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Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for Bioenergy. Appl Environ Microbiol 2020; 86:AEM.00880-20. [PMID: 32709729 PMCID: PMC7499029 DOI: 10.1128/aem.00880-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/20/2020] [Indexed: 01/08/2023] Open
Abstract
Learning more about the biodiversity and composition of arbuscular mycorrhizal fungi (AMF) under alternative agricultural management scenarios may be important to the sustainable intensification of switchgrass grown as a bioenergy crop. Using PacBio single-molecule sequencing and taxonomic resolution to the level of amplicon sequence variant (ASV), we assessed the effects of nitrogen amendment on AMF associating with switchgrass and explored relationships between AMF and switchgrass yield across three sites of various productivities in Wisconsin. Nitrogen amendment had little effect on AMF diversity metrics or community composition. While AMF ASV diversity was not correlated with switchgrass yield, AMF family richness and switchgrass yield had a strong, positive relationship at one of our three sites. Each of our sites was dominated by unique ASVs of the species Paraglomus brasilianum, indicating regional segregation of AMF at the intraspecific level. Our molecular biodiversity survey identified putative core members of the switchgrass microbiome, as well as novel clades of AMF, especially in the order Paraglomerales and the genus Nanoglomus Furthermore, our phylogenies unite the cosmopolitan, soil-inhabiting clade deemed GS24 with Pervetustaceae, an enigmatic family prevalent in stressful environments. Future studies should isolate and characterize the novel genetic diversity found in switchgrass agroecosystems and explore the potential yield benefits of AMF richness.IMPORTANCE We assessed the different species of beneficial fungi living in agricultural fields of switchgrass, a large grass grown for biofuels, using high-resolution DNA sequencing. Contrary to our expectations, the fungi were not greatly affected by fertilization. However, we found a positive relationship between plant productivity and the number of families of beneficial fungi at one site. Furthermore, we sequenced many species that could not be identified with existing reference databases. One group of fungi was highlighted in an earlier study for being widely distributed but of unknown taxonomy. We discovered that this group belonged to a family called Pervetustaceae, which may benefit switchgrass in stressful environments. To produce higher-yielding switchgrass in a more sustainable manner, it could help to study these undescribed fungi and the ways in which they may contribute to greater switchgrass yield in the absence of fertilization.
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Abstract
Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved. Understanding the basic biology that underpins soil microbiome interactions is required to predict the metaphenomic response to environmental shifts. A significant knowledge gap remains in how such changes affect microbial community dynamics and their metabolic landscape at microbially relevant spatial scales. Using a custom-built SoilBox system, here we demonstrated changes in microbial community growth and composition in different soil environments (14%, 24%, and 34% soil moisture), contingent upon access to reservoirs of nutrient sources. The SoilBox emulates the probing depth of a common soil core and enables determination of both the spatial organization of the microbial communities and their metabolites, as shown by confocal microscopy in combination with mass spectrometry imaging (MSI). Using chitin as a nutrient source, we used the SoilBox system to observe increased adhesion of microbial biomass on chitin islands resulting in degradation of chitin into N-acetylglucosamine (NAG) and chitobiose. With matrix-assisted laser desorption/ionization (MALDI)-MSI, we also observed several phospholipid families that are functional biomarkers for microbial growth on the chitin islands. Fungal hyphal networks bridging different chitin islands over distances of 27 mm were observed only in the 14% soil moisture regime, indicating that such bridges may act as nutrient highways under drought conditions. In total, these results illustrate a system that can provide unprecedented spatial information about interactions within soil microbial communities as a function of changing environments. We anticipate that this platform will be invaluable in spatially probing specific intra- and interkingdom functional relationships of microbiomes within soil. IMPORTANCE Microbial communities are key components of the soil ecosystem. Recent advances in metagenomics and other omics capabilities have expanded our ability to characterize the composition and function of the soil microbiome. However, characterizing the spatial metabolic and morphological diversity of microbial communities remains a challenge due to the dynamic and complex nature of soil microenvironments. The SoilBox system, demonstrated in this work, simulates an ∼12-cm soil depth, similar to a typical soil core, and provides a platform that facilitates imaging the molecular and topographical landscape of soil microbial communities as a function of environmental gradients. Moreover, the nondestructive harvesting of soil microbial communities for the imaging experiments can enable simultaneous multiomics analysis throughout the depth of the SoilBox. Our results show that by correlating molecular and optical imaging data obtained using the SoilBox platform, deeper insights into the nature of specific soil microbial interactions can be achieved.
