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Huusko K, Manninen OH, Myrsky E, Stark S. Soil fungal and bacterial communities reflect differently tundra vegetation state transitions and soil physico-chemical properties. THE NEW PHYTOLOGIST 2024; 243:407-422. [PMID: 38750646 DOI: 10.1111/nph.19808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/23/2024] [Indexed: 06/07/2024]
Abstract
Strong disturbances may induce ecosystem transitions into new alternative states that sustain through plant-soil interactions, such as the transition of dwarf shrub-dominated into graminoid-dominated vegetation by herbivory in tundra. Little evidence exists on soil microbial communities in alternative states, and along the slow process of ecosystem return into the predisturbance state. We analysed vegetation, soil microbial communities and activities as well as soil physico-chemical properties in historical reindeer enclosures in northernmost Finland in the following plot types: control heaths in the surrounding tundra; graminoid-dominated; 'shifting'; and recovered dwarf shrub-dominated vegetation inside enclosures. Soil fungal communities followed changes in vegetation, whereas bacterial communities were more affected by soil physico-chemical properties. Graminoid plots were characterized by moulds, pathotrophs and dark septate endophytes. Ericoid mycorrhizal and saprotrophic fungi were typical for control and recovered plots. Soil microbial communities inside the enclosures showed historical contingency, as their spatial variation was high in recovered plots despite the vegetation being more homogeneous. Self-maintaining feedback loops between plant functional types, soil microbial communities, and carbon and nutrient mineralization act effectively to stabilize alternative vegetation states, but once predisturbance vegetation reestablishes itself, soil microbial communities and physico-chemical properties return back towards their predisturbance state.
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Affiliation(s)
- Karoliina Huusko
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu, FI-90014, Finland
| | - Outi H Manninen
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
| | - Eero Myrsky
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
| | - Sari Stark
- Arctic Center, University of Lapland, PO Box 122, Rovaniemi, FI-96101, Finland
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2
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Fransson P, Robertson AHJ, Campbell CD. Carbon availability affects already large species-specific differences in chemical composition of ectomycorrhizal fungal mycelia in pure culture. MYCORRHIZA 2023; 33:303-319. [PMID: 37824023 PMCID: PMC10752919 DOI: 10.1007/s00572-023-01128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Although ectomycorrhizal (ECM) contribution to soil organic matter processes receives increased attention, little is known about fundamental differences in chemical composition among species, and how that may be affected by carbon (C) availability. Here, we study how 16 species (incl. 19 isolates) grown in pure culture at three different C:N ratios (10:1, 20:1, and 40:1) vary in chemical structure, using Fourier transform infrared (FTIR) spectroscopy. We hypothesized that C availability impacts directly on chemical composition, expecting increased C availability to lead to more carbohydrates and less proteins in the mycelia. There were strong and significant effects of ECM species (R2 = 0.873 and P = 0.001) and large species-specific differences in chemical composition. Chemical composition also changed significantly with C availability, and increased C led to more polysaccharides and less proteins for many species, but not all. Understanding how chemical composition change with altered C availability is a first step towards understanding their role in organic matter accumulation and decomposition.
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Affiliation(s)
- Petra Fransson
- Department of Forest Mycology and Plant Pathology, Uppsala BioCenter, Swedish University of Agricultural Sciences, PO Box 7026, SE-750 07, Uppsala, Sweden.
| | - A H Jean Robertson
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland
| | - Colin D Campbell
- The James Hutton Institute, Craigiebuckler, Aberdeen, AB15 8QH, Scotland
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3
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Verma KK, Song XP, Li DM, Singh M, Wu JM, Singh RK, Sharma A, Zhang BQ, Li YR. Silicon and soil microorganisms improve rhizospheric soil health with bacterial community, plant growth, performance and yield. PLANT SIGNALING & BEHAVIOR 2022; 17:2104004. [PMID: 35943127 PMCID: PMC9364706 DOI: 10.1080/15592324.2022.2104004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The interaction of silicon and soil microorganisms stimulates crop enhancement to ensure sustainable agriculture. Silicon may potentially increase nutrient availability in rhizosphere with improved plants' growth, development as it does not produce phytotoxicity. The rhizospheric microbiome accommodates a variety of microbial species that live in a small area of soil directly associated with the hidden half plants' system. Plant growth-promoting rhizobacteria (PGPR) play a major role in plant development in response to adverse climatic conditions. PGPRs may enhance the growth, quality, productivity in variety of crops, and mitigate abiotic stresses by reprogramming stress-induced physiological variations in plants via different mechanisms, such as synthesis of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate deaminase, exopolysaccharides, volatile organic compounds, atmospheric nitrogen fixation, and phosphate solubilization. Our article eye upon interactions of silicon and plant microbes which seems to be an opportunity for sustainable agriculture for series of crops and cropping systems in years to come, essential to safeguard the food security for masses.
