1
|
El Amrani B. Insights into the Biotic Factors Shaping Ectomycorrhizal Associations. BIOLOGY 2024; 13:1044. [PMID: 39765711 PMCID: PMC11673544 DOI: 10.3390/biology13121044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/11/2025]
Abstract
Ectomycorrhizal (EM) associations are essential symbiotic relationships that contribute significantly to the health and functioning of forest ecosystems. This review examines the biotic factors that influence EM associations, focusing on plant and fungal diversity, host specificity, and microbial interactions. Firstly, the diversity of host plants and ectomycorrhizal fungi (EMF) is discussed, highlighting how the richness of these organisms affects the formation and success of EM symbioses. Next, host specificity is explored, with a focus on the complex relationships between EMF and their host plants. Microbial interactions are examined in depth, with sections on both positive and negative influences of bacteria and different fungal groups on EM formation. Overall, this review provides a comprehensive overview of the biotic factors that shape EM associations, offering insights into the mechanisms that underpin these critical ecological interactions and their broader implications for ecosystem management and restoration.
Collapse
Affiliation(s)
- Belkacem El Amrani
- Lumbricidae, Improving Soil Productivity and Environment Unit (LAPSE), Higher Normal School (ENS), Mohammed V University in Rabat, Rabat P.O. Box 554, Morocco
| |
Collapse
|
2
|
Chaves T, Santos Xavier J, Gonçalves Dos Santos A, Martins-Cunha K, Karstedt F, Kossmann T, Sourell S, Leopoldo E, Fortuna Ferreira MN, Farias R, Titton M, Alves-Silva G, Bittencourt F, Bortolini D, Gumboski EL, von Wangenheim A, Góes-Neto A, Drechsler-Santos ER. Innovative infrastructure to access Brazilian fungal diversity using deep learning. PeerJ 2024; 12:e17686. [PMID: 39006015 PMCID: PMC11243970 DOI: 10.7717/peerj.17686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024] Open
Abstract
In the present investigation, we employ a novel and meticulously structured database assembled by experts, encompassing macrofungi field-collected in Brazil, featuring upwards of 13,894 photographs representing 505 distinct species. The purpose of utilizing this database is twofold: firstly, to furnish training and validation for convolutional neural networks (CNNs) with the capacity for autonomous identification of macrofungal species; secondly, to develop a sophisticated mobile application replete with an advanced user interface. This interface is specifically crafted to acquire images, and, utilizing the image recognition capabilities afforded by the trained CNN, proffer potential identifications for the macrofungal species depicted therein. Such technological advancements democratize access to the Brazilian Funga, thereby enhancing public engagement and knowledge dissemination, and also facilitating contributions from the populace to the expanding body of knowledge concerning the conservation of macrofungal species of Brazil.
Collapse
Affiliation(s)
- Thiago Chaves
- Brazilian National Institute for Digital Convergence-INCoD, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Joicymara Santos Xavier
- Institute of Agricultural Science, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Minas Gerais, Brazil
| | - Alfeu Gonçalves Dos Santos
- Brazilian National Institute for Digital Convergence-INCoD, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Kelmer Martins-Cunha
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Fernanda Karstedt
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Thiago Kossmann
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Susanne Sourell
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Eloisa Leopoldo
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Miriam Nathalie Fortuna Ferreira
- Brazilian National Institute for Digital Convergence-INCoD, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Roger Farias
- Brazilian National Institute for Digital Convergence-INCoD, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Mahatmã Titton
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Genivaldo Alves-Silva
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Felipe Bittencourt
- MIND.Funga/MICOLAB, Department of Botany, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Dener Bortolini
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Emerson L Gumboski
- Department of Biological Sciences, Regional University of Joinville (UNIVILLE), Joinville, Santa Catarina, Brazil
| | - Aldo von Wangenheim
- Brazilian National Institute for Digital Convergence-INCoD, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | |
Collapse
|
3
|
Vance-Chalcraft HD, Smith KC, Allen J, Bowser G, Cooper CB, Jelks NO, Karl C, Kodner R, Laslo M. Social Justice, Community Engagement, and Undergraduate STEM Education: Participatory Science as a Teaching Tool. CBE LIFE SCIENCES EDUCATION 2024; 23:es3. [PMID: 38728230 PMCID: PMC11235114 DOI: 10.1187/cbe.23-06-0123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Social justice is increasingly being seen as relevant to the science curriculum. We examine the intersection of participatory science, social justice, and higher education in the United States to investigate how instructors can teach about social justice and enhance collaborations to work toward enacting social justice. Participatory science approaches, like those that collect data over large geographic areas, can be particularly useful for teaching students about social justice. Conversely, local-scale approaches that integrate students into community efforts can create powerful collaborations to help facilitate social justice. We suggest a variety of large-scale databases, platforms, and portals that could be used as starting points to address a set of learning objectives about social justice. We also describe local-scale participatory science approaches with a social justice focus, developed through academic and community partnerships. Considerations for implementing participatory science with undergraduates are discussed, including cautions about the necessary time investment, cultural competence, and institutional support. These approaches are not always appropriate but can provide compelling learning experiences in the correct circumstances.
