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Lupini S, Nguyen HN, Morales D, House GL, Paudel S, Chain PSG, Rodrigues DF. Diversity of fungal microbiome obtained from plant rhizoplanes. Sci Total Environ 2023:164506. [PMID: 37295515 DOI: 10.1016/j.scitotenv.2023.164506] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023]
Abstract
Microbial communities, and their ecological importance, have been investigated in several habitats. However, so far, most studies could not describe the closest microbial interactions and their functionalities. This study investigates the co-occurring interactions between fungi and bacteria in plant rhizoplanes and their potential functions. The partnerships were obtained using fungal-highway columns with four plant-based media. The fungi and associated microbiomes isolated from the columns were identified by sequencing the ITS (fungi) and 16S rRNA genes (bacteria). Statistical analyses including Exploratory Graph and Network Analysis were used to visualize the presence of underlying clusters in the microbial communities and evaluate the metabolic functions associated with the fungal microbiome (PICRUSt2). Our findings characterize the presence of both unique and complex bacterial communities associated with different fungi. The results showed that Bacillus was associated as exo-bacteria in 80 % of the fungi but occurred as putative endo-bacteria in 15 %. A shared core of putative endo-bacterial genera, potentially involved in the nitrogen cycle was found in 80 % of the isolated fungi. The comparison of potential metabolic functions of the putative endo- and exo-communities highlighted the potential essential factors to establish an endosymbiotic relationship, such as the loss of pathways associated with metabolites obtained from the host while maintaining pathways responsible for bacterial survival within the hypha.
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Affiliation(s)
- Simone Lupini
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sachin Paudel
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Debora F Rodrigues
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA; Department of Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA.
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2
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Robinson AJ, House GL, Morales DP, Kelliher JM, Gallegos-Graves LV, LeBrun ES, Davenport KW, Palmieri F, Lohberger A, Bregnard D, Estoppey A, Buffi M, Paul C, Junier T, Hervé V, Cailleau G, Lupini S, Nguyen HN, Zheng AO, Gimenes LJ, Bindschedller S, Rodrigues DF, Werner JH, Young JD, Junier P, Chain PSG. Widespread bacterial diversity within the bacteriome of fungi. Commun Biol 2021; 4:1168. [PMID: 34621007 PMCID: PMC8497576 DOI: 10.1038/s42003-021-02693-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.
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Affiliation(s)
- Aaron J Robinson
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Geoffrey L House
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Demosthenes P Morales
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Julia M Kelliher
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - La Verne Gallegos-Graves
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Erick S LeBrun
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Danaé Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Simone Lupini
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Hang N Nguyen
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Amy O Zheng
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Luciana Jandelli Gimenes
- Center for Environmental Research and Training, University of São Paulo, Cubatão, São Paulo, 11.540 -990, Brazil
| | - Saskia Bindschedller
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - James H Werner
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves LV, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021; 97:6095729. [PMID: 33440006 PMCID: PMC7878174 DOI: 10.1093/femsec/fiab003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
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Affiliation(s)
- Pilar Junier
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Celine Vallotton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Olivia C Trautschold
- Materials Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH, 1015, Lausanne, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aaron Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | | | - Armand E K Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Simone Lupini
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Debora F Rodrigues
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | | | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
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Delavaux CS, Schemanski JL, House GL, Tipton AG, Sikes B, Bever JD. Root pathogen diversity and composition varies with climate in undisturbed grasslands, but less so in anthropogenically disturbed grasslands. ISME J 2020; 15:304-317. [PMID: 32958849 PMCID: PMC7852655 DOI: 10.1038/s41396-020-00783-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/25/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
Soil-borne pathogens structure plant communities, shaping their diversity, and through these effects may mediate plant responses to climate change and disturbance. Little is known, however, about the environmental determinants of plant pathogen communities. Therefore, we explored the impact of climate gradients and anthropogenic disturbance on root-associated pathogens in grasslands. We examined the community structure of two pathogenic groups-fungal pathogens and oomycetes-in undisturbed and anthropogenically disturbed grasslands across a natural precipitation and temperature gradient in the Midwestern USA. In undisturbed grasslands, precipitation and temperature gradients were important predictors of pathogen community richness and composition. Oomycete richness increased with precipitation, while fungal pathogen richness depended on an interaction of precipitation and temperature, with precipitation increasing richness most with higher temperatures. Disturbance altered plant pathogen composition and precipitation and temperature had a reduced effect on pathogen richness and composition in disturbed grasslands. Because pathogens can mediate plant community diversity and structure, the sensitivity of pathogens to disturbance and climate suggests that degradation of the pathogen community may mediate loss, or limit restoration of, native plant diversity in disturbed grasslands, and may modify plant community response to climate change.
