Pennsylvania State University University Park Pennsylvania 16802 USA
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23
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Chen W, Koide RT, Adams TS, DeForest JL, Cheng L, Eissenstat DM. Root morphology and mycorrhizal symbioses together shape nutrient foraging strategies of temperate trees. Proc Natl Acad Sci U S A 2016; 113:8741-6. [PMID: 27432986 PMCID: PMC4978252 DOI: 10.1073/pnas.1601006113] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [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] [Indexed: 11/18/2022] Open
Abstract
Photosynthesis by leaves and acquisition of water and minerals by roots are required for plant growth, which is a key component of many ecosystem functions. Although the role of leaf functional traits in photosynthesis is generally well understood, the relationship of root functional traits to nutrient uptake is not. In particular, predictions of nutrient acquisition strategies from specific root traits are often vague. Roots of nearly all plants cooperate with mycorrhizal fungi in nutrient acquisition. Most tree species form symbioses with either arbuscular mycorrhizal (AM) or ectomycorrhizal (EM) fungi. Nutrients are distributed heterogeneously in the soil, and nutrient-rich "hotspots" can be a key source for plants. Thus, predicting the foraging strategies that enable mycorrhizal root systems to exploit these hotspots can be critical to the understanding of plant nutrition and ecosystem carbon and nutrient cycling. Here, we show that in 13 sympatric temperate tree species, when nutrient availability is patchy, thinner root species alter their foraging to exploit patches, whereas thicker root species do not. Moreover, there appear to be two distinct pathways by which thinner root tree species enhance foraging in nutrient-rich patches: AM trees produce more roots, whereas EM trees produce more mycorrhizal fungal hyphae. Our results indicate that strategies of nutrient foraging are complementary among tree species with contrasting mycorrhiza types and root morphologies, and that predictable relationships between below-ground traits and nutrient acquisition emerge only when both roots and mycorrhizal fungi are considered together.
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Affiliation(s)
- Weile Chen
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802; Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
| | - Roger T Koide
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802; Department of Biology, Brigham Young University, Provo, UT 84602
| | - Thomas S Adams
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802; Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802
| | - Jared L DeForest
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701
| | - Lei Cheng
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - David M Eissenstat
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802; Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA 16802;
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24
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Chaudhary VB, Rúa MA, Antoninka A, Bever JD, Cannon J, Craig A, Duchicela J, Frame A, Gardes M, Gehring C, Ha M, Hart M, Hopkins J, Ji B, Johnson NC, Kaonongbua W, Karst J, Koide RT, Lamit LJ, Meadow J, Milligan BG, Moore JC, Pendergast IV TH, Piculell B, Ramsby B, Simard S, Shrestha S, Umbanhowar J, Viechtbauer W, Walters L, Wilson GWT, Zee PC, Hoeksema JD. MycoDB, a global database of plant response to mycorrhizal fungi. Sci Data 2016; 3:160028. [PMID: 27163938 PMCID: PMC4862322 DOI: 10.1038/sdata.2016.28] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/23/2016] [Indexed: 11/12/2022] Open
Abstract
Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems.