Collapse
Affiliation(s)
| | - Kalynda Chivon Smith
- Department of Psychology, North Carolina Agricultural and Technical State University, Greensboro, NC 27411
| | - Jessica Allen
- Department of Biological, Physical, and Health Sciences, Roosevelt University, Chicago, IL 60605
| | - Gillian Bowser
- Ecosystem Science and Sustainability, Colorado State University, Fort Collins, CO 80523
| | - Caren B Cooper
- Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695
| | | | | | - Robin Kodner
- Environmental Sciences, Western Washington University, Bellingham, WA 98225
| | - Mara Laslo
- Biological Sciences, Wellesley College, Wellesley, MA 02481
| |
Collapse
|
4
|
Haelewaters D, Quandt CA, Bartrop L, Cazabonne J, Crockatt ME, Cunha SP, De Lange R, Dominici L, Douglas B, Drechsler-Santos ER, Heilmann-Clausen J, Irga PJ, Jakob S, Lofgren L, Martin TE, Muchane MN, Stallman JK, Verbeken A, Walker AK, Gonçalves SC. The power of citizen science to advance fungal conservation. Conserv Lett 2024; 17:e13013. [PMID: 39371387 PMCID: PMC11452162 DOI: 10.1111/conl.13013] [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: 11/20/2023] [Accepted: 02/27/2024] [Indexed: 10/08/2024] Open
Abstract
Fungal conservation is gaining momentum globally, but many challenges remain. To advance further, more data are needed on fungal diversity across space and time. Fundamental information regarding population sizes, trends, and geographic ranges is also critical to accurately assess the extinction risk of individual species. However, obtaining these data is particularly difficult for fungi due to their immense diversity, complex and problematic taxonomy, and cryptic nature. This paper explores how citizen science (CS) projects can be lever-aged to advance fungal conservation efforts. We present several examples of past and ongoing CS-based projects to record and monitor fungal diversity. These include projects that are part of broad collecting schemes, those that provide participants with targeted sampling methods, and those whereby participants collect environmental samples from which fungi can be obtained. We also examine challenges and solutions for how such projects can capture fungal diversity, estimate species absences, broaden participation, improve data curation, and translate resulting data into actionable conservation measures. Finally, we close the paper with a call for professional mycologists to engage with amateurs and local communities, presenting a framework to determine whether a given project would likely benefit from participation by citizen scientists.
Collapse
Affiliation(s)
- Danny Haelewaters
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Entomology, České Budějovice, Czech Republic
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Lachlan Bartrop
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jonathan Cazabonne
- Forest Research Institute, Université du Québec en Abitibi-Témiscamingue, Amos, Canada
- Centre for Forest Research, Université du Québec à Montréal, Montréal, Canada
| | - Martha E. Crockatt
- Leverhulme Centre for Nature Recovery, School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Susana P. Cunha
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Ruben De Lange
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
| | - Laura Dominici
- Department of Environment, Land and Infrastructure Engineering, Politecnico di Torino, Turin, Italy
| | | | | | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peter J. Irga
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, Australia
| | - Sigrid Jakob
- Fungal Diversity Survey, Sebastopol, California, USA
| | - Lotus Lofgren
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Thomas E. Martin
- School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, Wales, UK
| | | | - Jeffery K. Stallman
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - Annemieke Verbeken
- Research Group Mycology, Department of Biology, Ghent University, Ghent, Belgium
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Susana C. Gonçalves
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| |
Collapse
|
5
|
Substrate affinities of wood decay fungi are foremost structured by wood properties not climate. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2023.101231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
6
|
Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, Chu H. Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China. SCIENCE CHINA LIFE SCIENCES 2022; 66:1134-1150. [PMID: 36462107 DOI: 10.1007/s11427-022-2174-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022]
Abstract
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.
Collapse
Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, 50409, Estonia
- College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Miao Sun
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Han-Yang Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210003, China
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
7
|
Yang H, Yang Z, Wang QC, Wang YL, Hu HW, He JZ, Zheng Y, Yang Y. Compartment and Plant Identity Shape Tree Mycobiome in a Subtropical Forest. Microbiol Spectr 2022; 10:e0134722. [PMID: 35863008 PMCID: PMC9430249 DOI: 10.1128/spectrum.01347-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/26/2022] [Indexed: 11/20/2022] Open
Abstract
Deciphering the relationships between microbes and their host plants is critical for a better understanding of microbial diversity maintenance and community stability. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a subtropical common-garden experiment. The results showed that fungal community structures significantly differed across compartments (leaf, root, and soil) and different tree species. Higher α-diversity was observed in the phyllosphere than in the roots and rhizospheric soil. Fungal community composition (β-diversity) was significantly affected by both compartment and species identity. The fungal community compositions were significantly correlated with soil pH in the roots and the soils as well as with soil nitrate and leaf total phosphorus in the leaves. We found that fungal community assemblies were mainly driven by deterministic processes, regardless of compartments. Moreover, host preference analyses indicated that stronger plant/fungus preferences occurred in leaves than in roots and soils. Our results highlight the differences in tree mycobiome between aboveground and belowground compartments and have important implications for the promotion of biodiversity conservation and management sustainability for the subtropical forest. IMPORTANCE Subtropical mountain forests are widely distributed in Southern China and are characterized by high biodiversity. The interactions between plants and fungi play pivotal roles in biodiversity maintenance and community stability. Nevertheless, knowledge of fungal diversity and of the community assembly patterns of woody plants is scarce. Here, we investigated fungal diversity and community assembly in the phyllosphere and rhizosphere of 13 tree species in a common-garden experiment. We found that both compartment and plant identity influenced fungal diversity, community, and guild compositions, while deterministic processes mainly governed the fungal community assembly, especially in the rhizospheric fungal communities. Our results demonstrate that tree leaves represent stronger host/fungi preferences than do roots and soils. Together, our findings enhance the understanding of the roles of compartment and plant identity in structuring fungal communities as well as promote fungal diversity maintenance in subtropical mountain forest ecosystems.
