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Zhang M, Wang K, Shi C, Li X, Qiu Z, Shi F. Responses of Fungal Assembly and Co-Occurrence Network of Rhizosphere Soil to Amaranthus palmeri Invasion in Northern China. J Fungi (Basel) 2023; 9:jof9050509. [PMID: 37233220 DOI: 10.3390/jof9050509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023] Open
Abstract
The interaction between invasive plants and soil microbial communities is critical for plant establishment. However, little is known about the assembly and co-occurrence patterns of fungal communities in the rhizosphere soil of Amaranthus palmeri. The soil fungal communities and co-occurrence networks were investigated in 22 invaded patches and 22 native patches using high-throughput Illumina sequencing. Despite having little effect on alpha diversity, plant invasion significantly altered the composition of the soil fungal community (ANOSIM, p < 0.05). Fungal taxa associated with plant invasion were identified using linear discriminant analysis effect size (LEfSe). In the rhizosphere soil of A. palmeri, Basidiomycota was significantly enriched, while Ascomycota and Glomeromycota were significantly reduced when compared to native plants. At the genus level, the invasion of A. palmeri dramatically increased the abundance of beneficial fungi and potential antagonists such as Dioszegia, Tilletiopsis, Colacogloea, and Chaetomium, while it significantly decreased the abundance of pathogenic fungi such as Alternaria and Phaeosphaeria. Plant invasion reduced the average degree and average path length, and increased the modularity value, resulting in a less complex but more effective and stable network. Our findings improved the knowledge of the soil fungal communities, network co-occurrence patterns, and keystone taxa in A. palmeri-invaded ecosystems.
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Affiliation(s)
- Mei Zhang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kefan Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Cong Shi
- School of Environmental Science and Engineering, Tiangong University, Tianjin 300387, China
| | - Xueying Li
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhenlu Qiu
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Fuchen Shi
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Zhang M, Shi C, Li X, Wang K, Qiu Z, Shi F. Changes in the structure and function of rhizosphere soil microbial communities induced by Amaranthus palmeri invasion. Front Microbiol 2023; 14:1114388. [PMID: 37056750 PMCID: PMC10089265 DOI: 10.3389/fmicb.2023.1114388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/09/2023] [Indexed: 03/30/2023] Open
Abstract
IntroductionPlant invasion can profoundly alter ecosystem processes driven by microorganisms. The fundamental mechanisms linking microbial communities, functional genes, and edaphic characteristics in invaded ecosystems are, nevertheless, poorly understood.MethodsHere, soil microbial communities and functions were determined across 22 Amaranthus palmeri (A. palmeri) invaded patches by pairwise 22 native patches located in the Jing-Jin-Ji region of China using high-throughput amplicon sequencing and quantitative microbial element cycling technologies.ResultsAs a result, the composition and structure of rhizosphere soil bacterial communities differed significantly between invasive and native plants according to principal coordinate analysis. A. palmeri soils exhibited higher abundance of Bacteroidetes and Nitrospirae, and lower abundance of Actinobacteria than native soils. Additionally, compared to native rhizosphere soils, A. palmeri harbored a much more complex functional gene network with higher edge numbers, average degree, and average clustering coefficient, as well as lower network distance and diameter. Furthermore, the five keystone taxa identified in A. palmeri rhizosphere soils belonged to the orders of Longimicrobiales, Kineosporiales, Armatimonadales, Rhizobiales and Myxococcales, whereas Sphingomonadales and Gemmatimonadales predominated in the native rhizosphere soils. Moreover, random forest model revealed that keystone taxa were more important indicators of soil functional attributes than edaphic variables in both A. palmeri and native rhizosphere soils. For edaphic variables, only ammonium nitrogen was a significant predictor of soil functional potentials in A. palmeri invaded ecosystems. We also found keystone taxa in A. palmeri rhizosphere soils had strong and positive correlations with functional genes compared to native soils.DiscussionOur study highlighted the importance of keystone taxa as a driver of soil functioning in invaded ecosystem.