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Affiliation(s)
- Krishan K. Verma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Xiu-Peng Song
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Dong-Mei Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Munna Singh
- Department of Botany, University of Lucknow, Lucknow, India
| | - Jian-Ming Wu
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Rajesh Kumar Singh
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Anjney Sharma
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Bao-Qing Zhang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Yang-Rui Li
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture and Rural Affairs/Guangxi Key Laboratory of Sugarcane Genetic Improvement/Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences/ Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Nanning, China
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4
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Wang G, Koziol L, Foster BL, Bever JD. Microbial mediators of plant community response to long-term N and P fertilization: Evidence of a role of plant responsiveness to mycorrhizal fungi. GLOBAL CHANGE BIOLOGY 2022; 28:2721-2735. [PMID: 35048483 DOI: 10.1111/gcb.16091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Climate changes and anthropogenic nutrient enrichment widely threaten plant diversity and ecosystem functions. Understanding the mechanisms governing plant species turnover across nutrient gradients is crucial to developing successful management and restoration strategies. We tested whether and how soil microbes, particularly arbuscular mycorrhizal fungi (AMF), could mediate plant community response to a 15 years long-term N (0, 4, 8, and 16 g N m-2 year-1 ) and P (0 and 8 g N m-2 year-1 ) enrichment in a grassland system. We found N and P enrichment resulted in plant community diversity decrease and composition change, in which perennial C4 graminoids were dramatically reduced while annuals and perennial forbs increased. Metabarcoding analysis of soil fungal community showed that N and P changed fungal diversity and composition, of which only a cluster of AMF identified by the co-occurrence networks analysis was highly sensitive to P treatments and was negatively correlated with shifts in percentage cover of perennial C4 graminoids. Moreover, by estimating the mycorrhizal responsiveness (MR) of 41 plant species in the field experiment from 264 independent tests, we found that the community weighted mean MR of the plant community was substantially reduced with nutrient enrichment and was positively correlated with C4 graminoids percentage cover. Both analyses of covariance and structural equation modeling indicated that the shift in MR rather than AMF composition change was the primary predictor of the decline in perennial C4 graminoids, suggesting that the energy cost invested by C4 plants on those sensitive AMF might drive the inferior competitive abilities compared with other groups. Our results suggest that shifts in the competitive ability of mycorrhizal responsive plants can drive plant community change to anthropogenic eutrophication, suggesting a functional benefit of mycorrhizal mutualism in ecological restoration following climatic or anthropogenic degradation of soil communities.
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Affiliation(s)
- Guangzhou Wang
- College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, People's Republic of China
- Kansas Biological Survey, University of Kansas, Lawrence, Kansas, USA
| | - Liz Koziol
- Kansas Biological Survey, University of Kansas, Lawrence, Kansas, USA
| | - Bryan L Foster
- Kansas Biological Survey, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - James D Bever
- Kansas Biological Survey, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
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5
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Influence of Tourism Disturbance on Soil Microbial Community Structure in Dawei Mountain National Forest Park. SUSTAINABILITY 2022. [DOI: 10.3390/su14031162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This research aimed to reveal the response characteristics of soil microbial community structure to different degrees of tourism disturbance. To explore the soil microbial community structure’s response mechanism, we set up continuous plots with different interference intensities: high disturbance, middle disturbance, and the control area. We collected 0–10 cm topsoil in all plots and used Illumina MiSeq high-throughput sequencing method to obtain and analyze the response characteristics of soil microbial community composition and structure under different tourism disturbances. These results were then combined with alpha diversity and environmental factors to explore the microbial response mechanism. In the tested soil, Acidobacteria, Chlorocurve, and Proteobacteria were the main bacterial phyla, while Basidiomycota and Ascomycota were the main fungal phyla. Based on the phylum, the relative abundance of the microbial community between the interference groups was compared using a significance test, with significant differences found between the interference groups in the phyla Chloroflexus, GAL15, Rokubacteria, and Blastomonas (p < 0.05). The relative abundance of the dominant phyla in the fungal community was significantly different among the groups (p < 0.05). A principal component analysis of the soil microbial community structure suggested that the soil microbial community structure was significantly different for different interference levels.
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6
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Brigham LM, Bueno de Mesquita CP, Smith JG, Sartwell SA, Schmidt SK, Suding KN. Do plant-soil interactions influence how the microbial community responds to environmental change? Ecology 2021; 103:e03554. [PMID: 34622953 DOI: 10.1002/ecy.3554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023]
Abstract
Global change alters ecosystems and their functioning, and biotic interactions can either buffer or amplify such changes. We utilized a long-term nitrogen (N) addition and species removal experiment in the Front Range of Colorado, USA to determine whether a codominant forb and a codominant grass, with different effects on nutrient cycling and plant community structure, would buffer or amplify the effects of simulated N deposition on soil bacterial and fungal communities. While the plant community was strongly shaped by both the presence of dominant species and N addition, we did not find a mediating effect of the plant community on soil microbial response to N. In contrast to our hypothesis, we found a decoupling of the plant and microbial communities such that the soil microbial community shifted under N independently of directional shifts in the plant community. These findings suggest there are not strong cascading effects of N deposition across the plant-soil interface in our system.