Collapse
Affiliation(s)
- Hao Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Zhijie Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
| | - Quan-Cheng Wang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Yong-Long Wang
- Faculty of Biological Science and Technology, Baotou Teacher’s College, Baotou, Inner Mongolia, China
| | - Hang-Wei Hu
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Ji-Zheng He
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
| | - Yong Zheng
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Yusheng Yang
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
- Sanming Forest Ecosystem National Observation and Research Station, Sanming, Fujian, China
| |
Collapse
|
8
|
Bruun HH, Brunbjerg AK, Dalby L, Fløjgaard C, Frøslev TG, Haarder S, Heilmann‐Clausen J, Høye TT, Læssøe T, Ejrnæs R. Simple attributes predict the value of plants as hosts to fungal and arthropod communities. OIKOS 2022. [DOI: 10.1111/oik.08823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Lars Dalby
- Dept of Ecoscience, Aarhus Univ. Rønde Denmark
| | | | | | | | | | | | - Thomas Læssøe
- Dept of Biology, Univ. of Copenhagen Copenhagen Denmark
- Centre for Macroecology, Evolution and Climate, Univ. of Copenhagen Copenhagen Denmark
| | | |
Collapse
|
9
|
Wang XW, Jiang JH, Liu SL, Gafforov Y, Zhou LW. Species Diversification of the Coniferous Pathogenic Fungal Genus Coniferiporia (Hymenochaetales, Basidiomycota) in Association with Its Biogeography and Host Plants. PHYTOPATHOLOGY 2022; 112:404-413. [PMID: 34170760 DOI: 10.1094/phyto-05-21-0181-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Coniferiporia, belonging to Hymenochaetaceae and now segregated from Phellinidium, is a wood-inhabiting fungal genus with three species, each having a specific geographic distribution and a strong host specificity as a forest pathogen of coniferous trees. In this study, the species diversity of Coniferiporia is further clarified with the aid of a wider sampling and multilocus-based phylogenetic analysis, which reveals a new species Coniferiporia uzbekistanensis. The molecular clock and ancestral geographic origin analyses indicate that the ancestor of Coniferiporia emerged in one of the Pinaceae and Cupressaceae, then jumped to the other plant family originated in eastern Eurasia 17.01 million years ago (Mya; 95% highest posterior density: 9.46 to 25.86 Mya), and later extended its distribution to western North America, Central Asia, and eastern Europe. Coniferiporia sulphurascens speciated on Pinaceae in eastern Eurasia 8.78 Mya (9.46 to 25.86 Mya) and then extended its distribution to western North America and eastern Europe. Coniferiporia qilianensis and C. uzbekistanensis speciated on Juniperus przewalskii in eastern Eurasia 3.67 Mya (0.36 to 8.02 Mya) and on Juniperus polycarpos in Central Asia 4.35 Mya (0.94 to 8.37 Mya), respectively. The speciation event of Coniferiporia weirii occurred 4.45 Mya (0.77 to 9.33 Mya) right after the emergence of its host, the endemic Cupressaceae species Thuja plicata, and soon after, this fungus evolved to also inhabit another endemic Cupressaceae species Calocedrus decurrens. In summary, this study for the first time unambiguously clarified and timed the adaptive evolutionary event of Coniferiporia in association with its biogeography and host plants.