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Affiliation(s)
- V. Bala Chaudhary
- Department of Environmental Science and Studies, DePaul University, Chicago, Illinois 60614, USA
| | - Megan A. Rúa
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, Tennessee 37996-3410, USA
- Department of Biology, University of Mississippi, University, Mississippi 38677, USA
| | - Anita Antoninka
- School of Forestry, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - James D. Bever
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jeffery Cannon
- Colorado Forest Restoration Institute, Colorado State University, Fort Collins, Colorado 80523-1472, USA
| | - Ashley Craig
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Jessica Duchicela
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
- Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas—ESPE, Sangolquí 1715231B, Ecuador
| | - Alicia Frame
- US Environmental Protection Agency, Office of Solid Waste and Emergency Response, Washington DC 20004, USA
| | - Monique Gardes
- Université Toulouse 3 Paul Sabatier, CNRS, ENFA; UMR5174 EDB (Évolution & Diversité Biologique); F-31062 Toulouse, France
| | - Catherine Gehring
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011, USA
| | - Michelle Ha
- Department of Biology, University of Mississippi, University, Mississippi 38677, USA
| | - Miranda Hart
- Department of Biology, University of British Columbia Okanagan, Kelowna BC, Canada V1V1V7
| | - Jacob Hopkins
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Baoming Ji
- College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Nancy Collins Johnson
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona 86011, USA
- School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff Arizona 86011, USA
| | - Wittaya Kaonongbua
- Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Justine Karst
- Department of Renewable Resources, University of Alberta, Edmonton, Canada T6G 2E3
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, Utah 84602, USA
| | - Louis J. Lamit
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931-1295, USA
| | - James Meadow
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, Montana 59717, USA
| | - Brook G. Milligan
- Department of Biology, New Mexico State University, Las Cruces, New Mexico 88003, USA
| | - John C. Moore
- Department of Ecosystem Science and Sustainability, and the Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA
| | | | - Bridget Piculell
- Department of Biology, University of Mississippi, University, Mississippi 38677, USA
| | - Blake Ramsby
- Department of Biology, University of Mississippi, University, Mississippi 38677, USA
| | - Suzanne Simard
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Shubha Shrestha
- Department of Biological Sciences, Winston Salem State University, Winston-Salem, North Carolina 27110, USA
| | - James Umbanhowar
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Neuropsychology, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Lawrence Walters
- Software Engineering, Enova International Inc., Chicago, Illinois 60604, USA
| | - Gail W. T. Wilson
- Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, Oklahoma 74078, USA
| | - Peter C. Zee
- Department of Biology, California State University—Northridge, Northridge, California 91330, USA
| | - Jason D. Hoeksema
- Department of Biology, University of Mississippi, University, Mississippi 38677, USA
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25
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Yang H, Xu J, Guo Y, Koide RT, Dai Y, Xu M, Bian L, Bian X, Zhang Q. Predicting plant response to arbuscular mycorrhizas: The role of host functional traits. FUNGAL ECOL 2016. [DOI: 10.1016/j.funeco.2015.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Yang H, Xu M, Koide RT, Liu Q, Dai Y, Liu L, Bian X. Effects of ditch-buried straw return on water percolation, nitrogen leaching and crop yields in a rice-wheat rotation system. J Sci Food Agric 2016; 96:1141-9. [PMID: 25847361 DOI: 10.1002/jsfa.7196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 11/04/2014] [Revised: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 05/28/2023]
Abstract
BACKGROUND Crop residue management and nitrogen loss are two important environmental problems in the rice-wheat rotation system in China. This study investigated the effects of burial of straw on water percolation, nitrogen loss by leaching, crop growth and yield. Greenhouse mesocosm experiments were conducted over the course of three simulated cropping seasons in a rice1-wheat-rice2 rotation. RESULTS Greater amounts of straw resulted in more water percolation, irrespective of crop season. Burial at 20 and 35 cm significantly reduced, but burial at 50 cm increased nitrogen leaching. Straw at 500 kg ha(-1) reduced, but at 1000 kg ha(-1) and at 1500 kg ha(-1) straw increased nitrogen leaching in three consecutive crop rotations. In addition, straw at 500 kg ha(-1) buried at 35 cm significantly increased yield and its components for both crops. CONCLUSIONS This study suggests that N losses via leaching from the rice-wheat rotation may be reduced by the burial of the appropriate amount of straw at the appropriate depth. Greater amounts of buried straw, however, may promote nitrogen leaching and negatively affect crop growth and yields. Complementary field experiments must be performed to make specific agronomic recommendations.