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Affiliation(s)
- Laurel M Brigham
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Clifton P Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Jane G Smith
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Samuel A Sartwell
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Katharine N Suding
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
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7
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Zhang J, Cook J, Nearing JT, Zhang J, Raudonis R, Glick BR, Langille MGI, Cheng Z. Harnessing the plant microbiome to promote the growth of agricultural crops. Microbiol Res 2021; 245:126690. [PMID: 33460987 DOI: 10.1016/j.micres.2020.126690] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 12/11/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022]
Abstract
The rhizosphere microbiome is composed of diverse microbial organisms, including archaea, viruses, fungi, bacteria as well as eukaryotic microorganisms, which occupy a narrow region of soil directly associated with plant roots. The interactions between these microorganisms and the plant can be commensal, beneficial or pathogenic. These microorganisms can also interact with each other, either competitively or synergistically. Promoting plant growth by harnessing the soil microbiome holds tremendous potential for providing an environmentally friendly solution to the increasing food demands of the world's rapidly growing population, while also helping to alleviate the associated environmental and societal issues of large-scale food production. There recently have been many studies on the disease suppression and plant growth promoting abilities of the rhizosphere microbiome; however, these findings largely have not been translated into the field. Therefore, additional research into the dynamic interactions between crop plants, the rhizosphere microbiome and the environment are necessary to better guide the harnessing of the microbiome to increase crop yield and quality. This review explores the biotic and abiotic interactions that occur within the plant's rhizosphere as well as current agricultural practices, and how these biotic and abiotic factors, as well as human practices, impact the plant microbiome. Additionally, some limitations, safety considerations, and future directions to the study of the plant microbiome are discussed.
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Affiliation(s)
- Janie Zhang
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jamie Cook
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Jacob T Nearing
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Junzeng Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Halifax, NS, Canada
| | - Renee Raudonis
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Morgan G I Langille
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada; Department of Pharmacology, Dalhousie University, Halifax, NS, Canada; CGEB-Integrated Microbiome Resource (IMR), Dalhousie University, Halifax, NS, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada.
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8
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Phragmites australis Associates with Belowground Fungal Communities Characterized by High Diversity and Pathogen Abundance. DIVERSITY 2020. [DOI: 10.3390/d12090363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Microbial symbionts are gaining attention as crucial drivers of invasive species spread and dominance. To date, much research has quantified the net effects of plant–microbe interactions on the relative success of native and invasive species. However, little is known about how the structure (composition and diversity) of microbial symbionts can differ among native and invasive species, or vary across the invasive landscape. Here, we explore the structure of endosphere and soil fungal communities associated with a monoculture-forming widespread invader, Phragmites australis, and co-occurring native species. Using field survey data from marshes in coastal Louisiana, we tested three hypotheses: (1) Phragmites australis root and soil fungal communities differ from that of co-occurring natives, (2) Phragmites australis monocultures harbor distinct fungal communities at the expanding edge compared to the monodominant center, and (3) proximity to the P. australis invading front alters native root endosphere and soil fungal community structure. We found that P. australis cultivates root and soil fungal communities with higher richness, diversity, and pathogen abundances compared to native species. While P. australis was found to have higher endosphere pathogen abundances at its expanding edge compared to the monodominant center, we found no evidence of compositional changes or pathogen spillover in native species in close proximity to the invasion front. This work suggests that field measurements of fungal endosphere communities in native and invasive plants are useful to help understand (or rule out) mechanisms of invasion.
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9
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Rotter P, Loreau M, de Mazancourt C. Why do forests respond differently to nitrogen deposition? A modelling approach. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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10
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Nguyen DQ, Schneider D, Brinkmann N, Song B, Janz D, Schöning I, Daniel R, Pena R, Polle A. Soil and root nutrient chemistry structure root-associated fungal assemblages in temperate forests. Environ Microbiol 2020; 22:3081-3095. [PMID: 32383336 DOI: 10.1111/1462-2920.15037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022]
Abstract
Root-associated fungi (RAF) link nutrient fluxes between soil and roots and thus play important roles in ecosystem functioning. To enhance our understanding of the factors that control RAF, we fitted statistical models to explain variation in RAF community structure using data from 150 temperate forest sites covering a broad range of environmental conditions and chemical root traits. We found that variation in RAF communities was related to both root traits (e.g., cations, carbohydrates, NO3 - ) and soil properties (pH, cations, moisture, C/N). The identified drivers were the combined result of distinct response patterns of fungal taxa (determined at the rank of orders) to biotic and abiotic factors. Our results support that RAF community variation is related to evolutionary adaptedness of fungal lineages and consequently, drivers of RAF communities are context-dependent.