Collapse
Affiliation(s)
- Xue-Wei Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji-Hang Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shi-Liang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yusufjon Gafforov
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Laboratory of Mycology, Institute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent 100125, Uzbekistan
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Li-Wei Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| |
Collapse
|
10
|
Picek L, Šulc M, Matas J, Heilmann-Clausen J, Jeppesen TS, Lind E. Automatic Fungi Recognition: Deep Learning Meets Mycology. SENSORS 2022; 22:s22020633. [PMID: 35062595 PMCID: PMC8779018 DOI: 10.3390/s22020633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 02/04/2023]
Abstract
The article presents an AI-based fungi species recognition system for a citizen-science community. The system's real-time identification too - FungiVision - with a mobile application front-end, led to increased public interest in fungi, quadrupling the number of citizens collecting data. FungiVision, deployed with a human-in-the-loop, reaches nearly 93% accuracy. Using the collected data, we developed a novel fine-grained classification dataset - Danish Fungi 2020 (DF20) - with several unique characteristics: species-level labels, a small number of errors, and rich observation metadata. The dataset enables the testing of the ability to improve classification using metadata, e.g., time, location, habitat and substrate, facilitates classifier calibration testing and finally allows the study of the impact of the device settings on the classification performance. The continual flow of labelled data supports improvements of the online recognition system. Finally, we present a novel method for the fungi recognition service, based on a Vision Transformer architecture. Trained on DF20 and exploiting available metadata, it achieves a recognition error that is 46.75% lower than the current system. By providing a stream of labeled data in one direction, and an accuracy increase in the other, the collaboration creates a virtuous cycle helping both communities.
Collapse
Affiliation(s)
- Lukáš Picek
- Department of Cybernetics, Faculty of Applied Sciences, University of West Bohemia, 30100 Pilsen, Czech Republic
- Correspondence: or
| | - Milan Šulc
- Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, 16636 Prague, Czech Republic; (M.Š.); (J.M.)
| | - Jiří Matas
- Department of Cybernetics, Faculty of Electrical Engineering, Czech Technical University in Prague, 16636 Prague, Czech Republic; (M.Š.); (J.M.)
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, Biological Institute, University of Copenhagen, 1165 Copenhagen, Denmark; (J.H.-C.); (E.L.)
| | | | - Emil Lind
- Center for Macroecology, Evolution and Climate, Biological Institute, University of Copenhagen, 1165 Copenhagen, Denmark; (J.H.-C.); (E.L.)
| |
Collapse
|
11
|
Moll J, Roy F, Bässler C, Heilmann-Clausen J, Hofrichter M, Kellner H, Krabel D, Schmidt JH, Buscot F, Hoppe B. First Evidence That Nematode Communities in Deadwood Are Related to Tree Species Identity and to Co-Occurring Fungi and Prokaryotes. Microorganisms 2021; 9:microorganisms9071454. [PMID: 34361890 PMCID: PMC8304250 DOI: 10.3390/microorganisms9071454] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/02/2023] Open
Abstract
Nematodes represent a diverse and ubiquitous group of metazoans in terrestrial environments. They feed on bacteria, fungi, plants, other nematodes or parasitize a variety of animals and hence may be considered as active members of many food webs. Deadwood is a structural component of forest ecosystems which harbors many niches for diverse biota. As fungi and bacteria are among the most prominent decomposing colonizers of deadwood, we anticipated frequent and diverse nematode populations to co-occur in such ecosystems. However, knowledge about their ability to colonize this habitat is still limited. We applied DNA-based amplicon sequencing (metabarcoding) of the 18S rRNA gene to analyze nematode communities in sapwood and heartwood of decaying logs from 13 different tree species. We identified 247 nematode ASVs (amplicon sequence variants) from 27 families. Most of these identified families represent bacterial and fungal feeders. Their composition strongly depended on tree species identity in both wood compartments. While pH and water content were the only wood properties that contributed to nematodes' distribution, co-occurring fungal and prokaryotic (bacteria and archaea) α- and β-diversities were significantly related to nematode communities. By exploring thirteen different tree species, which exhibit a broad range of wood characteristics, this study provides first and comprehensive insights into nematode diversity in deadwood of temperate forests and indicates connectivity to other wood-inhabiting organisms.
Collapse
Affiliation(s)
- Julia Moll
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Correspondence: (J.M.); (B.H.)
| | - Friederike Roy
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Claus Bässler
- Department of Conservation Biology, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany;
- Department of Research, National Park Bavarian Forest, 94481 Grafenau, Germany
| | - Jacob Heilmann-Clausen
- Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Martin Hofrichter
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Harald Kellner
- Institute of Environmental Biotechnology, Technische Universität Dresden, IHI Zittau, 02763 Zittau, Germany; (M.H.); (H.K.)
| | - Doris Krabel
- Institute of Forest Botany, Technische Universität Dresden, 01737 Tharandt, Germany;
| | - Jan Henrik Schmidt
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany;
| | - François Buscot
- Helmholtz Centre for Environmental Research—UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany; (F.R.); (F.B.)
- German Centre for Integrative Biodiversity Research (iDiv) Halle—Jena—Leipzig, 04103 Leipzig, Germany
| | - Björn Hoppe
- Institute for National and International Plant Health, Julius Kühn Institute (JKI)—Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany
- Correspondence: (J.M.); (B.H.)
| |
Collapse
|
12
|
Li T, Wu S, Yang W, Selosse MA, Gao J. How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics. FRONTIERS IN PLANT SCIENCE 2021; 12:647114. [PMID: 34025695 PMCID: PMC8138319 DOI: 10.3389/fpls.2021.647114] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 04/13/2021] [Indexed: 05/04/2023]
Abstract
Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.