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Affiliation(s)
- Mei Zhang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cong Shi
- School of Environmental Science and Engineering, Tiangong University, Tianjin, China
| | - Xueying Li
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Kefan Wang
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Zhenlu Qiu
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
| | - Fuchen Shi
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, China
- *Correspondence: Fuchen Shi,
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Razgulin SM. Mycorrhizal Complexes and Their Role in the Ecology of Boreal Forests (Review). BIOL BULL+ 2022. [DOI: 10.1134/s1062359022060140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Defending Earth's terrestrial microbiome. Nat Microbiol 2022; 7:1717-1725. [PMID: 36192539 DOI: 10.1038/s41564-022-01228-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/17/2022] [Indexed: 11/08/2022]
Abstract
Microbial life represents the majority of Earth's biodiversity. Across disparate disciplines from medicine to forestry, scientists continue to discover how the microbiome drives essential, macro-scale processes in plants, animals and entire ecosystems. Yet, there is an emerging realization that Earth's microbial biodiversity is under threat. Here we advocate for the conservation and restoration of soil microbial life, as well as active incorporation of microbial biodiversity into managed food and forest landscapes, with an emphasis on soil fungi. We analyse 80 experiments to show that native soil microbiome restoration can accelerate plant biomass production by 64% on average, across ecosystems. Enormous potential also exists within managed landscapes, as agriculture and forestry are the dominant uses of land on Earth. Along with improving and stabilizing yields, enhancing microbial biodiversity in managed landscapes is a critical and underappreciated opportunity to build reservoirs, rather than deserts, of microbial life across our planet. As markets emerge to engineer the ecosystem microbiome, we can avert the mistakes of aboveground ecosystem management and avoid microbial monocultures of single high-performing microbial strains, which can exacerbate ecosystem vulnerability to pathogens and extreme events. Harnessing the planet's breadth of microbial life has the potential to transform ecosystem management, but it requires that we understand how to monitor and conserve the Earth's microbiome.
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Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P. Fungal communities in soils under global change. Stud Mycol 2022; 103:1-24. [PMID: 36760734 PMCID: PMC9886077 DOI: 10.3114/sim.2022.103.01] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022] Open
Abstract
Soil fungi play indispensable roles in all ecosystems including the recycling of organic matter and interactions with plants, both as symbionts and pathogens. Past observations and experimental manipulations indicate that projected global change effects, including the increase of CO2 concentration, temperature, change of precipitation and nitrogen (N) deposition, affect fungal species and communities in soils. Although the observed effects depend on the size and duration of change and reflect local conditions, increased N deposition seems to have the most profound effect on fungal communities. The plant-mutualistic fungal guilds - ectomycorrhizal fungi and arbuscular mycorrhizal fungi - appear to be especially responsive to global change factors with N deposition and warming seemingly having the strongest adverse effects. While global change effects on fungal biodiversity seem to be limited, multiple studies demonstrate increases in abundance and dispersal of plant pathogenic fungi. Additionally, ecosystems weakened by global change-induced phenomena, such as drought, are more vulnerable to pathogen outbreaks. The shift from mutualistic fungi to plant pathogens is likely the largest potential threat for the future functioning of natural and managed ecosystems. However, our ability to predict global change effects on fungi is still insufficient and requires further experimental work and long-term observations. Citation: Baldrian P, Bell-Dereske L, Lepinay C, Větrovský T, Kohout P (2022). Fungal communities in soils under global change. Studies in Mycology 103: 1-24. doi: 10.3114/sim.2022.103.01.
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Affiliation(s)
- P. Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic,*Corresponding author: Petr Baldrian,
| | - L. Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - C. Lepinay
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - T. Větrovský
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
| | - P. Kohout
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeòská 1083, 142 20 Prague, Czech Republic
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Anthony MA, Crowther TW, van der Linde S, Suz LM, Bidartondo MI, Cox F, Schaub M, Rautio P, Ferretti M, Vesterdal L, De Vos B, Dettwiler M, Eickenscheidt N, Schmitz A, Meesenburg H, Andreae H, Jacob F, Dietrich HP, Waldner P, Gessler A, Frey B, Schramm O, van den Bulk P, Hensen A, Averill C. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. THE ISME JOURNAL 2022; 16:1327-1336. [PMID: 35001085 PMCID: PMC9038731 DOI: 10.1038/s41396-021-01159-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 11/08/2022]
Abstract
Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.
