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Faticov M, Amorim JH, Abdelfattah A, van Dijk LJA, Carvalho AC, Laforest-Lapointe I, Tack AJM. Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree. AMBIO 2024; 53:1673-1685. [PMID: 38871928 PMCID: PMC11436615 DOI: 10.1007/s13280-024-02041-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/12/2024] [Accepted: 05/17/2024] [Indexed: 06/15/2024]
Abstract
Foliar fungi on urban trees are important for tree health, biodiversity and ecosystem functioning. Yet, we lack insights into how urbanization influences foliar fungal communities. We created detailed maps of Stockholm region's climate and air quality and characterized foliar fungi from mature oaks (Quercus robur) across climatic, air quality and local habitat gradients. Fungal richness was higher in locations with high growing season relative humidity, and fungal community composition was structured by growing season maximum temperature, NO2 concentration and leaf litter cover. The relative abundance of mycoparasites and endophytes increased with temperature. The relative abundance of pathogens was lowest with high concentrations of NO2 and particulate matter (PM2.5), while saprotrophs increased with leaf litter cover. Our findings show that urbanization influences foliar fungi, providing insights for developing management guidelines to promote tree health, prevent disease outbreaks and maintain biodiversity within urban landscapes.
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Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Frescativägen 40, 114 18, Stockholm, Sweden.
- Département de Biologie, Université de Sherbrooke, 2500, boul. de l'Université, J1K 2R, Sherbrooke, QC, Canada.
| | - Jorge H Amorim
- Swedish Meteorological and Hydrological Institute (SMHI), Folkborgsvägen 17, Norrköping, Sweden
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth-Allee 100, 14469, Potsdam, Germany
| | - Laura J A van Dijk
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Frescativägen 40, 114 18, Stockholm, Sweden
| | - Ana Cristina Carvalho
- Swedish Meteorological and Hydrological Institute (SMHI), Folkborgsvägen 17, Norrköping, Sweden
| | - Isabelle Laforest-Lapointe
- Département de Biologie, Université de Sherbrooke, 2500, boul. de l'Université, J1K 2R, Sherbrooke, QC, Canada
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Frescativägen 40, 114 18, Stockholm, Sweden
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Hoefle D, Sommer M, Wassermann B, Faticov M, Serra D, Berg G, Tack AJM, Abdelfattah A. Oak seedling microbiome assembly under climate warming and drought. ENVIRONMENTAL MICROBIOME 2024; 19:62. [PMID: 39198873 PMCID: PMC11360865 DOI: 10.1186/s40793-024-00602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024]
Abstract
Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.
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Affiliation(s)
- Daniel Hoefle
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
| | - Milena Sommer
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Maria Faticov
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Demetrio Serra
- Fondazione Mediterranea Terina Onlus, Zona industriale Benedetto XVI, 88046, Ficarella, CZ, Italy
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam OT, Golm, Germany
| | - Ayco J M Tack
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany.
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden.
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Mukhebi DW, Musangi CR, Isoe EM, Neondo JO, Mbinda WM. Endophytic and epiphytic metabarcoding reveals fungal communities on cashew phyllosphere in Kenya. PLoS One 2024; 19:e0305600. [PMID: 39018319 PMCID: PMC11253924 DOI: 10.1371/journal.pone.0305600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 07/19/2024] Open
Abstract
Plants intimately coexist with diverse taxonomically structured microbial communities that influence host health and productivity. The coexistence of plant microbes in the phyllosphere benefits biodiversity maintenance, ecosystem function, and community stability. However, differences in community composition and network structures of phyllosphere epiphytic and endophytic fungi are widely unknown. Using Illumina Miseq sequencing of internal transcribed spacer (ITS) and 28S rRNA gene amplicons, we characterised the epiphytic and endophytic fungal communities associated with cashew phyllosphere (leaf, flower and fruit) from Kwale, Kilifi and Lamu counties in Kenya. The ITS and 28S rRNA gene sequences were clustered into 267 and 108 operational taxonomic units (OTUs) at 97% sequence similarity for both the epiphytes and endophytes. Phylum Ascomycota was abundant followed by Basidiomycota, while class Saccharomycetes was most dominant followed by Dothideomycetes. The major non-ascomycete fungi were associated only with class Tremellales. The fungal communities detected had notable ecological functions as saprotrophs and pathotrophs in class Saccharomyectes and Dothideomycetes. The community composition of epiphytic and endophytic fungi significantly differed between the phyllosphere organs which was statistically confirmed by the Analysis of Similarity test (ANOSIM Statistic R: 0.3273, for 28S rRNA gene and ANOSIM Statistic R: 0.3034 for ITS). The network analysis revealed that epiphytic and endophytic structures were more specialized, modular and had less connectance. Our results comprehensively describe the phyllosphere cashew-associated fungal community and serve as a foundation for understanding the host-specific microbial community structures among cashew trees.
