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Geng X, Zuo J, Meng Y, Zhuge Y, Zhu P, Wu N, Bai X, Ni G, Hou Y. Changes in nitrogen and phosphorus availability driven by secondary succession in temperate forests shape soil fungal communities and function. Ecol Evol 2023; 13:e10593. [PMID: 37818249 PMCID: PMC10560873 DOI: 10.1002/ece3.10593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/25/2023] [Indexed: 10/12/2023] Open
Abstract
The soil fungal community plays an important role in forest ecosystems and is crucially influenced by forest secondary succession. However, the driving factors of fungal community and function during temperate forest succession and their potential impact on succession processes remain poorly understood. In this study, we investigated the dynamics of the soil fungal community in three temperate forest secondary successional stages (shrublands, coniferous forests, and deciduous broad-leaved forests) using high-throughput DNA sequencing coupled with functional prediction via the FUNGuild database. We found that fungal community richness, α-diversity, and evenness decreased significantly during the succession process. Soil available phosphorus and nitrate nitrogen decreased significantly after initial succession occurred, and redundancy analysis showed that both were significant predictors of soil fungal community structure. Among functional groups, fungal saprotrophs and pathotrophs represented by plant pathogens were significantly enriched in the early-successional stage, while fungal symbiotrophs represented by ectomycorrhiza were significantly increased in the late-successional stage. The abundance of both saprotroph and pathotroph fungal guilds was positively correlated with soil nitrate nitrogen and available phosphorus content. Ectomycorrhizal fungi were negatively correlated with nitrate nitrogen and available phosphorus content and positively correlated with ammonium nitrogen content. These results indicate that the dynamics of fungal community and function reflected the changes in nitrogen and phosphorus availability caused by the secondary succession in temperate forests. The fungal plant pathogen accumulated in the early-successional stage and ectomycorrhizal fungi accumulated in the late-successional stage may have a potential role in promoting forest succession. These findings contribute to a better understanding of the response of soil fungal communities to secondary forest succession and highlight the importance of fungal communities during the successional process.
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Affiliation(s)
- Xinze Geng
- College of Life SciencesLudong UniversityYantaiChina
| | - Jincheng Zuo
- College of Life SciencesLudong UniversityYantaiChina
| | - Yunhao Meng
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Yanhui Zhuge
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Ping Zhu
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Nan Wu
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Xinfu Bai
- School of Resources and Environmental EngineeringLudong UniversityYantaiChina
| | - Guangyan Ni
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Yuping Hou
- College of Life SciencesLudong UniversityYantaiChina
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2
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An X, Han S, Ren X, Sichone J, Fan Z, Wu X, Zhang Y, Wang H, Cai W, Sun F. Succession of Fungal Community during Outdoor Deterioration of Round Bamboo. J Fungi (Basel) 2023; 9:691. [PMID: 37367627 DOI: 10.3390/jof9060691] [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: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.
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Affiliation(s)
- Xiaojiao An
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuaibo Han
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xin Ren
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - John Sichone
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiwei Fan
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinxing Wu
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Wei Cai
- Anji Zhujing Bamboo Technology Co., Ltd., Huzhou 313300, China
| | - Fangli Sun
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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3
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Liu X, Zhou W, Wang X, Wu H, Dong W. Microbial gradual shifts during the process of species replacement in Taihang Mountain. Front Microbiol 2023; 14:1158731. [PMID: 37089536 PMCID: PMC10113637 DOI: 10.3389/fmicb.2023.1158731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/16/2023] [Indexed: 04/08/2023] Open
Abstract
IntroductionUnderstanding microbial gradual shifts along species replacement can help elucidate the mechanisms driving secondary succession, and predict microbial responses to changing environments. However, how climate-induced species replacement alters microbial processes, and whether microbial shifts follow predictable assembly trajectories remain unclear.MethodsUsing space-for-time substitution approach, we studied shifts in bacterial and fungal communities in the succession from Leptodermis oblonga to Vitex negundo var. heterophylla shrubland in Taihang Mountain.Results and DiscussionSpecies replacement, induced by climate related environmental change, significantly increased the above-ground biomass of shrublands, and TP and TK contents in topsoil. The succession from L. oblonga to V. negundo var. heterophylla communities resulted in the gradually replacement of cold-tolerant microbes with warm-affinity ones, and alterations of microbial communities involved in soil biogeochemical processes. Soil and plant variables, such as above-ground biomass, soil pH, total phosphorus, and total potassium, well explained the variations in microbial communities, indicating that the coordinated changes in plant communities and soil properties during secondary succession caused accompanied shifts in microbial diversity and composition.