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Affiliation(s)
- Haishui Yang
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingmin Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Qian Liu
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yajun Dai
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Liu
- College of Agriculture, Henan University of Science and Technology, Luoyang, 471003, China
| | - Xinmin Bian
- Key Laboratory of Crop Physiology, Ecology and Production Management, Nanjing Agricultural University, Nanjing, 210095, China
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Williams A, Kane DA, Ewing PM, Atwood LW, Jilling A, Li M, Lou Y, Davis AS, Grandy AS, Huerd SC, Hunter MC, Koide RT, Mortensen DA, Smith RG, Snapp SS, Spokas KA, Yannarell AC, Jordan NR. Soil Functional Zone Management: A Vehicle for Enhancing Production and Soil Ecosystem Services in Row-Crop Agroecosystems. Front Plant Sci 2016; 7:65. [PMID: 26904043 PMCID: PMC4743437 DOI: 10.3389/fpls.2016.00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/14/2016] [Indexed: 05/08/2023]
Abstract
There is increasing global demand for food, bioenergy feedstocks and a wide variety of bio-based products. In response, agriculture has advanced production, but is increasingly depleting soil regulating and supporting ecosystem services. New production systems have emerged, such as no-tillage, that can enhance soil services but may limit yields. Moving forward, agricultural systems must reduce trade-offs between production and soil services. Soil functional zone management (SFZM) is a novel strategy for developing sustainable production systems that attempts to integrate the benefits of conventional, intensive agriculture, and no-tillage. SFZM creates distinct functional zones within crop row and inter-row spaces. By incorporating decimeter-scale spatial and temporal heterogeneity, SFZM attempts to foster greater soil biodiversity and integrate complementary soil processes at the sub-field level. Such integration maximizes soil services by creating zones of 'active turnover', optimized for crop growth and yield (provisioning services); and adjacent zones of 'soil building', that promote soil structure development, carbon storage, and moisture regulation (regulating and supporting services). These zones allow SFZM to secure existing agricultural productivity while avoiding or minimizing trade-offs with soil ecosystem services. Moreover, the specific properties of SFZM may enable sustainable increases in provisioning services via temporal intensification (expanding the portion of the year during which harvestable crops are grown). We present a conceptual model of 'virtuous cycles', illustrating how increases in crop yields within SFZM systems could create self-reinforcing feedback processes with desirable effects, including mitigation of trade-offs between yield maximization and soil ecosystem services. Through the creation of functionally distinct but interacting zones, SFZM may provide a vehicle for optimizing the delivery of multiple goods and services in agricultural systems, allowing sustainable temporal intensification while protecting and enhancing soil functioning.
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Affiliation(s)
- Alwyn Williams
- Department of Agronomy and Plant Genetics, University of Minnesota, St PaulMN, USA
| | - Daniel A. Kane
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East LansingMI, USA
| | - Patrick M. Ewing
- Department of Agronomy and Plant Genetics, University of Minnesota, St PaulMN, USA
| | - Lesley W. Atwood
- Department of Natural Resources and the Environment, University of New Hampshire, DurhamNH, USA
| | - Andrea Jilling
- Department of Natural Resources and the Environment, University of New Hampshire, DurhamNH, USA
| | - Meng Li
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Yi Lou
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Adam S. Davis
- Global Change and Photosynthesis Research Unit, United States Department of Agriculture – Agricultural Research Service, UrbanaIL, USA
| | - A. Stuart Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, DurhamNH, USA