Collapse
Affiliation(s)
- Taiqiang Li
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Shimao Wu
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Wenke Yang
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| | - Marc-André Selosse
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
- Institut de Systématique, Évolution, Biodiversité, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum National d’Histoire Naturelle, Sorbonne Universités, Paris, France
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Gdańsk, Poland
| | - Jiangyun Gao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, China
- Laboratory of Ecology and Evolutionary Biology, Yunnan University, Kunming, China
| |
Collapse
|
13
|
Current distribution data for the red-listed species of aphyllophoroid fungi in Ukraine. UKRAINIAN BOTANICAL JOURNAL 2021. [DOI: 10.15407/ukrbotj78.01.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The article provides current information on distribution patterns of six species of aphyllophoroid fungi (Agaricomycetes, Basidiomycota) listed in the Red Data Book of Ukraine: Clavariadelphus pistillaris, Gomphus clavatus, Hericium coralloides, Picipes rhizophilus, Polyporus umbellatus, and Sparassis crispa. Altogether, about 500 occurrences of the fungal fruitbodies in the country are reported. Of them, over 410 recent observations have been added to those published in the Red Data Book of Ukraine in 2009. Majority of that data has been provided over the last few years via mushroom citizen science, i.e. involvement of volunteers in collecting distribution data for macrofungi with large and distinctive fruitbodies. Only specialist-verified observations were included in the datasets reported in the article. The compiled data will serve as a considerably improved basis for future re-assessments of the conservation status of these threatened species for the next edition of the Red Data Book of Ukraine.
Collapse
|
14
|
Amplicon Sequencing-Based Bipartite Network Analysis Confirms a High Degree of Specialization and Modularity for Fungi and Prokaryotes in Deadwood. mSphere 2021; 6:6/1/e00856-20. [PMID: 33441408 PMCID: PMC7845612 DOI: 10.1128/msphere.00856-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. Fungi and prokaryotes are dominant colonizers of wood and mediate its decomposition. Much progress has been achieved to unravel these communities and link them to specific wood properties. However, comparative studies considering both groups of organisms and assessing their relationships to wood resources are largely missing. Bipartite interaction networks provide an opportunity to investigate this colonizer-resource relationship more in detail and aim to directly compare results between different biotic groups. The main questions were as follows. Are network structures reflecting the trophic relationship between fungal and prokaryotic colonizers and their resources? If so, do they reflect the critical role of these groups, especially that of fungi, during decomposition? We used amplicon sequencing data to analyze fungal and prokaryotic interaction networks from deadwood of 13 temperate tree species at an early to middle stage of decomposition. Several diversity- and specialization-related indices were determined and the observed network structures were related to intrinsic wood traits. We hypothesized nonrandom bipartite networks for both groups and a higher degree of specialization for fungi, as they are the key players in wood decomposition. The results reveal highly modular and specialized interaction networks for both groups of organisms, demonstrating that many fungi and prokaryotes are resource-specific colonizers. However, as the level of specialization of fungi significantly surpassed that of prokaryotes, our findings reflect the strong association between fungi and their host. Our novel approach shows that the application of bipartite interaction networks is a useful tool to explore, quantify, and compare the deadwood-colonizers relationship based on sequencing data. IMPORTANCE Deadwood is important for our forest ecosystems. It feeds and houses many organisms, e.g., fungi and prokaryotes, with many different species contributing to its decomposition and nutrient cycling. The aim of this study was to explore and quantify the relationship between these two main wood-inhabiting organism groups and their corresponding host trees. Two independent DNA-based amplicon sequencing data sets (fungi and prokaryotes) were analyzed via bipartite interaction networks. The links in the networks represent the interactions between the deadwood colonizers and their deadwood hosts. The networks allowed us to analyze whether many colonizing species interact mostly with a restricted number of deadwood tree species, so-called specialization. Our results demonstrate that many prokaryotes and fungi are resource-specific colonizers. The direct comparison between both groups revealed significantly higher specialization values for fungi, emphasizing their strong association to respective host trees, which reflects their dominant role in exploiting this resource.
Collapse
|
15
|
Lee MR, Oberle B, Olivas W, Young DF, Zanne AE. Wood construction more strongly shapes deadwood microbial communities than spatial location over 5 years of decay. Environ Microbiol 2020; 22:4702-4717. [PMID: 32840945 DOI: 10.1111/1462-2920.15212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 07/12/2020] [Accepted: 07/30/2020] [Indexed: 01/18/2023]
Abstract
Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3-98.8% mass loss while decaying in common garden 'rotplots' in a temperate oak-hickory forest in the Ozark Highlands, MO, USA. Communities were isolated from 21 woody species that had been decomposing for 1-5 years in spatially distinct habitats at the landscape scale (top and bottom of watersheds) and within stems (top and bottom of stems). Microbial community structure varied more strongly with wood traits than with spatial locations, mirroring the relative role of these factors on decay rates on the same pieces of wood even after 5 years. Co-occurring fungal and bacterial communities persistently influenced one another independently from their shared environmental conditions. However, the relative influence of wood construction versus spatial locations differed between fungi and bacteria, suggesting that life history characteristics of these clades structure diversity differently across space and time in decomposing wood.