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Affiliation(s)
- Mark A Anthony
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
| | - Thomas W Crowther
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Sietse van der Linde
- Netherlands Food and Consumer Product Safety Authority, National Reference Centre, Wageningen, The Netherlands
| | | | - Martin I Bidartondo
- Royal Botanic Gardens, Kew, TW9 3DS, UK
- Department of Life Sciences, Imperial College London, Ascot, SL5 7PY, UK
| | - Filipa Cox
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Marcus Schaub
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pasi Rautio
- Natural Resources Institute Finland, Rovaniemi, Finland
| | - Marco Ferretti
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Bruno De Vos
- Environment & Climate Unit, Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Mike Dettwiler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Nadine Eickenscheidt
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, 45657, Recklinghausen, Germany
| | - Andreas Schmitz
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, 45657, Recklinghausen, Germany
- Thuenen Institut of Forest Ecosystems, 16225, Eberswalde, Germany
| | | | | | - Frank Jacob
- Sachsenforst State Forest, 01796, Pirna OT Graupa, Germany
| | | | - Peter Waldner
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Arthur Gessler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Oliver Schramm
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pim van den Bulk
- The Netherlands Organization for Applied Scientific Research at Petten, 1755LE, Petten, The Netherlands
| | - Arjan Hensen
- The Netherlands Organization for Applied Scientific Research at Petten, 1755LE, Petten, The Netherlands
| | - Colin Averill
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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7
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Edwards JD, Yang WH, Yannarell AC. Soil microbial communities are not altered by garlic mustard in recently invaded central Illinois forests. Ecosphere 2022. [DOI: 10.1002/ecs2.3967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Joseph D. Edwards
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Wendy H. Yang
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Department of Geology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Anthony C. Yannarell
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Department of Natural Resources and Environmental Science University of Illinois at Urbana‐Champaign Urbana Illinois USA
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8
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Trautwig AN, Anthony MA, Frey SD, Stinson KA. Effects of an introduced mustard, Thlaspi arvense, on soil fungal communities in subalpine meadows. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2021.101135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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9
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Martín‐Forés I, Bywaters SL, Sparrow B, Guerin GR. Simultaneous effect of habitat remnancy, exotic species, and anthropogenic disturbance on orchid diversity in South Australia. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Irene Martín‐Forés
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Samantha L. Bywaters
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Ben Sparrow
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
- Terrestrial Ecosystem Research Network (TERN) University of Adelaide Adelaide South Australia Australia
| | - Greg R. Guerin
- School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
- Terrestrial Ecosystem Research Network (TERN) University of Adelaide Adelaide South Australia Australia
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Rodgers VL, Scanga SE, Kolozsvary MB, Garneau DE, Kilgore JS, Anderson LJ, Hopfensperger KN, Aguilera AG, Urban RA, Juneau KJ. OUP accepted manuscript. Bioscience 2022; 72:521-537. [PMID: 35677290 PMCID: PMC9169898 DOI: 10.1093/biosci/biac012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The invasive plant Alliaria petiolata (garlic mustard) has spread throughout forest understory and edge communities in much of North America, but its persistence, density, and impacts have varied across sites and time. Surveying the literature since 2008, we evaluated both previously proposed and new mechanisms for garlic mustard's invasion success and note how they interact and vary across ecological contexts. We analyzed how and where garlic mustard has been studied and found a lack of multisite and longitudinal studies, as well as regions that may be under- or overstudied, leading to poor representation for understanding and predicting future invasion dynamics. Inconsistencies in how sampling units are scaled and defined can also hamper our understanding of invasive species. We present new conceptual models for garlic mustard invasion from a macrosystems perspective, emphasizing the importance of synergies and feedbacks among mechanisms across spatial and temporal scales to produce variable ecological contexts.
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Affiliation(s)
| | | | | | - Danielle E Garneau
- State University of New York Plattsburgh, Plattsburgh, New York, United States
| | - Jason S Kilgore
- Washington and Jefferson College, Washington, Pennsylvania, United States
| | | | | | | | - Rebecca A Urban
- Lebanon Valley College, Annville, Pennsylvania, United States
| | - Kevyn J Juneau
- University of Wisconsin–River Falls, River Falls, Wisconsin, United States
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11
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Williams JP, Gornish ES, Barberán A. Effects of buffelgrass removal and nitrogen addition on soil microbial communities during an extreme drought in the Sonoran Desert. Restor Ecol 2021. [DOI: 10.1111/rec.13570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jared P. Williams
- Department of Environmental Science University of Arizona Tucson AZ 85721 U.S.A
| | - Elise S. Gornish
- School of Natural Resources and the Environment University of Arizona Tucson AZ 85721 U.S.A
| | - Albert Barberán
- Department of Environmental Science University of Arizona Tucson AZ 85721 U.S.A
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12
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Fehmi JS, Rasmussen C, Arnold AE. The pioneer effect advantage in plant invasions: site priming of native grasslands by invasive grasses. Ecosphere 2021. [DOI: 10.1002/ecs2.3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Jeffrey S. Fehmi
- School of Natural Resources and the Environment University of Arizona Tucson Arizona 85719 USA
| | - Craig Rasmussen
- Department of Environmental Science University of Arizona Tucson Arizona 85719 USA
| | - A. Elizabeth Arnold
- School of Plant Sciences and Department of Ecology and Evolutionary Biology University of Arizona Tucson Arizona 85719 USA
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