| | - Sheri C. Huerd
- Department of Agronomy and Plant Genetics, University of Minnesota, St PaulMN, USA
| | - Mitchell C. Hunter
- Department of Plant Science, The Pennsylvania State University, University ParkPA, USA
| | - Roger T. Koide
- Department of Biology, Brigham Young University, ProvoUT, USA
| | - David A. Mortensen
- Department of Plant Science, The Pennsylvania State University, University ParkPA, USA
| | - Richard G. Smith
- Department of Natural Resources and the Environment, University of New Hampshire, DurhamNH, USA
| | - Sieglinde S. Snapp
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East LansingMI, USA
| | - Kurt A. Spokas
- Soil and Water Management Unit, United States Department of Agriculture – Agricultural Research Service, St PaulMN, USA
| | - Anthony C. Yannarell
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana–Champaign, UrbanaIL, USA
| | - Nicholas R. Jordan
- Department of Agronomy and Plant Genetics, University of Minnesota, St PaulMN, USA
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Eissenstat DM, Kucharski JM, Zadworny M, Adams TS, Koide RT. Linking root traits to nutrient foraging in arbuscular mycorrhizal trees in a temperate forest. New Phytol 2015; 208:114-24. [PMID: 25970701 DOI: 10.1111/nph.13451] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/05/2015] [Indexed: 05/05/2023]
Affiliation(s)
- David M. Eissenstat
- Intercollege Graduate Degree Program in Plant Biology Penn State University University Park PA 16802 USA
- Department of Ecosystem Science and Management Penn State University University Park PA 16802 USA
| | - Joshua M. Kucharski
- Intercollege Graduate Degree Program in Plant Biology Penn State University University Park PA 16802 USA
| | - Marcin Zadworny
- Intercollege Graduate Degree Program in Plant Biology Penn State University University Park PA 16802 USA
- Institute of Dendrology Polish Academy of Sciences Parkowa 5 62‐035 Kórnik Poland
| | - Thomas S. Adams
- Department of Ecosystem Science and Management Penn State University University Park PA 16802 USA
| | - Roger T. Koide
- Intercollege Graduate Degree Program in Plant Biology Penn State University University Park PA 16802 USA
- Department of Biology Brigham Young University Provo UT 84602 USA
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Liu B, Li H, Zhu B, Koide RT, Eissenstat DM, Guo D. Complementarity in nutrient foraging strategies of absorptive fine roots and arbuscular mycorrhizal fungi across 14 coexisting subtropical tree species. New Phytol 2015; 208:125-36. [PMID: 25925733 DOI: 10.1111/nph.13434] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 01/27/2015] [Accepted: 03/29/2015] [Indexed: 05/05/2023]
Abstract
In most cases, both roots and mycorrhizal fungi are needed for plant nutrient foraging. Frequently, the colonization of roots by arbuscular mycorrhizal (AM) fungi seems to be greater in species with thick and sparsely branched roots than in species with thin and densely branched roots. Yet, whether a complementarity exists between roots and mycorrhizal fungi across these two types of root system remains unclear. We measured traits related to nutrient foraging (root morphology, architecture and proliferation, AM colonization and extramatrical hyphal length) across 14 coexisting AM subtropical tree species following root pruning and nutrient addition treatments. After root pruning, species with thinner roots showed more root growth, but lower mycorrhizal colonization, than species with thicker roots. Under multi-nutrient (NPK) addition, root growth increased, but mycorrhizal colonization decreased significantly, whereas no significant changes were found under nitrogen or phosphate additions. Moreover, root length proliferation was mainly achieved by altering root architecture, but not root morphology. Thin-root species seem to forage nutrients mainly via roots, whereas thick-root species rely more on mycorrhizal fungi. In addition, the reliance on mycorrhizal fungi was reduced by nutrient additions across all species. These findings highlight complementary strategies for nutrient foraging across coexisting species with contrasting root traits.