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Affiliation(s)
- Camille S Delavaux
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA. .,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA.
| | - Josh L Schemanski
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - Geoffrey L House
- National Ecological Observatory Network, Boulder, CO, 80301, USA
| | - Alice G Tipton
- Department of Science, Technology, and Mathematics, Lincoln University, 821 Taylor Drive, 205 Daniel Hall, Jefferson City, MO, 65101, USA
| | - Benjamin Sikes
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, KS, 66045, USA.,Kansas Biological Survey, The University of Kansas, 106 Higuchi Hall, 2101 Constant Ave, Lawrence, KS, 66047, USA
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5
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House GL, Bever JD. Biochar soil amendments in prairie restorations do not interfere with benefits from inoculation with native arbuscular mycorrhizal fungi. Restor Ecol 2020. [DOI: 10.1111/rec.12924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Geoffrey L. House
- Department of Biology Indiana University 1001 East Third Street Bloomington IN 47405 U.S.A
| | - James D. Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey The University of Kansas 2041 Haworth Hall, 1200 Sunnyside Avenue Lawrence KS 66045 U.S.A
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6
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Palmieri F, Estoppey A, House GL, Lohberger A, Bindschedler S, Chain PSG, Junier P. Oxalic acid, a molecule at the crossroads of bacterial-fungal interactions. Adv Appl Microbiol 2018; 106:49-77. [PMID: 30798804 DOI: 10.1016/bs.aambs.2018.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oxalic acid is the most ubiquitous and common low molecular weight organic acid produced by living organisms. Oxalic acid is produced by fungi, bacteria, plants, and animals. The aim of this review is to give an overview of current knowledge about the microbial cycling of oxalic acid through ecosystems. Here we review the production and degradation of oxalic acid, as well as its implications in the metabolism for fungi, bacteria, plants, and animals. Indeed, fungi are well known producers of oxalic acid, while bacteria are considered oxalic acid consumers. However, this framework may need to be modified, because the ability of fungi to degrade oxalic acid and the ability of bacteria to produce it, have been poorly investigated. Finally, we will highlight the role of fungi and bacteria in oxalic acid cycling in soil, plant and animal ecosystems.
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Affiliation(s)
- Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Paul C, Filippidou S, Jamil I, Kooli W, House GL, Estoppey A, Hayoz M, Junier T, Palmieri F, Wunderlin T, Lehmann A, Bindschedler S, Vennemann T, Chain PSG, Junier P. Bacterial spores, from ecology to biotechnology. Adv Appl Microbiol 2018; 106:79-111. [PMID: 30798805 DOI: 10.1016/bs.aambs.2018.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The production of a highly specialized cell structure called a spore is a remarkable example of a survival strategy displayed by bacteria in response to challenging environmental conditions. The detailed analysis and description of the process of sporulation in selected model organisms have generated a solid background to understand the cellular processes leading to the formation of this specialized cell. However, much less is known regarding the ecology of spore-formers. This research gap needs to be filled as the feature of resistance has important implications not only on the survival of spore-formers and their ecology, but also on the use of spores for environmental prospection and biotechnological applications.
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Affiliation(s)
- Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Sevasti Filippidou
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Isha Jamil
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Wafa Kooli
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Mathilda Hayoz
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland; Vital-IT group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Anael Lehmann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Torsten Vennemann
- Laboratory of stable isotope geochemistry, Institute of Earth Surface Dynamics, University of Lausanne, Lausanne, Switzerland
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland.