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Affiliation(s)
- Dung Quang Nguyen
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany.,Forest Protection Research Centre, Vietnamese Academy of Forest Sciences, Duc Thang Ward, Bac Tu Liem District, Hanoi, Vietnam
| | - Dominik Schneider
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Grisebachstraße 8, 37077, Germany
| | - Nicole Brinkmann
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Bin Song
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Dennis Janz
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Ingo Schöning
- Biogeochemical Processes, Max Planck Institute for Biogeochemistry, Hans-Knöll-Str. 10, 07745 Jena, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Grisebachstraße 8, 37077, Germany
| | - Rodica Pena
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
| | - Andrea Polle
- Forest Botany and Tree Physiology, Büsgen-Institut, University of Göttingen, Göttingen, Büsgenweg 2, 37077, Germany
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11
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Knapp DG, Imrefi I, Boldpurev E, Csíkos S, Akhmetova G, Berek-Nagy PJ, Otgonsuren B, Kovács GM. Root-Colonizing Endophytic Fungi of the Dominant Grass Stipa krylovii From a Mongolian Steppe Grassland. Front Microbiol 2019; 10:2565. [PMID: 31781068 PMCID: PMC6861457 DOI: 10.3389/fmicb.2019.02565] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/23/2019] [Indexed: 11/25/2022] Open
Abstract
In several terrestrial ecosystems such as grasslands, plants live together with various root-colonizing dark septate endophytes (DSEs), fungi that are relatively frequent colonizers of healthy belowground tissues of plants in these environments. They are important members of the plant microbiota and may have various effects on plant survival under different stress conditions; however, their general functions in relation to plants and the greater ecosystem remain elusive. Although an increasing number of studies has been published focusing on DSEs in Asian grasslands, our knowledge is limited. Especially in Mongolia, where the steppe region represents a significant area, information is not available on these root colonizers. In this study, we aimed to characterize DSEs of a common dominant gramineous plant species, Stipa krylovii in a semiarid grassland of Mongolia. Root samples were collected in a natural steppe and were processed for isolation of fungal endophytes. For molecular identification of the isolates, the internal transcribed spacer (ITS) region of the nrDNA was obtained for all the isolates investigated; furthermore, the partial translation elongation factor 1-α (TEF) gene and large subunit (LSU) and small subunit (SSU) of rDNA were also amplified and sequenced in case of representative isolates. In vitro tests were used to examine the rough symbiotic nature of the fungi, and root colonization was visualized. A majority of the 135 isolates examined in detail was found to belong to several orders of Ascomycota (110 isolates) and some to Basidiomycota (25 isolates). A significant number of the isolates represented presumably novel taxa, and dominant similarities of the lineages have been found with relatively frequent and known grass root endophytes of semiarid areas in other geographic regions. These endophytes included Periconia macrospinosa, Microdochium bolley, and Darksidea, the genus of which comprised one fourth of the isolates. We found numerous lineages, which have been detected not only from Asian steppe ecosystems, but also from prairies in North America and sandy grasslands in Europe. Therefore, our results strengthen the hypothesized worldwide presence of a common and dominant core group of a DSE community in arid and semiarid grasslands.
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Affiliation(s)
- Dániel G. Knapp
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Ildikó Imrefi
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Enkhtuul Boldpurev
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Sándor Csíkos
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Galiya Akhmetova
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | - Péter János Berek-Nagy
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | | | - Gábor M. Kovács
- Department of Plant Anatomy, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
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12
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Sandona K, Billingsley Tobias TL, Hutchinson MI, Natvig DO, Porras-Alfaro A. Diversity of thermophilic and thermotolerant fungi in corn grain. Mycologia 2019; 111:719-729. [PMID: 31348716 DOI: 10.1080/00275514.2019.1631137] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Corn bins in the midwestern United States can reach temperatures up to 52 C. High temperatures combined with sufficient moisture and humidity in bins provide the perfect environment to promote the growth of thermophilic and thermotolerant fungi. In this article, we characterize for the first time thermophilic and thermotolerant fungi in corn grain bins using culture-based methods and pyrosequencing techniques. Corn samples were collected from local farms in western Illinois. Samples were plated and incubated at 50 C using a variety of approaches. Of several hundred kernels examined, more than 90% showed colonization. Species identified using culture methods included Thermomyces lanuginosus, Thermomyces dupontii, Aspergillus fumigatus, Thermoascus crustaceus, and Rhizomucor pusillus. Pyrosequencing was also performed directly on corn grain using fungal-specific primers to determine whether thermophilic fungi could be detected using this technique. Sequences were dominated by pathogenic fungi, and thermophiles were represented by less than 2% of the sequences despite being isolated from 90% of the grain samples using culturing techniques. The high abundance of previously undocumented viable fungi in corn could have negative implications for grain quality and pose a potential risk for workers and consumers of corn-derived products in the food industry. Members of the Sordariales were absent among thermophile isolates and were not represented in nuc rDNA internal transcribed spacer (ITS) sequences. This is in striking contrast with results obtained with other substrates such as litter, dung, and soils, where mesophilic and thermophilic members of the Sordariaceae and Chaetomiaceae are common. This absence appears to reflect an important difference between the ecology of Sordariales and other orders within the Ascomycota in terms of their ability to compete in microhabitats rich in sugars and living tissues.