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Crognale S, Stazi SR, Firrincieli A, Pesciaroli L, Fedi S, Petruccioli M, D'Annibale A. Time-Dependent Changes in Morphostructural Properties and Relative Abundances of Contributors in Pleurotus ostreatus/ Pseudomonas alcaliphila Mixed Biofilms. Front Microbiol 2019; 10:1819. [PMID: 31447819 PMCID: PMC6695841 DOI: 10.3389/fmicb.2019.01819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/23/2019] [Indexed: 11/13/2022] Open
Abstract
Pleurotus ostreatus dual biofilms with bacteria are known to be involved in rock phosphate solubilization, endophytic colonization, and even in nitrogen fixation. Despite these relevant implications, no information is currently available on the architecture of P. ostreatus-based dual biofilms. In addition to this, there is a limited amount of information regarding the estimation of the temporal changes in the relative abundances of the partners in such binary systems. To address these issues, a dual biofilm model system with this fungus was prepared by using Pseudomonas alcaliphila 34 as the bacterial partner due to its very fast biofilm-forming ability. The application of the bacterial inoculum to already settled fungal biofilm on a polystyrene surface coated with hydroxyapatite was the most efficient approach to the production of the mixed system the ultrastructure of which was investigated by a multi-microscopy approach. Transmission electron microscopy analysis showed that the adhesion of bacterial cells onto the mycelial cell wall appeared to be mediated by the presence of an abundant layer of extracellular matrix (ECM). Scanning electron microscopy analysis showed that ECM filaments of bacterial origin formed initially a reticular structure that assumed a tabular semblance after 72 h, thus overshadowing the underlying mycelial network. Across the thickness of the mixed biofilms, the presence of an extensive network of channels with large aggregates of viable bacteria located on the edges of their lumina was found by confocal laser scanning microscopy; on the outermost biofilm layer, a significant fraction of dead bacterial cells was evident. Albeit with tangible differences, similar results regarding the estimation of the temporal shifts in the relative abundances of the two partners were obtained by two independent methods, the former relying on qPCR targeting of 16S and 18S rRNA genes and the latter on ester-linked fatty acid methyl esters analysis.
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Affiliation(s)
- Silvia Crognale
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Silvia Rita Stazi
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Andrea Firrincieli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Lorena Pesciaroli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Stefano Fedi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Maurizio Petruccioli
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Alessandro D'Annibale
- Department for Innovation in Biological, Agro-Food and Forest Systems (DIBAF), University of Tuscia, Viterbo, Italy
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Docherty KM, Gutknecht JLM. Soil microbial restoration strategies for promoting climate-ready prairie ecosystems. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2019; 29:e01858. [PMID: 30680826 PMCID: PMC9286448 DOI: 10.1002/eap.1858] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/10/2018] [Accepted: 01/03/2019] [Indexed: 05/20/2023]
Abstract
Tractable practices for soil microbial restoration in tallgrass prairies reclaimed from agriculture are a critical gap in traditional ecological restoration. Long-term fertilization and tilling permanently alter soil bacterial and fungal communities, requiring microbe-targeted restoration methods to improve belowground ecosystem services and carbon storage in newly restored prairies. These techniques are particularly important when restoring for climate-ready ecosystems, adapted to altered temperature regimes. To approach these issues, we conducted a multi-factorial greenhouse experiment to test the effects of plant species richness, soil amendment and elevated temperature on soil microbial diversity, growth, and function. Treatments consisted of three seedlings of one plant species (Andropogon gerardii) or one seedling each of three plant species (A. gerardii, Echinacea pallida, Coreopsis lanceolata). Soil amendments included cellulose addition, inoculation with a microbial community collected from an undisturbed remnant prairie, and a control. We assessed microbial communities using extracellular enzyme assays, Illumina sequencing of the bacterial 16S rRNA