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Affiliation(s)
- Xiuping Liu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wangming Zhou
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Xinzhen Wang
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Hongliang Wu
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Hebei Key Laboratory of Soil Ecology, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- *Correspondence: Wenxu Dong,
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4
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Current Insight into Traditional and Modern Methods in Fungal Diversity Estimates. J Fungi (Basel) 2022; 8:jof8030226. [PMID: 35330228 PMCID: PMC8955040 DOI: 10.3390/jof8030226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/19/2022] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Fungi are an important and diverse component in various ecosystems. The methods to identify different fungi are an important step in any mycological study. Classical methods of fungal identification, which rely mainly on morphological characteristics and modern use of DNA based molecular techniques, have proven to be very helpful to explore their taxonomic identity. In the present compilation, we provide detailed information on estimates of fungi provided by different mycologistsover time. Along with this, a comprehensive analysis of the importance of classical and molecular methods is also presented. In orderto understand the utility of genus and species specific markers in fungal identification, a polyphasic approach to investigate various fungi is also presented in this paper. An account of the study of various fungi based on culture-based and cultureindependent methods is also provided here to understand the development and significance of both approaches. The available information on classical and modern methods compiled in this study revealed that the DNA based molecular studies are still scant, and more studies are required to achieve the accurate estimation of fungi present on earth.
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Prada-Salcedo LD, Goldmann K, Heintz-Buschart A, Reitz T, Wambsganss J, Bauhus J, Buscot F. Fungal guilds and soil functionality respond to tree community traits rather than to tree diversity in European forests. Mol Ecol 2020; 30:572-591. [PMID: 33226697 DOI: 10.1111/mec.15749] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022]
Abstract
At the global scale, most forest research on biodiversity focuses on aboveground organisms. However, understanding the structural associations between aboveground and belowground communities provides relevant information about important functions linked to biogeochemical cycles. Microorganisms such as soil fungi are known to be closely coupled to the dominant tree vegetation, and we hypothesize that tree traits affect fungal guilds and soil functionality in multiple ways. By analysing fungal diversity of 64 plots from four European forest types using Illumina DNA sequencing, we show that soil fungal communities respond to tree community traits rather than to tree species diversity. To explain changes in fungal community structure and measured soil enzymatic activities, we used a trait-based ecological approach and community-weighted means of tree traits to define 'fast' (acquisitive) versus 'slow' (conservative) tree communities. We found specific tree trait effects on different soil fungal guilds and soil enzymatic activities: tree traits associated with litter and absorptive roots correlated with fungal, especially pathogen diversity, and influenced community composition of soil fungi. Relative abundance of the symbiotrophic and saprotrophic guilds mirrored the litter quality, while the root traits of fast tree communities enhanced symbiotrophic abundance. We found that forest types of higher latitudes, which are dominated by fast tree communities, correlated with high carbon-cycling enzymatic activities. In contrast, Mediterranean forests with slow tree communities showed high enzymatic activities related to nitrogen and phosphorous. Our findings highlight that tree trait effects of either 'fast' or 'slow' tree communities drive different fungal guilds and influence biogeochemical cycles.
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Affiliation(s)
- Luis Daniel Prada-Salcedo
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany.,Department of Biology, University of Leipzig, Leipzig, Germany
| | - Kezia Goldmann
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany
| | - Anna Heintz-Buschart
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Thomas Reitz
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Janna Wambsganss
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany.,Chair of Geobotany, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jürgen Bauhus
- Chair of Silviculture, Faculty of Environment and Natural Resources, University of Freiburg, Freiburg, Germany
| | - François Buscot
- Department of Soil Ecology, Helmholtz-Centre for Environmental Research - UFZ, Halle (Saale), Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
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6
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Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
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Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
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7
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Fahey C, Koyama A, Antunes PM, Dunfield K, Flory SL. Plant communities mediate the interactive effects of invasion and drought on soil microbial communities. THE ISME JOURNAL 2020; 14:1396-1409. [PMID: 32076127 PMCID: PMC7242364 DOI: 10.1038/s41396-020-0614-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/15/2020] [Accepted: 02/07/2020] [Indexed: 01/05/2023]
Abstract
Soil microbiomes could play a major role in ecosystem responses to escalating anthropogenic global change. However, we currently have a poor understanding of how soil microbes will respond to interacting global change factors and if responses will be mediated by changes in plant community structure. We used a field experiment to assess changes in soil fungal and bacterial communities in response to plant invasion, experimental drought, and their combination. In addition, we evaluated the relative importance of direct versus indirect pathways of invasion and drought through changes in associated plant communities with structural equation models. We found that fungal communities were interactively structured by invasion and drought, where fungal richness was lowest with invasion under ambient conditions but highest with invasion under drought conditions. Bacterial richness was lower under drought but unaffected by invasion. Changes in the plant community, including lower plant richness and higher root biomass, moderated the direct effects of invasion on microbial richness. Fungal and bacterial functional groups, including pathogens, mutualists, and nitrogen metabolizers, were also influenced by plant community changes. In sum, plant communities mediated the effects of interacting global change drivers on soil microbial community structure, with significant potential consequences for community dynamics and ecosystem functions.