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Affiliation(s)
- Katrina Sandona
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Terri L Billingsley Tobias
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455
| | - Miriam I Hutchinson
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Donald O Natvig
- Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
| | - Andrea Porras-Alfaro
- Department of Biological Sciences, Western Illinois University , 1 University Circle, Macomb , Illinois 61455.,Department of Biology, University of New Mexico , 1 University of New Mexico, Albuquerque , New Mexico 87131
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13
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Potter TS, Owens WM, Bowman WD. Do plant–microbe interactions and aluminum tolerance influence alpine sedge species’ responses to nitrogen deposition? Ecosphere 2019. [DOI: 10.1002/ecs2.2775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Teal S. Potter
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado 80309‐0334 USA
| | - William M. Owens
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado 80309‐0334 USA
| | - William D. Bowman
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado 80309‐0334 USA
- Institute of Arctic and Alpine Research University of Colorado Boulder Colorado 80309‐0450 USA
- Mountain Research Station University of Colorado Nederland Colorado 80466 USA
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14
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Purahong W, Wubet T, Kahl T, Arnstadt T, Hoppe B, Lentendu G, Baber K, Rose T, Kellner H, Hofrichter M, Bauhus J, Krüger D, Buscot F. Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy ensure ecosystem function. Environ Microbiol 2018; 20:1693-1710. [PMID: 29473288 DOI: 10.1111/1462-2920.14081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/13/2018] [Accepted: 02/20/2018] [Indexed: 01/07/2023]
Abstract
Nitrogen deposition can strongly affect biodiversity, but its specific effects on terrestrial microbial communities and their roles for ecosystem functions and processes are still unclear. Here, we investigated the impacts of N deposition on wood-inhabiting fungi (WIF) and their related ecological functions and processes in a highly N-limited deadwood habitat. Based on high-throughput sequencing, enzymatic activity assay and measurements of wood decomposition rates, we show that N addition has no significant effect on the overall WIF community composition or on related ecosystem functions and processes in this habitat. Nevertheless, we detected several switches in presence/absence (gain/loss) of wood-inhabiting fungal OTUs due to the effect of N addition. The responses of WIF differed from previous studies carried out with fungi living in soil and leaf-litter, which represent less N-limited fungal habitats. Our results suggest that adaptation at different levels of organization and functional redundancy may explain this buffered response and the resistant microbial-mediated ecosystem function and processes against N deposition in highly N-limited habitats.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany
| | - Tesfaye Wubet
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
| | - Tiemo Kahl
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany.,Biosphere Reserve Vessertal-Thuringian Forest, Brunnenstr. 1, Schmiedefeld am Rennsteig, D-98711, Germany
| | - Tobias Arnstadt
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Björn Hoppe
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Julius Kühn-Institute - Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Messeweg 11/12, Braunschweig, D-38104, Germany
| | - Guillaume Lentendu
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,Department of Ecology, University of Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern, 67663, Germany
| | - Kristin Baber
- Department of Systematic Botany and Functional Biodiversity, University of Leipzig, Institute of Biology Johannisallee 21-23, Leipzig, D-04103, Germany
| | - Tyler Rose
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany
| | - Harald Kellner
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Martin Hofrichter
- Technische Universität Dresden - International Institute (IHI) Zittau, Department of Bio- and Environmental Sciences, Markt 23, Zittau, D-02763, Germany
| | - Jürgen Bauhus
- University of Freiburg, Faculty of Environment and Natural Resources, Chair of Silviculture, Tennenbacherstr. 4, Freiburg im Breisgau, D-79085, Germany
| | - Dirk Krüger
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany
| | - François Buscot
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Theodor-Lieser-Str. 4, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, D-04103, Germany
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15
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Ma M, Jiang X, Wang Q, Ongena M, Wei D, Ding J, Guan D, Cao F, Zhao B, Li J. Responses of fungal community composition to long-term chemical and organic fertilization strategies in Chinese Mollisols. Microbiologyopen 2018; 7:e00597. [PMID: 29573192 PMCID: PMC6182557 DOI: 10.1002/mbo3.597] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 11/07/2022] Open
Abstract
How fungi respond to long-term fertilization in Chinese Mollisols as sensitive indicators of soil fertility has received limited attention. To broaden our knowledge, we used high-throughput pyrosequencing and quantitative PCR to explore the response of soil fungal community to long-term chemical and organic fertilization strategies. Soils were collected in a 35-year field experiment with four treatments: no fertilizer, chemical phosphorus, and potassium fertilizer (PK), chemical phosphorus, potassium, and nitrogen fertilizer (NPK), and chemical phosphorus and potassium fertilizer plus manure (MPK). All fertilization differently changed soil properties and fungal community. The MPK application benefited soil acidification alleviation and organic matter accumulation, as well as soybean yield. Moreover, the community richness indices (Chao1 and ACE) were higher under the MPK regimes, indicating the resilience of microbial diversity and stability. With regards to fungal community composition, the phylum Ascomycota was dominant in all samples, followed by Zygomycota, Basidiomycota, Chytridiomycota, and Glomeromycota. At each taxonomic level, the community composition dramatically differed under different fertilization strategies, leading to different soil quality. The NPK application caused a loss of Leotiomycetes but an increase in Eurotiomycetes, which might reduce the plant-fungal symbioses and increase nitrogen losses and greenhouse gas emissions. According to the linear discriminant analysis (LDA) coupled with effect size (LDA score > 3.0), the NPK application significantly increased the abundances of fungal taxa with known pathogenic traits, such as order Chaetothyriales, family Chaetothyriaceae and Pleosporaceae, and genera Corynespora, Bipolaris, and Cyphellophora. In contrast, these fungi were detected at low levels under the MPK regime. Soil organic matter and pH were the two most important contributors to fungal community composition.