gene, predicted bacterial metabolic pathways from sequence data and phospholipid fatty acid analysis (PLFA), which includes both bacterial and fungal lipid abundances. Our results indicate that addition of cellulose selects for slow-growing bacterial taxa (Verrucomicrobia) and fungi at ambient temperature. However, at elevated temperature, selection for slow-growing bacterial taxa is enhanced, while selection for fungi is lost, indicating temperature sensitivity among fungi. Cellulose addition was a more effective means of altering soil community composition than addition of microbial communities harvested from a remnant prairie. Soil water content was typically higher in the A. gerardii treatment alone, regardless of temperature, but at ambient temperature only, predicted metagenomics pathways for bacterial carbon metabolism were more abundant with A. gerardii. In summary, these results from a mesocosm test case indicate that adding cellulose to newly restored soil and increasing the abundance of C4 grasses, such as A. gerardii, can select for microbial communities adapted for slow growth and carbon storage. Further testing is required to determine if these approaches yield the same results in a field-level experiment.
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Affiliation(s)
- Kathryn M. Docherty
- Department of Biological SciencesWestern Michigan University1903 West Michigan Avenue, Mailstop 5410KalamazooMichigan49008USA
| | - Jessica L. M. Gutknecht
- Department of Soil, Water, and ClimateUniversity of Minnesota Twin CitiesSt. PaulMinnesota55108USA
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Trogisch S, Schuldt A, Bauhus J, Blum JA, Both S, Buscot F, Castro-Izaguirre N, Chesters D, Durka W, Eichenberg D, Erfmeier A, Fischer M, Geißler C, Germany MS, Goebes P, Gutknecht J, Hahn CZ, Haider S, Härdtle W, He JS, Hector A, Hönig L, Huang Y, Klein AM, Kühn P, Kunz M, Leppert KN, Li Y, Liu X, Niklaus PA, Pei Z, Pietsch KA, Prinz R, Proß T, Scherer-Lorenzen M, Schmidt K, Scholten T, Seitz S, Song Z, Staab M, von Oheimb G, Weißbecker C, Welk E, Wirth C, Wubet T, Yang B, Yang X, Zhu CD, Schmid B, Ma K, Bruelheide H. Toward a methodical framework for comprehensively assessing forest multifunctionality. Ecol Evol 2017; 7:10652-10674. [PMID: 29299246 PMCID: PMC5743643 DOI: 10.1002/ece3.3488] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/27/2017] [Accepted: 09/02/2017] [Indexed: 01/30/2023] Open
Abstract
Biodiversity-ecosystem functioning (BEF) research has extended its scope from communities that are short-lived or reshape their structure annually to structurally complex forest ecosystems. The establishment of tree diversity experiments poses specific methodological challenges for assessing the multiple functions provided by forest ecosystems. In particular, methodological inconsistencies and nonstandardized protocols impede the analysis of multifunctionality within, and comparability across the increasing number of tree diversity experiments. By providing an overview on key methods currently applied in one of the largest forest biodiversity experiments, we show how methods differing in scale and simplicity can be combined to retrieve consistent data allowing novel insights into forest ecosystem functioning. Furthermore, we discuss and develop recommendations for the integration and transferability of diverse methodical approaches to present and future forest biodiversity experiments. We identified four principles that should guide basic decisions concerning method selection for tree diversity experiments and forest BEF research: (1) method selection should be directed toward maximizing data density to increase the number of measured variables in each plot. (2) Methods should cover all relevant scales of the experiment to consider scale dependencies of biodiversity effects. (3) The same variable should be evaluated with the same method across space and time for adequate larger-scale and longer-time data analysis and to reduce errors due to changing measurement protocols. (4) Standardized, practical and rapid methods for assessing biodiversity and ecosystem functions should be promoted to increase comparability among forest BEF experiments. We demonstrate that currently available methods provide us with a sophisticated toolbox to improve a synergistic understanding of forest multifunctionality. However, these methods require further adjustment to the specific requirements of structurally complex and long-lived forest ecosystems. By applying methods connecting relevant scales, trophic levels, and above- and belowground ecosystem compartments, knowledge gain from large tree diversity experiments can be optimized.