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Affiliation(s)
- Bitao Liu
- Center of Forest Ecosystem Studies and Qianyanzhou Ecological Station, Key Laboratory of Ecosystem Network Observation and Modeling, Synthesis Research Center of Chinese Ecosystem Research Network, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongbo Li
- Center of Forest Ecosystem Studies and Qianyanzhou Ecological Station, Key Laboratory of Ecosystem Network Observation and Modeling, Synthesis Research Center of Chinese Ecosystem Research Network, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Biao Zhu
- Department of Ecology, College of Urban and Environmental Sciences, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing, 100871, China
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
| | - David M Eissenstat
- Department of Ecosystem Science and Management, and Intercollege Graduate Degree Program in Plant Biology, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dali Guo
- Center of Forest Ecosystem Studies and Qianyanzhou Ecological Station, Key Laboratory of Ecosystem Network Observation and Modeling, Synthesis Research Center of Chinese Ecosystem Research Network, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing, 100101, China
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Affiliation(s)
- Ian A Dickie
- Bio-Protection Research Centre, Lincoln University, Lincoln, 7640, New Zealand
| | - Roger T Koide
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
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Koide RT, Fernandez C, Malcolm G. Determining place and process: functional traits of ectomycorrhizal fungi that affect both community structure and ecosystem function. New Phytol 2014. [PMID: 26207269 DOI: 10.1111/nph.12538] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
There is a growing interest amongst community ecologists in functional traits. Response traits determine membership in communities. Effect traits influence ecosystem function. One goal of community ecology is to predict the effect of environmental change on ecosystem function. Environmental change can directly and indirectly affect ecosystem function. Indirect effects are mediated through shifts in community structure. It is difficult to predict how environmental change will affect ecosystem function via the indirect route when the change in effect trait distribution is not predictable from the change in response trait distribution. When response traits function as effect traits, however, it becomes possible to predict the indirect effect of environmental change on ecosystem function. Here we illustrate four examples in which key attributes of ectomycorrhizal fungi function as both response and effect traits. While plant ecologists have discussed response and effect traits in the context of community structuring and ecosystem function, this approach has not been applied to ectomycorrhizal fungi. This is unfortunate because of the large effects of ectomycorrhizal fungi on ecosystem function. We hope to stimulate further research in this area in the hope of better predicting the ecosystem- and landscape-level effects of the fungi as influenced by changing environmental conditions.
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Abstract
Ectomycorrhizal fungal tissues comprise a significant forest-litter pool. Ectomycorrhizal (EM) fungi may also influence the decomposition of other forest-litter components via competitive interactions with decomposer fungi and by ensheathing fine roots. Because of these direct and indirect effects of ectomycorrhizal fungi, the factors that control the decomposition of EM fungi will strongly control forest-litter decomposition as a whole and, thus, ecosystem nutrient and carbon cycling. Some have suggested that chitin, a component of fungal cell walls, reduces fungal tissue decomposition because it is relatively recalcitrant. We therefore examined the change in chitin concentrations of EM fungal tissues during decomposition. Our results show that chitin is not recalcitrant relative to other compounds in fungal tissues and that its concentration is positively related to the decomposition of fungal tissues. Variation existing among EM fungal isolates in chitin concentration suggests that EM fungal community structure influences C and nutrient cycling.
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Affiliation(s)
- Christopher W Fernandez
- Intercollege Graduate Program in Ecology, 103 Tyson Building, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
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Abstract
In many forest ecosystems, fine root litter comprises a large pool of organic carbon and nutrients. In temperate climates ectomycorrhizal fungi colonize the roots of many forest plant species. If ectomycorrhizal colonization influenced root decomposition, it could significantly influence carbon sequestration and nutrient cycling. Fungal tissues and fine roots may decompose at different rates and, therefore, ectomycorrhizal colonization may either hasten or retard root decomposition. Unfortunately, no comparisons of the decomposition of roots and ectomycorrhizal fungi have yet been made. Therefore, we compared decomposition of Pinus resinosa fine roots and ectomycorrhizal fungi from a Pinus resinosa plantation. We also compared the decomposition rates of nonmycorrhizal Pinus resinosa fine roots with roots colonized by nine species of ectomycorrhizal fungi. We found that the several tested isolates of ectomycorrhizal fungi decomposed far more rapidly than the fine roots and that ectomycorrhizal colonization either had no significant effect on root decomposition or significantly increased root decomposition depending on the isolate of fungus. We conclude that the composition of an ectomycorrhizal fungal community may affect carbon and nutrient cycling through its influence on root decomposition.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, 102 Tyson Building, The Pennsylvania State University, University Park, PA 16802, USA
- Graduate Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher W Fernandez
- Graduate Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew S Peoples
- Department of Horticulture, 102 Tyson Building, The Pennsylvania State University, University Park, PA 16802, USA
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35
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Hoeksema JD, Chaudhary VB, Gehring CA, Johnson NC, Karst J, Koide RT, Pringle A, Zabinski C, Bever JD, Moore JC, Wilson GWT, Klironomos JN, Umbanhowar J. A meta-analysis of context-dependency in plant response to inoculation with mycorrhizal fungi. Ecol Lett 2010; 13:394-407. [PMID: 20100237 DOI: 10.1111/j.1461-0248.2009.01430.x] [Citation(s) in RCA: 482] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason D Hoeksema
- Department of Biology, University of Mississippi, University, MS 38677, USA.