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Affiliation(s)
- Mingchao Ma
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xin Jiang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Qingfeng Wang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Marc Ongena
- Microbial Processes and Interactions Research Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Dan Wei
- The Institute of Soil Fertility and Environmental Sources, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jianli Ding
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Dawei Guan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Fengming Cao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Baisuo Zhao
- Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
| | - Jun Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China.,Laboratory of Quality & Safety Risk Assessment for Microbial Products, Ministry of Agriculture, Beijing, China
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16
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Tian D, Jiang L, Ma S, Fang W, Schmid B, Xu L, Zhu J, Li P, Losapio G, Jing X, Zheng C, Shen H, Xu X, Zhu B, Fang J. Effects of nitrogen deposition on soil microbial communities in temperate and subtropical forests in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 607-608:1367-1375. [PMID: 28738512 DOI: 10.1016/j.scitotenv.2017.06.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
Increasing nitrogen (N) deposition has aroused large concerns because of its potential negative effects on forest ecosystems. Although microorganisms play a vital role in ecosystem carbon (C) and nutrient cycling, the effect of N deposition on soil microbiota still remains unclear. In this study, we investigated the responses of microbial biomass C (MBC) and N (MBN) and microbial community composition to 4-5years of experimentally simulated N deposition in temperate needle-leaf forests and subtropical evergreen broadleaf forests in eastern China, using chloroform fumigation extraction and phospholipid fatty acid (PLFA) methods. We found idiosyncratic effects of N addition on microbial biomass in these two types of forest ecosystems. In the subtropical forests, N addition showed a significant negative effect on microbial biomass and community composition, while the effect of N addition was not significant in the temperate forests. The N addition decreased MBC, MBN, arbuscular mycorrhizal fungi, and the F/B ratio (ratio of fungi to bacteria biomass) in the subtropical forests, likely due to a decreased soil pH and changes in the plant community composition. These results showed that microbial biomass and community composition in subtropical forests, compared with the temperate forests, were sensitive to N deposition. Our findings suggest that N deposition may have negative influence on soil microorganisms and potentially alter carbon and nutrient cycling in subtropical forests, rather than in temperate forests.
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Affiliation(s)
- Di Tian
- 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
| | - Lai Jiang
- 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
| | - Suhui Ma
- 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
| | - Wenjing Fang
- 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
| | - Bernhard Schmid
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Longchao Xu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jianxiao 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
| | - Peng Li
- 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
| | - Gianalberto Losapio
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Xin Jing
- 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
| | - Chengyang Zheng
- 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
| | - Haihua Shen
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoniu Xu
- Department of Forestry, Anhui Agricultural University, 230036 Hefei, Anhui, 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
| | - Jingyun Fang
- 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.