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Affiliation(s)
- Catherine Fahey
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, USA.
| | - Akihiro Koyama
- Department of Forestry, Michigan State University, East Lansing, MI, USA
| | - Pedro M Antunes
- Biology Department, Algoma University, Sault Ste. Marie, Ontario, Canada
| | - Kari Dunfield
- School of Environmental Science, University of Guelph, Guelph, ON, Canada
| | - S Luke Flory
- Agronomy Department, University of Florida, Gainesville, FL, USA
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8
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Martorelli I, Helwerda LS, Kerkvliet J, Gomes SIF, Nuytinck J, van der Werff CRA, Ramackers GJ, Gultyaev AP, Merckx VSFT, Verbeek FJ. Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB). J Integr Bioinform 2020; 17:jib-2019-0046. [PMID: 32463383 PMCID: PMC7734503 DOI: 10.1515/jib-2019-0046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 04/20/2020] [Indexed: 11/15/2022] Open
Abstract
Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.
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Affiliation(s)
- Irene Martorelli
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Leon S. Helwerda
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Jesse Kerkvliet
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Sofia I. F. Gomes
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Jorinde Nuytinck
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | - Guus J. Ramackers
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Alexander P. Gultyaev
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
| | - Vincent S. F. T. Merckx
- Understanding Evolution, Naturalis Biodiversity Center, Leiden, The Netherlands
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Fons J. Verbeek
- Leiden Institute of Advanced Computer Science (LIACS), Leiden University, Leiden, The Netherlands
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9
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Ngugi MR, Fechner N, Neldner VJ, Dennis PG. Successional dynamics of soil fungal diversity along a restoration chronosequence post‐coal mining. Restor Ecol 2020. [DOI: 10.1111/rec.13112] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Michael R. Ngugi
- Department of Environment and ScienceQueensland Herbarium, Mt Coot‐tha Road, Toowong Brisbane QLD 4066 Australia
| | - Nigel Fechner
- Department of Environment and ScienceQueensland Herbarium, Mt Coot‐tha Road, Toowong Brisbane QLD 4066 Australia
| | - Victor J. Neldner
- Department of Environment and ScienceQueensland Herbarium, Mt Coot‐tha Road, Toowong Brisbane QLD 4066 Australia
| | - Paul G. Dennis
- School of Earth and Environmental SciencesThe University of Queensland QLD Brisbane 4072 Australia
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10
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Plant Taxonomic Diversity Better Explains Soil Fungal and Bacterial Diversity than Functional Diversity in Restored Forest Ecosystems. PLANTS 2019; 8:plants8110479. [PMID: 31698841 PMCID: PMC6918236 DOI: 10.3390/plants8110479] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 10/24/2019] [Accepted: 11/04/2019] [Indexed: 12/17/2022]
Abstract
Plant attributes have direct and indirect effects on soil microbes via plant inputs and plant-mediated soil changes. However, whether plant taxonomic and functional diversities can explain the soil microbial diversity of restored forest ecosystems remains elusive. Here, we tested the linkage between plant attributes and soil microbial communities in four restored forests (Acacia species, Eucalyptus species, mixed coniferous species, mixed native species). The trait-based approaches were applied for plant properties and high-throughput Illumina sequencing was applied for fungal and bacterial diversity. The total number of soil microbial operational taxonomic units (OTUs) varied among the four forests. The highest richness of fungal OTUs was found in the Acacia forest. However, bacterial OTUs were highest in the Eucalyptus forest. Species richness was positively and significantly related to fungal and bacterial richness. Plant taxonomic diversity (species richness and species diversity) explained more of the soil microbial diversity than the functional diversity and soil properties. Prediction of fungal richness was better than that of bacterial richness. In addition, root traits explained more variation than the leaf traits. Overall, plant taxonomic diversity played a more important role than plant functional diversity and soil properties in shaping the soil microbial diversity of the four forests.
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