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Affiliation(s)
| | | | - Everlyne Moraa Isoe
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Johnstone Omukhulu Neondo
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Wilton Mwema Mbinda
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Pwani University Biosciences Research Centre (PUBReC), Pwani University, Kilifi, Kenya
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4
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Mizuno T, Sato H, Itioka T. Foraging ants affect community composition and diversity of phyllosphere fungi on a myrmecophilous plants, Mallotus japonicus. Ecol Evol 2024; 14:e11423. [PMID: 38751826 PMCID: PMC11094773 DOI: 10.1002/ece3.11423] [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: 12/31/2023] [Revised: 04/06/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Many microorganisms inhabit the aboveground parts of plants (i.e. the phyllosphere), which mainly comprise leaves. Understanding the structure of phyllosphere microbial communities and their drivers is important because they influence host plant fitness and ecosystem functions. Despite the high prevalence of ant-plant associations, few studies have used quantitative community data to investigate the effects of ants on phyllosphere microbial communities. In the present study, we investigated the effects of ants on the phyllosphere fungal communities of Mallotus japonicus using high-throughput sequencing. Mallotus japonicus is a myrmecophilous plants that bears extrafloral nectaries, attracting several ant species, but does not provide specific ant species with nest sites like myrmecophytes do. We experimentally excluded ants with sticky resins from the target plants and collected leaf discs to extract fungal DNA. The ribosomal DNA internal transcribed spacer 1 (ITS1) regions of the phyllosphere fungi were amplified and sequenced to obtain fungal community data. Our results showed that the exclusion of ants changed the phyllosphere fungal community composition; however, the effect of ants on OTU richness was not clear. These results indicate that ants can change the community of phyllosphere fungi, even if the plant is not a myrmecophyte.
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Affiliation(s)
- Takafumi Mizuno
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Hirotoshi Sato
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Takao Itioka
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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Cambon MC, Trillat M, Lesur-Kupin I, Burlett R, Chancerel E, Guichoux E, Piouceau L, Castagneyrol B, Le Provost G, Robin S, Ritter Y, Van Halder I, Delzon S, Bohan DA, Vacher C. Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems. Mol Ecol 2023; 32:5944-5958. [PMID: 37815414 DOI: 10.1111/mec.17149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.
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Affiliation(s)
- Marine C Cambon
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
- School of Natural Sciences, Bangor University, Bangor, UK
| | | | - Isabelle Lesur-Kupin
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
- HelixVenture, Mérignac, France
| | - Régis Burlett
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
| | | | | | | | | | | | | | - Yves Ritter
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
| | | | | | - David A Bohan
- Agroécologie, INRAE, Université Bourgogne Franche-Comté, Dijon, France
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7
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Small CM, Beck EA, Currey MC, Tavalire HF, Bassham S, Cresko WA. Host genomic variation shapes gut microbiome diversity in threespine stickleback fish. mBio 2023; 14:e0021923. [PMID: 37606367 PMCID: PMC10653670 DOI: 10.1128/mbio.00219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/30/2023] [Indexed: 08/23/2023] Open
Abstract
IMPORTANCE A major focus of host-microbe research is to understand how genetic differences, of various magnitudes, among hosts translate to differences in their microbiomes. This has been challenging for animal hosts, including humans, because it is difficult to control environmental variables tightly enough to isolate direct genetic effects on the microbiome. Our work in stickleback fish is a significant contribution because our experimental approach allowed strict control over environmental factors, including standardization of the microbiome from the earliest stage of development and unrestricted co-housing of fish in a truly common environment. Furthermore, we measured host genetic variation over 2,000 regions of the stickleback genome, comparing this information and microbiome composition data among fish from very similar and very different genetic backgrounds. Our findings highlight how differences in the host genome influence microbiome diversity and make a case for future manipulative microbiome experiments that use host systems with naturally occurring genetic variation.
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Affiliation(s)
- Clayton M. Small
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Emily A. Beck
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
| | - Mark C. Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Hannah F. Tavalire
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
- Presidential Initiative in Data Science, University of Oregon, Eugene, Oregon, USA
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8
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Dong X, Jiang F, Duan D, Tian Z, Liu H, Zhang Y, Hou F, Nan Z, Chen T. Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species. J Fungi (Basel) 2023; 9:1016. [PMID: 37888272 PMCID: PMC10608051 DOI: 10.3390/jof9101016] [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: 09/14/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.
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Affiliation(s)
- Xin Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Feifei Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Dongdong Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China
| | - Zhen Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Huining Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Yinan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Tao Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
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Calvert J, McTaggart A, Carvalhais LC, Rensink S, Dennis PG, Drenth A, Shivas R. Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:860-870. [PMID: 37647418 DOI: 10.1111/plb.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.