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Koziol L, Schultz PA, House GL, Bauer JT, Middleton EL, Bever JD. The Plant Microbiome and Native Plant Restoration: The Example of Native Mycorrhizal Fungi. Bioscience 2018. [DOI: 10.1093/biosci/biy125] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Liz Koziol
- Kansas Biological Survey, at the University of Kansas, in Lawrence
| | - Peggy A Schultz
- Kansas Biological Survey, at the University of Kansas, in Lawrence
| | | | | | | | - James D Bever
- Kansas Biological Survey, at the University of Kansas, in Lawrence
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House GL, Bever JD. Disturbance reduces the differentiation of mycorrhizal fungal communities in grasslands along a precipitation gradient. Ecol Appl 2018; 28:736-748. [PMID: 29314434 DOI: 10.1002/eap.1681] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 08/08/2017] [Revised: 11/22/2017] [Accepted: 12/11/2017] [Indexed: 05/14/2023]
Abstract
Given that mycorrhizal fungi play key roles in shaping plant communities, greater attention should be focused on factors that determine the composition of mycorrhizal fungal communities and their sensitivity to anthropogenic disturbance. We investigate changes in arbuscular mycorrhizal (AM) fungal community composition across a precipitation gradient in North American grasslands as well as changes occurring with varying degrees of site disturbance that have resulted in invasive plant establishment. We find strong differentiation of AM fungal communities in undisturbed remnant grasslands across the precipitation gradient, whereas communities in disturbed grasslands were more homogeneous. These changes in community differentiation with disturbance are consistent with more stringent environmental filtering of AM fungal communities in undisturbed sites that may also be promoted by more rigid functional constraints imposed on AM fungi by the native plant communities in these areas. The AM fungal communities in eastern grasslands were particularly sensitive to anthropogenic disturbance, with disturbed sites having low numbers of AM fungal operational taxonomic units (OTUs) commonly found in undisturbed sites, and also the proliferation of AM fungal OTUs in disturbed sites. This proliferation of AM fungi in eastern disturbed sites coincided with increased soil phosphorus availability and is consistent with evidence suggesting the fungi represented by these OTUs would provide reduced benefits to native plants. The differentiation of AM fungal communities along the precipitation gradient in undisturbed grasslands but not in disturbed sites is consistent with AM fungi aiding plant adaptation to climate, and suggests they may be especially important targets for conservation and restoration in order to help maintain or re-establish diverse grassland plant communities.
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Affiliation(s)
- Geoffrey L House
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, Indiana, 47405, USA
| | - James D Bever
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, The University of Kansas, 2041 Haworth Hall, 1200 Sunnyside Avenue, Lawrence, Kansas, 66045, USA
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House GL, Hahn MW. Evaluating methods to visualize patterns of genetic differentiation on a landscape. Mol Ecol Resour 2018; 18:448-460. [PMID: 29282875 DOI: 10.1111/1755-0998.12747] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 12/19/2017] [Indexed: 01/25/2023]
Abstract
With advances in sequencing technology, research in the field of landscape genetics can now be conducted at unprecedented spatial and genomic scales. This has been especially evident when using sequence data to visualize patterns of genetic differentiation across a landscape due to demographic history, including changes in migration. Two recent model-based visualization methods that can highlight unusual patterns of genetic differentiation across a landscape, SpaceMix and EEMS, are increasingly used. While SpaceMix's model can infer long-distance migration, EEMS' model is more sensitive to short-distance changes in genetic differentiation, and it is unclear how these differences may affect their results in various situations. Here, we compare SpaceMix and EEMS side by side using landscape genetics simulations representing different migration scenarios. While both methods excel when patterns of simulated migration closely match their underlying models, they can produce either un-intuitive or misleading results when the simulated migration patterns match their models less well, and this may be difficult to assess in empirical data sets. We also introduce unbundled principal components (un-PC), a fast, model-free method to visualize patterns of genetic differentiation by combining principal components analysis (PCA), which is already used in many landscape genetics studies, with the locations of sampled individuals. Un-PC has characteristics of both SpaceMix and EEMS and works well with simulated and empirical data. Finally, we introduce msLandscape, a collection of tools that streamline the creation of customizable landscape-scale simulations using the popular coalescent simulator ms and conversion of the simulated data for use with un-PC, SpaceMix and EEMS.
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