Collapse
Affiliation(s)
- Marissa R Lee
- Department of Plant and Microbial Biology, North Carolina State University, Campus Box 7612, Raleigh, NC, 27695, USA
| | - Brad Oberle
- Division of Natural Sciences, New College of Florida, 5800 Bay Shore Rd., Sarasota, FL, 34243, USA
| | - Wendy Olivas
- Department of Biology, University of Missouri, St Louis, MO, 63108, USA
| | - Darcy F Young
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW Suite 6000, Washington, DC, 20052, USA
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW Suite 6000, Washington, DC, 20052, USA
| |
Collapse
|
16
|
Müller J, Ulyshen M, Seibold S, Cadotte M, Chao A, Bässler C, Vogel S, Hagge J, Weiß I, Baldrian P, Tláskal V, Thorn S. Primary determinants of communities in deadwood vary among taxa but are regionally consistent. OIKOS 2020. [DOI: 10.1111/oik.07335] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Jörg Müller
- Field Station Fabrikschleichach, Dept of Animal Ecology and Tropical Biology, Biocenter, Univ. of Würzburg Glashüttenstraße 5 DE‐96181 Rauhenebrach Germany
- Bavarian Forest National Park Grafenau Germany
| | - Mike Ulyshen
- USDA Forest Service, Southern Research Station Athens GA USA
| | - Sebastian Seibold
- Dept of Ecology and Ecosystem Management, Technical Univ. of Munich Freising Germany
- Berchtesgaden National Park Berchtesgaden Germany
| | - Marc Cadotte
- Dept of Biological Sciences, Univ. of Toronto–Scarborough Toronto ON Canada
| | - Anne Chao
- Inst. of Statistics, National Tsing Hua Univ. Hsin‐Chu Taiwan
| | - Claus Bässler
- Field Station Fabrikschleichach, Dept of Animal Ecology and Tropical Biology, Biocenter, Univ. of Würzburg Glashüttenstraße 5 DE‐96181 Rauhenebrach Germany
- Bavarian Forest National Park Grafenau Germany
- Dept of Biodiversity Conservation, Institute for Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt Frankfurt am Main Germany
| | - Sebastian Vogel
- Field Station Fabrikschleichach, Dept of Animal Ecology and Tropical Biology, Biocenter, Univ. of Würzburg Glashüttenstraße 5 DE‐96181 Rauhenebrach Germany
| | - Jonas Hagge
- Forest Nature Conservation, Georg‐August‐Univ. Göttingen Göttingen Germany
| | - Ingmar Weiß
- Bavarian Forest National Park Grafenau Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Inst. of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Inst. of Microbiology of the Czech Academy of Sciences Prague Czech Republic
| | - Simon Thorn
- Field Station Fabrikschleichach, Dept of Animal Ecology and Tropical Biology, Biocenter, Univ. of Würzburg Glashüttenstraße 5 DE‐96181 Rauhenebrach Germany
| |
Collapse
|
17
|
A Comparison of the Formation Rates and Composition of Tree-Related Microhabitats in Beech-Dominated Primeval Carpathian and Hyrcanian Forests. FORESTS 2020. [DOI: 10.3390/f11020144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Primeval forests in the temperate zone exist only as a few remnants, but theses serve as important reference areas for conservation. As key habitats, tree-related microhabitats (TreMs) are of intense interest to forest ecologists, but little is known about their natural composition and dynamics in different tree species. Beech forms a major part of the temperate forests that extend from Europe, home to European beech Fagus sylvatica L. (Fs), eastward to Iran, where Oriental beech Fagus orientalis Lipsky (Fo) is the dominant species. In this study, we compared TreMs in primeval forests of both species, using data from Fo growing in 25 inventory plots throughout the Hyrcanian forest belt in Iran and from Fs growing in a 9 ha permanent plot in the Uholka Forest of Ukraine. TreMs based on 47 types and 11 subgroups were recorded. Beech trees in the Hyrcanian forest had a higher mean diameter at breast height (dbh) than beech trees in Uholka and contained twice as many TreMs per hectare. Although the mean richness of TreMs per TreM bearing tree was similar in the two species, on the basis of the comparison single trees in two groups (n = 405 vs. 2251), the composition of the TreMs clearly differed, as the proportions of rot holes, root-buttress concavities, and crown deadwood were higher in the Hyrcanian Forest, and those of bark losses, exposed heartwood, and burrs and cankers higher in Uholka Forest. Estimates of TreMs dynamics based on dbh and using Weibull models showed a significantly faster cumulative increase of TreMs in Fo, in which saturation occurred already in trees with a dbh of 70–80 cm. By contrast, the increase in TreMs in Fs was continuous. In both species, the probability density was highest at a dbh of about 30 cm, but was twice as high in Fo. Because of limitations of our study design, the reason behind observed differences of TreM formation and composition between regions remains unclear, as it could be either result of the tree species or the environment, or their interaction. However, the observed differences were more likely the result of differences in the environment than in the two tree species. Nevertheless, our findings demonstrate that the Hyrcanian Forest, recently designated as a natural heritage site in Iran, is unique, not only as a tertiary relict or due to its endemic trees, herbs and arthropods, but also because of its TreMs, which form a distinct and rich habitat for associated taxa, including endemic saproxylic species.