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17
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Seed-associated fungi in the alpine tundra: Both mutualists and pathogens could impact plant recruitment. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Ekanayaka AH, Ariyawansa HA, Hyde KD, Jones EBG, Daranagama DA, Phillips AJL, Hongsanan S, Jayasiri SC, Zhao Q. DISCOMYCETES: the apothecial representatives of the phylum Ascomycota. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0389-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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19
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Dean SL, Billingsley Tobias T, Phippen WB, Clayton AW, Gruver J, Porras-Alfaro A. A study of Glycine max (soybean) fungal communities under different agricultural practices. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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20
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21
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Farrer EC, Suding KN. Teasing apart plant community responses to N enrichment: the roles of resource limitation, competition and soil microbes. Ecol Lett 2016; 19:1287-96. [DOI: 10.1111/ele.12665] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 04/26/2016] [Accepted: 07/18/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Emily C. Farrer
- Department of Ecology and Evolutionary Biology Tulane University New Orleans LA70118 USA
- Institute of Arctic and Alpine Research University of Colorado Boulder Boulder CO80303 USA
| | - Katharine N. Suding
- Institute of Arctic and Alpine Research University of Colorado Boulder Boulder CO80303 USA
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22
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Purahong W, Wubet T, Lentendu G, Schloter M, Pecyna MJ, Kapturska D, Hofrichter M, Krüger D, Buscot F. Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition. Mol Ecol 2016; 25:4059-74. [DOI: 10.1111/mec.13739] [Citation(s) in RCA: 205] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 06/08/2016] [Accepted: 06/22/2016] [Indexed: 02/07/2023]
Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - Tesfaye Wubet
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e D-04103 Leipzig Germany
| | - Guillaume Lentendu
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - Michael Schloter
- Helmholtz Zentrum München; Research Unit for Environmental Genomics; Ingolstädter Landstr. 1 D-85758 Oberschleissheim Germany
| | - Marek J. Pecyna
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Danuta Kapturska
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Martin Hofrichter
- Technische Universität Dresden; International Institute (IHI) Zittau; Markt 23 D-02763 Zittau Germany
| | - Dirk Krüger
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
| | - François Buscot
- Department of Soil Ecology; UFZ-Helmholtz Centre for Environmental Research; Theodor-Lieser-Str. 4 D-06120 Halle (Saale) Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig; Deutscher Platz 5e D-04103 Leipzig Germany
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23
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Revillini D, Gehring CA, Johnson NC. The role of locally adapted mycorrhizas and rhizobacteria in plant–soil feedback systems. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12668] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Revillini
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Catherine A. Gehring
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
| | - Nancy Collins Johnson
- Department of Biological Sciences Northern Arizona University PO Box 5640 Flagstaff AZ 86011 USA
- School of Earth Sciences and Environmental Sustainability Northern Arizona University PO Box 5694 Flagstaff AZ 86011 USA
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24
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Chen D, Sun J, Bai M, Dassanayake KB, Denmead OT, Hill J. A new cost-effective method to mitigate ammonia loss from intensive cattle feedlots: application of lignite. Sci Rep 2015; 5:16689. [PMID: 26584639 PMCID: PMC4653648 DOI: 10.1038/srep16689] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022] Open
Abstract
In open beef feedlot systems, more than 50% of dietary nitrogen (N) is lost as ammonia (NH3). Here we report an effective and economically-viable method to mitigate NH3 emissions by the application of lignite. We constructed two cattle pens (20 × 20 m) to determine the effectiveness of lignite in reducing NH3 emissions. Twenty-four steers were fed identical commercial rations in each pen. The treatment pen surface was dressed with 4.5 kg m−2 lignite dry mass while no lignite was applied in the control pen. We measured volatilised NH3 concentrations using Ecotech EC9842 NH3 analysers in conjunction with a mass balance method to calculate NH3 fluxes. Application of lignite decreased NH3 loss from the pen by approximately 66%. The cumulative NH3 losses were 6.26 and 2.13 kg N head−1 in the control and lignite treatment, respectively. In addition to the environmental benefits of reduced NH3 losses, the value of retained N nutrient in the lignite treated manure is more than $37 AUD head−1 yr−1, based on the current fertiliser cost and estimated cost of lignite application. We show that lignite application is a cost-effective method to reduce NH3 loss from cattle feedlots.
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Affiliation(s)
- Deli Chen
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Jianlei Sun
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Mei Bai
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Kithsiri B Dassanayake
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Owen T Denmead
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - Julian Hill
- Ternes Agricultural Consulting Pty Ltd, Upwey, Victoria 3158, Australia
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25
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Yang A, Liu N, Tian Q, Bai W, Williams M, Wang Q, Li L, Zhang WH. Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition. Front Microbiol 2015; 6:789. [PMID: 26322024 PMCID: PMC4533001 DOI: 10.3389/fmicb.2015.00789] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 07/20/2015] [Indexed: 12/23/2022] Open
Abstract
We evaluated effects of 9-year simulated nitrogen (N) deposition on microbial composition and diversity in the rhizosphere of two dominant temperate grassland species: grass Stipa krylovii and forb Artemisia frigida. Microbiomes in S. krylovii and A. frigida rhizosphere differed, but changed consistently along the N gradient. These changes were correlated to N-induced shifts to plant community. Hence, as plant biomass changed, so did bacterial rhizosphere communities, a result consistent with the role that N fertilizer has been shown to play in altering plant-microbial mutualisms. A total of 23 bacterial phyla were detected in the two rhizospheric soils by pyrosequencing, with Proteobacteria, Acidobacteria, and Bacteroidetes dominating the sequences of all samples. Bacterioidetes and Proteobacteria tended to increase, while Acidobacteria declined with increase in N addition rates. TM7 increased >5-fold in the high N addition rates, especially in S. krylovii rhizosphere. Nitrogen addition also decreased diversity of OTUs (operational taxonomic units), Shannon and Chao1 indices of rhizospheric microbes regardless of plant species. These results suggest that there were both similar but also specific changes in microbial communities of temperate steppes due to N deposition. These findings would contribute to our mechanistic understanding of impacts of N deposition on grassland ecosystem by linking changes in plant traits to their rhizospheric microbes-mediated processes.