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López-Gutiérrez JC, Malcolm GM, Koide RT, Eissenstat DM. Ectomycorrhizal fungi from Alaska and Pennsylvania: adaptation of mycelial respiratory response to temperature? New Phytol 2008; 180:741-4. [PMID: 19138230 DOI: 10.1111/j.1469-8137.2008.02655.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA (*Author for correspondence: tel +1 814 863 0710; fax +1 814 863 6139; email )
| | - Jori N Sharda
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA (*Author for correspondence: tel +1 814 863 0710; fax +1 814 863 6139; email )
| | - Joshua R Herr
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA (*Author for correspondence: tel +1 814 863 0710; fax +1 814 863 6139; email )
| | - Glenna M Malcolm
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA (*Author for correspondence: tel +1 814 863 0710; fax +1 814 863 6139; email )
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Abstract
* The basis for significant interspecific variability in colonization by arbuscular mycorrhizal fungi is poorly understood. Limited evidence suggests that, for species with a dimorphic hypodermis, colonization of the root cortex occurs only through hypodermal passage cells. Therefore, the hypothesis that interspecific variability in mycorrhizal colonization is accounted for by interspecific variation in passage cell distribution was tested. * The arbuscular mycorrhizal colonization and distribution of fungal penetration points and hypodermal passage cells in the root systems of eight species (seven plant families) possessing a dimorphic hypodermis were characterized. * Mycorrhizal fungal penetration of the hypodermis occurred exclusively through passage cells. Moreover, the proportion of root length with passage cells explained nearly 99% of the variability among the eight plant species in the proportion of root length with penetration points. * In dimorphic hypodermal species, passage cells appear to be key determinants of mycorrhizal colonization because they are the cells through which fungal penetration of the hypodermis occurs. Variation among such species in mycorrhizal colonization may be at least partly determined by variation in the proportion of root length with passage cells.
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Affiliation(s)
- J N Sharda
- Intercollege Graduate Degree Program in Plant Biology
| | - R T Koide
- Intercollege Graduate Degree Program in Plant Biology
- Department of Horticulture, and
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Several mechanisms may contribute to the high species richness often reported in ectomycorrhizal (ECM) fungal communities, including spatial and temporal partitioning. Here, we focus on temporal partitioning. Using molecular methods, we determined the frequencies of occurrence of ECM fungal species detected as hyphae and ECM roots in the forest floor of a Pinus resinosa plantation during a 13-month period. We then used a novel statistical procedure to place the most frequently occurring ECM fungal species into groups distinguished by their patterns of relative frequency over time. Three groups with contrasting temporal patterns were distinguishable for fungal species detected as hyphae. Two groups were distinguishable for species detected as ECM roots. Our results support the hypothesis that temporal partitioning occurs among the species of ECM fungi in this community, but we did not address its causes, which may have involved interactions among species' physiological tolerances, temporal environmental variability, temporal patterns of root production, and variation in fungal genet lifespan. These interactions should be the subjects of future research.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Durland L Shumway
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bing Xu
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jori N Sharda
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA 16802, USA
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA
| | - Pierre-Emmanuel Courty