Collapse
|
18
|
Lee MR, Powell JR, Oberle B, Cornwell WK, Lyons M, Rigg JL, Zanne AE. Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats. Ecology 2019; 100:e02790. [PMID: 31228251 DOI: 10.1002/ecy.2790] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 04/14/2019] [Accepted: 05/06/2019] [Indexed: 12/13/2022]
Abstract
Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.
Collapse
Affiliation(s)
- Marissa R Lee
- Department of Biological Sciences, The George Washington University, Washington, D.C., 20052, USA
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Brad Oberle
- Division of Natural Sciences, New College of Florida, Sarasota, Florida, 34243, USA
| | - William K Cornwell
- School of Biological, Earth & Environmental Sciences, Ecology and Evolution Research Centre, UNSW Australia, Sydney, New South Wales, 2052, Australia
| | - Mitchell Lyons
- School of Biological, Earth & Environmental Sciences, Centre for Ecosystem Science, UNSW Australia, Sydney, New South Wales, 2052, Australia
| | - Jessica L Rigg
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Meanagle, New South Wales, 2568, Australia
| | - Amy E Zanne
- Department of Biological Sciences, The George Washington University, Washington, D.C., 20052, USA
| |
Collapse
|
19
|
Wang Z, Jiang Y, Deane DC, He F, Shu W, Liu Y. Effects of host phylogeny, habitat and spatial proximity on host specificity and diversity of pathogenic and mycorrhizal fungi in a subtropical forest. THE NEW PHYTOLOGIST 2019; 223:462-474. [PMID: 30861145 DOI: 10.1111/nph.15786] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 03/04/2019] [Indexed: 05/04/2023]
Abstract
Soil plant-pathogenic (PF) and mycorrhizal fungi (MF) are both important in maintaining plant diversity, for example via host-specialized effects. However, empirical knowledge on the degree of host specificity and possible factors affecting the fungal assemblages is lacking. We identified PF and MF in fine roots of 519 individuals across 45 subtropical tree species in southern China in order to quantify the importance of host phylogeny (including via its effects on functional traits), habitat and space in determining fungal communities. We also compared host specificity in PF and MF at different host-phylogenetic scales. In both PF and MF, host phylogeny independently accounted for > 19% of the variation in fungal richness and composition, whereas environmental and spatial factors each explained no more than 4% of the variation. Over 77% of the variation explained by phylogeny was attributable to covariation in plant functional traits. Host specificity was phylogenetically scale-dependent, being stronger in PF than in MF at low host-phylogenetic scales (e.g. within genus) but similar at larger scales. Our study suggests that host-phylogenetic effects dominate the assembly of both PF and MF communities, resulting from phylogenetically clustered plant traits. The scale-dependent host specificity implies that PF were specialized at lower-level and MF at higher-level host taxa.
Collapse
Affiliation(s)
- Zihui Wang
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510271, China
| | - Yuan Jiang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510271, China
| | - David C Deane
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Fangliang He
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Wensheng Shu
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Yu Liu
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecological and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| |
Collapse
|
20
|
Martín González AM, Ornelas JF, Dalsgaard B, Márquez-Luna U, Lara C. Meta-networks for the study of biogeographical traits in ecological networks: the Mexican hummingbird-plant assemblage. Naturwissenschaften 2018; 105:54. [PMID: 30291455 DOI: 10.1007/s00114-018-1578-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/03/2018] [Accepted: 08/05/2018] [Indexed: 02/05/2023]
Abstract
Recent studies on ecological networks have quantified the contribution of ecological, historical, and evolutionary factors on the structure of local communities of interacting species. However, the influence of species' biogeographical traits, such as migratory habits or phylogeographical history, on ecological networks is poorly understood. Meta-networks, i.e., networks that cover large spatial extensions and include species not co-occurring locally, enable us to investigate mechanisms that operate at larger spatial scales such as migratory patterns or phylogeographical distributions, as well as indirect relationships among species through shared partners. Using a meta-network of hummingbird-plant interaction across Mexico, we illustrate the usefulness of this approach by investigating (1) how biogeographical and morphological factors associate with observed interactions and (2) how species-specific biogeographical characteristics associate with species' network roles. Our results show that all studied hummingbird and plant species in the meta-network were interrelated, either directly or through shared partners. The meta-network was structured into modules, resulting from hummingbirds and plants interacting preferentially with subsets of species, which differed in biogeographical, and, to a lesser extent, morphological traits. Furthermore, migrants and hummingbirds from Nearctic, Transition, and widespread regions had a higher topological importance in the meta-network. Our study illustrates how meta-networks may contribute to our current knowledge on species' biogeographical traits and biotic interactions, providing a perspective complementary to local-scale networks.
Collapse
Affiliation(s)
- Ana M Martín González
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark.