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Affiliation(s)
- An Yang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Nana Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China ; University of Chinese Academy of Sciences Beijing, China
| | - Qiuying Tian
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Wenming Bai
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Mark Williams
- Department of Horticulture, Virginia Polytechnic Institute and State University Blacksburg, VA, USA
| | - Qibing Wang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Linghao Li
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China
| | - Wen-Hao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences Beijing, China ; Research Network of Global Change Biology, Beijing Institutes of Life Science, Chinese Academy of Sciences Beijing, China
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26
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Dean SL, Farrer EC, Porras-Alfaro A, Suding KN, Sinsabaugh RL. Assembly of root-associated bacteria communities: interactions between abiotic and biotic factors. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:102-110. [PMID: 25870878 DOI: 10.1111/1758-2229.12194] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Nitrogen (N) deposition in many areas of the world is over an order of magnitude greater than it would be in absence of human activity. We ask how abiotic (N)and biotic (plant host and neighborhood) effects interact to influence root-associated bacterial (RAB)community assembly. Using 454 pyrosequencing, we examined RAB communities from two dominantal pine tundra plants, Geum rossii and Deschampsia cespitosa, under control, N addition and D. cespitosa removal treatments, implemented in a factorial design. We hypothesized that host would have the strongest effect on RAB assembly, followed by N,then neighbor effects.The most dominant phyla were Proteobacteria (mostly Gammaproteobacteria), Actinobacteria,Bacteroidetes and Acidobacteria. We found RAB communities were host specific, with only 17% overlap in operational taxonomic units. Host effects on composition were over twice as strong as Neffects. D. cespitosa RAB diversity declined with N, while G. rossii RAB did not. D. cespitosa removal did not influence G. rossii RAB community composition, but G. rossii RAB diversity declined with N only when D. cespitosa was absent. We conclude that RAB of both hosts are sensitive to N enrichment, and RAB response to N is influenced by host identity and plant neighborhood.
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Affiliation(s)
- Sarah L Dean
- Department of Biology, University of New Mexico Albuquerque, NM, USA.
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27
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Rieseberg L, Vines T, Gow J, Geraldes A. Editorial 2015. Mol Ecol 2015; 24:1-17. [DOI: 10.1111/mec.12997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 11/10/2014] [Indexed: 11/30/2022]
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28
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Russell JA, Dubilier N, Rudgers JA. Nature's microbiome: introduction. Mol Ecol 2014; 23:1225-1237. [PMID: 24628935 DOI: 10.1111/mec.12676] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 01/18/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, PA, 19104, USA
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29
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Farrer EC, Ashton IW, Knape J, Suding KN. Separating direct and indirect effects of global change: a population dynamic modeling approach using readily available field data. GLOBAL CHANGE BIOLOGY 2014; 20:1238-1250. [PMID: 24115317 DOI: 10.1111/gcb.12401] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 09/03/2013] [Indexed: 06/02/2023]
Abstract
Two sources of complexity make predicting plant community response to global change particularly challenging. First, realistic global change scenarios involve multiple drivers of environmental change that can interact with one another to produce non-additive effects. Second, in addition to these direct effects, global change drivers can indirectly affect plants by modifying species interactions. In order to tackle both of these challenges, we propose a novel population modeling approach, requiring only measurements of abundance and climate over time. To demonstrate the applicability of this approach, we model population dynamics of eight abundant plant species in a multifactorial global change experiment in alpine tundra where we manipulated nitrogen, precipitation, and temperature over 7 years. We test whether indirect and interactive effects are important to population dynamics and whether explicitly incorporating species interactions can change predictions when models are forecast under future climate change scenarios. For three of the eight species, population dynamics were best explained by direct effect models, for one species neither direct nor indirect effects were important, and for the other four species indirect effects mattered. Overall, global change had negative effects on species population growth, although species responded to different global change drivers, and single-factor effects were slightly more common than interactive direct effects. When the fitted population dynamic models were extrapolated under changing climatic conditions to the end of the century, forecasts of community dynamics and diversity loss were largely similar using direct effect models that do not explicitly incorporate species interactions or best-fit models; however, inclusion of species interactions was important in refining the predictions for two of the species. The modeling approach proposed here is a powerful way of analyzing readily available datasets which should be added to our toolbox to tease apart complex drivers of global change.
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Affiliation(s)
- Emily C Farrer
- Department of Environmental Science, Policy & Management, University of California, Berkeley, 94720, CA, USA
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