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Affiliation(s)
- J Calvert
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - A McTaggart
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - L C Carvalhais
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - S Rensink
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - P G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - A Drenth
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
| | - R Shivas
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Dutton Park, QLD, Australia
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10
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Feng R, Wang H, Liu T, Wang F, Cai L, Chen X, Zhang S. Response of microbial communities in the phyllosphere ecosystem of tobacco exposed to the broad-spectrum copper hydroxide. Front Microbiol 2023; 14:1229294. [PMID: 37840714 PMCID: PMC10568630 DOI: 10.3389/fmicb.2023.1229294] [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] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Copper hydroxide is a broad-spectrum copper fungicide, which is often used to control crop fungal and bacterial diseases. In addition to controlling targeted pathogens, copper hydroxide may also affect other non-targeted microorganisms in the phyllosphere ecosystem. At four time points (before spraying, and 5, 10 and 15 days after fungicide application), the response of diseased and healthy tobacco phyllosphere microorganisms to copper hydroxide stress was studied by using Illumina high-throughput sequencing technology, and Biolog tools. The results showed that the microbiome communities of the healthy group were more affected than the disease group, and the fungal community was more sensitive than the bacterial community. The most common genera in the disease group were Alternaria, Boeremia, Cladosporium, Pantoea, Ralstonia, Pseudomonas, and Sphingomonas; while in the healthy group, these were Alternaria, Cladosporium, Symmetrospora, Ralstonia, and Pantoea. After spraying, the alpha diversity of the fungal community decreased at 5 days for both healthy and diseased groups, and then showed an increasing trend, with a significant increase at 15 days for the healthy group. The alpha diversity of bacterial community in healthy and diseased groups increased at 15 days, and the healthy group had a significant difference. The relative abundance of Alternaria and Cladosporium decreased while that of Boeremia, Stagonosporopsis, Symmetrospora, Epicoccum and Phoma increased in the fungal communities of healthy and diseased leaves. The relative abundance of Pantoea decreased first and then increased, while that of Ralstonia, Pseudomonas and Sphingomonas increased first and then decreased in the bacterial communities of healthy and diseased leaves. While copper hydroxide reduced the relative abundance of pathogenic fungi Alternaria and Cladosporium, it also resulted in the decrease of beneficial bacteria such as Actinomycetes and Pantoea, and the increase of potential pathogens such as Boeremia and Stagonosporopsis. After treatment with copper hydroxide, the metabolic capacity of the diseased group improved, while that of the healthy group was significantly suppressed, with a gradual recovery of metabolic activity as the application time extended. The results revealed changes in microbial community composition and metabolic function of healthy and diseased tobacco under copper hydroxide stress, providing a theoretical basis for future studies on microecological protection of phyllosphere.
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Affiliation(s)
- Ruichao Feng
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co- construction by Ministry and Province), Yangtze University, Jingzhou, Hubei, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Hancheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Tingting Liu
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Liuti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Xingjiang Chen
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Songbai Zhang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co- construction by Ministry and Province), Yangtze University, Jingzhou, Hubei, China
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11
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Tie Z, Wang P, Chen W, Tang B, Yu Y, Liu Z, Zhao S, Khan FH, Zhang X, Xi H. Different responses of the rhizosphere microbiome to Verticillium dahliae infection in two cotton cultivars. Front Microbiol 2023; 14:1229454. [PMID: 37637103 PMCID: PMC10450913 DOI: 10.3389/fmicb.2023.1229454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 07/31/2023] [Indexed: 08/29/2023] Open
Abstract
Verticillium wilt is a disastrous disease caused by Verticillium dahliae that severely damages the production of cotton in China. Even under homogeneous conditions, the same cotton cultivar facing V. dahliae tends to either stay healthy or become seriously ill and die. This binary outcome may be related to the interactions between microbiome assembly and plant health. Understanding how the rhizosphere microbiome responds to V. dahliae infection is vital to controlling Verticillium wilt through the manipulation of the microbiome. In this study, we evaluated the healthy and diseased rhizosphere microbiome of two upland cotton cultivars that are resistant to V. dahliae, Zhong 2 (resistant) and Xin 36 (susceptible), using 16S rRNA and ITS high-throughput sequencing. The results showed that the healthy rhizosphere of both resistant cultivar and susceptible cultivar had more unique bacterial ASVs than the diseased rhizosphere, whereas fewer unique fungal ASVs were found in the healthy rhizosphere of resistant cultivar. There were no significant differences in alpha diversity and beta diversity between the resistant cultivar and susceptible cultivar. In both resistant cultivar and susceptible cultivar, bacterial genera such as Pseudomonas and Acidobacteria bacterium LP6, and fungal genera such as Cephalotrichum and Mortierella were both highly enriched in the diseased rhizosphere, and Pseudomonas abundance in diseased rhizospheres was significantly higher than that in the healthy rhizosphere regardless of the cultivar type. However, cultivar and V. dahliae infection can cause composition changes in the rhizosphere bacterial and fungal communities, especially in the relative abundances of core microbiome members, which varied significantly, with different responses in the two cotton cultivars. Analysis of co-occurrence networks showed that resistant cultivar has a more complex network relationship than susceptible cultivar in the bacterial communities, and V. dahliae has a significant impact on the bacterial community structure. These findings will further broaden the understanding of plant-rhizosphere microbiome interactions and provide an integrative perspective on the cotton rhizosphere microbiome, which is beneficial to cotton health and production.