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Affiliation(s)
- Stefan Trogisch
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Andreas Schuldt
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Jürgen Bauhus
- Chair of Silviculture Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany
| | - Juliet A Blum
- Institute of Plant Sciences University of Bern Bern Switzerland
| | - Sabine Both
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen UK
| | - François Buscot
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Department of Soil Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | - Nadia Castro-Izaguirre
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | | | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Department of Community Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | - David Eichenberg
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Institute of Biology University of Leipzig Leipzig Germany
| | - Alexandra Erfmeier
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Institute for Ecosystem Research/Geobotany Kiel University Kiel Germany
| | - Markus Fischer
- Institute of Plant Sciences University of Bern Bern Switzerland
| | - Christian Geißler
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Markus S Germany
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Institute for Ecosystem Research/Geobotany Kiel University Kiel Germany
| | - Philipp Goebes
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Jessica Gutknecht
- Department of Soil Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany.,Department of Soil, Water, and Climate University of Minnesota, Twin Cities Saint Paul MN USA
| | - Christoph Zacharias Hahn
- Department of Community Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | - Sylvia Haider
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Werner Härdtle
- Institute of Ecology Leuphana University of Lüneburg Lüneburg Germany
| | - Jin-Sheng He
- Department of Ecology College of Urban and Environmental Sciences Key Laboratory for Earth Surface Processes of the Ministry of Education Peking University Beijing China
| | - Andy Hector
- Department of Plant Sciences University of Oxford Oxford UK
| | - Lydia Hönig
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany
| | - Yuanyuan Huang
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Alexandra-Maria Klein
- Nature Conservation and Landscape Ecology Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany
| | - Peter Kühn
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Matthias Kunz
- Institute of General Ecology and Environmental Protection Technische Universität Dresden Tharandt Germany
| | - Katrin N Leppert
- Faculty of Biology University of Freiburg Geobotany, Freiburg Germany
| | - Ying Li
- Faculty of Soil and Water Conservation Beijing Forestry University Haidian District Beijing China
| | - Xiaojuan Liu
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Pascal A Niklaus
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Zhiqin Pei
- Department of Soil Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | | | - Ricarda Prinz
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,Senckenberg Biodiversity and Climate Research Centre (BIK-F) Frankfurt am Main Germany
| | - Tobias Proß
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | | | - Karsten Schmidt
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Thomas Scholten
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Steffen Seitz
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Zhengshan Song
- Institute of Geography, Soil Science and Geomorphology University of Tübingen Tübingen Germany
| | - Michael Staab
- Nature Conservation and Landscape Ecology Faculty of Environment and Natural Resources University of Freiburg Freiburg Germany
| | - Goddert von Oheimb
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Institute of General Ecology and Environmental Protection Technische Universität Dresden Tharandt Germany
| | - Christina Weißbecker
- Department of Soil Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | - Erik Welk
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Christian Wirth
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Institute of Biology University of Leipzig Leipzig Germany
| | - Tesfaye Wubet
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.,Department of Soil Ecology Helmholtz Centre for Environmental Research - UFZ Halle (Saale) Germany
| | - Bo Yang
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,Key Laboratory of Speciality Plant Resources of Jiangxi Province Jingdezhen University Jingdezhen China
| | - Xuefei Yang
- Kunming Institute of Botany Chinese Academy of Sciences Kunming China
| | - Chao-Dong Zhu
- Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change Institute of Botany Chinese Academy of Sciences Beijing China
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden Martin Luther University Halle-Wittenberg Halle (Saale) Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
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