- INRA Nancy, UMR 1136 INRA/UHP Interactions Arbres-Microorganismes, 54280 Champenoux, France
| | - Jean Garbaye
- INRA Nancy, UMR 1136 INRA/UHP Interactions Arbres-Microorganismes, 54280 Champenoux, France
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Lekberg Y, Koide RT. Is plant performance limited by abundance of arbuscular mycorrhizal fungi? A meta-analysis of studies published between 1988 and 2003. New Phytol 2005; 168:189-204. [PMID: 16159333 DOI: 10.1111/j.1469-8137.2005.01490.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We conducted meta-analyses of 290 published field and glasshouse trials to determine the effects of various agricultural practices on mycorrhizal colonization in nonsterile soils, and the consequence of those effects on yield, biomass, and phosphorus (P) concentration. Mycorrhizal colonization was increased most by inoculation (29% increase), followed by shortened fallow (20%) and reduced soil disturbance (7%). The effect of crop rotation depended on whether the crop was mycorrhizal. Increased colonization resulted in a yield increase in the field of 23% across all management practices. Biomass at harvest and shoot P concentration in early season were increased by inoculation (57 and 33%, respectively) and shortened fallow (55 and 24%). Reduced disturbance increased shoot P concentration by 27%, but biomass was not significantly affected. Biomass was significantly reduced in 2% of all trials in which there was a significant increase in colonization. Irrespective of management practice, an increased mycorrhizal colonization was less likely to increase biomass if either soil P or indigenous inoculum potential was high.
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Affiliation(s)
- Y Lekberg
- Department of Horticulture and Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
Ectomycorrhizal fungal communities have been characterized in a number of ways. Here we compare colonized root-tip and mycelia views of an ectomycorrhizal fungal community. Ectomycorrhizal fungi, both as mycelia and colonized root tips, were identified in soil samples taken from a pine plantation. We determined that for some ectomycorrhizal fungal species multiple root tips from a single soil sample were not independent. Therefore in the comparison of root-tip and mycelia views, we considered species to be present or absent from each soil sample irrespective of the number of root tips colonized by the species. We observed 39 ectomycorrhizal fungal species in total, but 12 were observed exclusively as mycelia and 11 exclusively colonizing root tips. The relative frequencies of 10 species occurring as both mycelia and root tips were not independent of the method of observation. Our results suggest that ectomycorrhizal fungal species differ in their spatial distributions on root tips, and that root-tip and mycelia views of the community are different.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA.
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Abstract
Ectomycorrhizal fungal communities can be structured by abiotic and biotic factors. Here, we present evidence for community structuring by species interactions. We sampled ectomycorrhizas and forest floor seven times during a 13-month period. The presence of various ectomycorrhizal fungal species was determined for each sample, and species co-occurrence analyses were performed. For both ectomycorrhizas and forest floor samples there was significantly less co-occurrence among species within the community than expected by chance, mostly because of negative associations involving Cenococcum geophilum or Clavulina cinerea. For some species pairs, there was significantly more co-occurrence than expected by chance. Both nitrogen and tannin additions to the forest floor altered some interactions among species. The causes of these nonrandom distributions are currently unknown. Future investigations on competition, antibiosis, parasitism and facilitation among ectomycorrhizal fungal species appear to be warranted.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA.