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C. (INECOL), Carretera Antigua a Coatepec No. 351, El Haya, 91070, Xalapa, Veracruz, Mexico
| | - Bo Dalsgaard
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen Ø, Denmark
| | - Ubaldo Márquez-Luna
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340, Iztapalapa, Mexico
| | - Carlos Lara
- Centro de Investigación en Ciencias Biológicas, Universidad Autónoma de Tlaxcala, Km 10.5 Autopista Tlaxcala-San Martín Texmelucan, San Felipe Ixtacuixtla, 90120, Tlaxcala, Mexico
| |
Collapse
|
21
|
Põlme S, Bahram M, Jacquemyn H, Kennedy P, Kohout P, Moora M, Oja J, Öpik M, Pecoraro L, Tedersoo L. Host preference and network properties in biotrophic plant-fungal associations. THE NEW PHYTOLOGIST 2018; 217:1230-1239. [PMID: 29165806 DOI: 10.1111/nph.14895] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/13/2017] [Indexed: 05/04/2023]
Abstract
Analytical methods can offer insights into the structure of biological networks, but mechanisms that determine the structure of these networks remain unclear. We conducted a synthesis based on 111 previously published datasets to assess a range of ecological and evolutionary mechanisms that may influence the plant-associated fungal interaction networks. We calculated the relative host effect on fungal community composition and compared nestedness and modularity among different mycorrhizal types and endophytic fungal guilds. We also assessed how plant-fungal network structure was related to host phylogeny, environmental and sampling properties. Orchid mycorrhizal fungal communities responded most strongly to host identity, but the effect of host was similar among all other fungal guilds. Community nestedness, which did not differ among fungal guilds, declined significantly with increasing mean annual precipitation on a global scale. Orchid and ericoid mycorrhizal fungal communities were more modular than ectomycorrhizal and root endophytic communities, with arbuscular mycorrhizal fungi in an intermediate position. Network properties among a broad suite of plant-associated fungi were largely comparable and generally unrelated to phylogenetic distance among hosts. Instead, network metrics were predominantly affected by sampling and matrix properties, indicating the importance of study design in properly inferring ecological patterns.
Collapse
Affiliation(s)
- Sergei Põlme
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
| | - Mohammad Bahram
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Hans Jacquemyn
- Department of Biology, Plant Conservation and Population Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001, Heverlee, Belgium
| | - Peter Kennedy
- Department of Plant Biology, University of Minnesota, 1445 Gortner Ave, St Paul, MN, 55108, USA
| | - Petr Kohout
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
- Institute of Botany, Academy of Sciences of the Czech Republic, CZ-252 43, Průhonice, Czech Republic
- Faculty of Science, Charles University, CZ-128 44, Prague 2, Czech Republic
| | - Mari Moora
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
| | - Jane Oja
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
| | - Maarja Öpik
- Department of Botany, University of Tartu, 40 Lai Street, 51005, Tartu, Estonia
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, 518114, Shenzhen, China
- Center for Biotechnology & BioMedicine and Division of Life & Health Sciences, Graduate School at Shenzhen, Tsinghua University, 518055, Shenzhen, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Leho Tedersoo
- Natural History Museum, University of Tartu, 14a Ravila, 50411, Tartu, Estonia
| |
Collapse
|
22
|
Plant-endophytes interaction influences the secondary metabolism in Echinacea purpurea (L.) Moench: an in vitro model. Sci Rep 2017; 7:16924. [PMID: 29208923 PMCID: PMC5717142 DOI: 10.1038/s41598-017-17110-w] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/22/2017] [Indexed: 12/11/2022] Open
Abstract
The influence of the interaction(s) between the medicinal plant Echinacea purpurea (L.) Moench and its endophytic communities on the production of alkamides is investigated. To mimic the in vivo conditions, we have set up an infection model of axenic in vitro E. purpurea plants inoculated with a pool of bacterial strains isolated from the E. purpurea stems and leaves. Here we show different alkamide levels between control (not-inoculated) and inoculated plants, suggesting that the alkamide biosynthesis may be modulated by the bacterial infection. Then, we have analysed the branched-chain amino acids (BCCA) decarboxylase gene (GenBank Accession #LT593930; the enzymatic source for the amine moiety formation of the alkamides) expression patterns. The expression profile shows a higher expression level in the inoculated E. purpurea tissues than in the control ones. These results suggest that the plant-endophyte interaction can influence plant secondary metabolism affecting the therapeutic properties of E. purpurea.
Collapse
|
23
|
Interaction type and intimacy structure networks between forest-dwelling organisms and their host trees. Basic Appl Ecol 2017. [DOI: 10.1016/j.baae.2017.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
24
|
Andrew C, Heegaard E, Kirk PM, Bässler C, Heilmann-Clausen J, Krisai-Greilhuber I, Kuyper TW, Senn-Irlet B, Büntgen U, Diez J, Egli S, Gange AC, Halvorsen R, Høiland K, Nordén J, Rustøen F, Boddy L, Kauserud H. Big data integration: Pan-European fungal species observations' assembly for addressing contemporary questions in ecology and global change biology. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.01.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|