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Koide RT. Nucleic Acid Isolation from Ecological Samples—Fungal Associations, Mycorrhizae. Methods Enzymol 2005; 395:58-72. [PMID: 15865961 DOI: 10.1016/s0076-6879(05)95005-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mycorrhizal fungi are among the most common symbioses found in terrestrial ecosystems, both natural and managed. They are important for many reasons, but most notably because of their positive effects on plant growth, which are mediated by their uptake of nutrients from the soil and transport of these to the roots. Moreover, many edible fungi are mycorrhizal. The study of mycorrhizal fungi has been hampered by the inability to identify species and individuals in the soil. This has been greatly aided by DNA-based methods, which first require the extraction of DNA. Herein, I discuss some general concerns that must be considered when extracting and purifying DNA from ecological samples and offer specific methods for soil, mycorrhizal roots, and fruiting bodies. These methods are rapid, safe, effective, relatively inexpensive, and convenient because they are based on commercially available kits.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Abstract
This is not a review paper in the traditional sense, of which there are many. Three of the most influential reviews that summarized well some of the "older" literature include those by Nicolson (1967), Gerdemann (1968) and Mosse (1973). Instead, in this brief and incomplete work, we attempt to show the historical development of research on arbuscular mycorrhizas. We owe much to those who have written other historical accounts, including Rayner (1926-1927), Trappe and Berch (1985), Mosse (1985), Schenck (1985), Harley (1991) and Allen (1996), but the contents of this work naturally reflect our own ignorance, interests and biases. It was often difficult to distinguish between the historical and the contemporary, and we did not use any specific cutoff date in making this distinction. The degree to which we include "contemporary" literature was determined by our own assessment of its connectedness to older literature. In any case, we hope this will be of some interest to those of you who study the arbuscular mycorrhiza, and that it will serve the purpose of providing what we consider to be an important historical context for current researchers. We wish you good fortune in your research.
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Affiliation(s)
- Roger T Koide
- Department of Horticulture, Pennsylvania State University, University Park, 16802, USA.
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Wu T, Sharda JN, Koide RT. Exploring interactions between saprotrophic microbes and ectomycorrhizal fungi using a protein-tannin complex as an N source by red pine (Pinus resinosa). New Phytol 2003; 159:131-139. [PMID: 33873681 DOI: 10.1046/j.1469-8137.2003.00800.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• Recent studies suggest that some plants may circumvent N mineralization carried out by saprotrophs because their ectomycorrhizal fungi have the capacity to hydrolyse protein. When complexed by tannins, however, proteins may be unavailable to some ectomycorrhizal fungi. • Here we tested the hypothesis that when protein-tannin complex is the N source, Pisolithus tinctorius will promote N uptake into red pine (Pinus resinosa) only in the presence of saprotrophs. • The model protein-tannin complex was stable at field pH. P. tinctorius could not obtain N from it, but saprotrophs could. Pre-treatment of the complex by saprotrophs did make its N available to ectomycorrhizal fungi. However, when the protein-tannin complex was the major N source, P. tinctorius increased shoot P but not N content, even in the presence of saprotrophs. • Interactions between saprotrophs and ectomycorrhizal fungi may be different for N and P because of immobilization of N by ectomycorrhizal fungi, or by the more rapid diffusion of ammonium than phosphate, rendering the absorptive surface area of ectomycorrhizal fungi superfluous for uptake of N but not for P.
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Affiliation(s)
- Tiehang Wu
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jori N Sharda
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
| | - Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
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Abstract
• Niche differentiation for different soil substrates has been proposed as a mechanism contributing to ectomycorrhizal fungal diversity. This hypothesis has been largely untestable because of a lack of techniques to study the in situ distribution of ectomycorrhizal hyphae. • We developed a technique involving soil DNA extraction, PCR and terminal restriction fragment length polymorphism (T-RFLP) analysis for species identification to investigate the vertical distribution of fungal hyphae in four distinct layers of the forest floor (lower litter, F-layer, H-layer, and B-horizon) of a Pinus resinosa plantation. • Fungal communities differed markedly among the four layers. Cluster analysis suggested six different patterns of resource utilization: litter-layer specialists, litter-layer generalists, F-layer, H-layer, and B-horizon species, and multilayer generalists. Known ectomycorrhizal species were found in all six clusters. • This spatial partitioning observed among ectomycorrhizal fungi along a single, relatively simple substrate-resource gradient supports the niche differentiation hypothesis as an important mechanism contributing to ectomycorrhizal fungal diversity.
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Affiliation(s)
- Ian A Dickie
- Current address: Department of Forest Resources, University of Minnesota, 115 Green Hall, 1530 N. Cleveland Ave., St. Paul, MN 55108, USA
| | - Bing Xu
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA
| | - Roger T Koide
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802 USA
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Affiliation(s)
- Roger T Koide
- The Pennsylvania State University, University Park 16802, USA.
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