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Affiliation(s)
- Zhanjiang Tie
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Peng Wang
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Weijian Chen
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Binghui Tang
- Cotton Research Institute, Shihezi Academy of Agricultural Sciences, Shihezi, Xinjiang, China
| | - Yu Yu
- Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, Xinjiang, China
| | - Zheng Liu
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Sifeng Zhao
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Faisal Hayat Khan
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - XueKun Zhang
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
| | - Hui Xi
- College of Agriculture, Shihezi University, Shihezi, Xinjiang, China
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12
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Huang S, Zha X, Fu G. Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2891. [PMID: 37631103 PMCID: PMC10458011 DOI: 10.3390/plants12162891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.
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Affiliation(s)
- Shaolin Huang
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xinjie Zha
- Xi’an University of Finance and Economics, Xi’an 710100, China;
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
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13
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Elyamine AM, Wang H, Oummu-Kulthum MAH, Raissa S, Nahdhoit AR, Meng S, Tao P, Hu Z. Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105920. [PMID: 36931048 DOI: 10.1016/j.marenvres.2023.105920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r2 = 0.904), nitrogen (r2 = 0.72), phosphorus content (r2 = 0.62) and the water factor (r2 = 0.93). It was however highly and negatively correlated with the canopy cover (r2 = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China; Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Han Wang
- Huanhuai University, Zhumadian, 46000, China
| | | | - Sailine Raissa
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Ahamada Rachid Nahdhoit
- Institute of Graduate Studies, Fundamental and Industrial Microbiology, Istanbul University, 34134, Vezneciler Faith, Istanbul, Turkey
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China.
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14
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Zhang Y, Cao B, Pan Y, Tao S, Zhang N. Metabolite-Mediated Responses of Phyllosphere Microbiota to Rust Infection in Two Malus Species. Microbiol Spectr 2023; 11:e0383122. [PMID: 36916990 PMCID: PMC10101083 DOI: 10.1128/spectrum.03831-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/24/2023] [Indexed: 03/15/2023] Open
Abstract
Plants recruit beneficial microbes to enhance their ability to fight pathogens. However, the current understanding of microbial recruitment is largely limited to belowground systems (root exudates and the rhizosphere). It remains unclear whether the changes in leaf metabolites induced by infectious pathogens can actively recruit beneficial microbes to mitigate the growth of foliar pathogens. In this study, we integrated microbiome and metabolomic analyses to systematically explore the dynamics of phyllosphere fungal and bacterial communities and key leaf metabolites in two crabapple species (Malus sp. "Flame" and Malus sp. "Kelsey") at six stages following infection with Gymnosporangium yamadae. Our results showed that the phyllosphere microbiome changed during lesion expansion, as highlighted by a reduction in bacterial alpha-diversity and an increase in fungal alpha-diversity; a decreasing and then an increasing complexity of the microbial co-occurrence network was observed in Kelsey and a decreasing complexity occurred in Flame. In addition, nucleotide sugars, diarylheptanoids, and carboxylic acids with aromatic rings were more abundant in early stages of collection, which positively regulated the abundance of bacterial orders Pseudomonadales (in Kelsey), Acidimicrobiales, Bacillales, and Flavobacteriales (in Flame). In addition, metabolites such as flavonoids, lignin precursors, terpenoids, coumarins, and quaternary ammonium salts enriched with the expansion of lesions had a positive regulatory effect on fungal families Rhynchogastremataceae and Golubeviaceae (in Flame) and the bacterial order Actinomycetales (in Kelsey). Our findings highlight that plants may also influence phyllosphere microorganisms by adjusting leaf metabolites in response to biotic stress. IMPORTANCE Our findings demonstrate the response patterns of bacterial and fungal communities in the Malus phyllosphere to rust fungus G. yamadae infection, and they also reveal how the phyllosphere microbiome changes with the expansion of lesions. We identified several metabolites whose relative abundance varied significantly with lesion expansion. Using a framework for assessing the role of leaf metabolites in shaping the phyllosphere microbiome of the two Malus species, we identified several specific metabolites that have profoundly selective effects on the microbial community. In conclusion, our study provides new evidence of the ecological niche of the phyllosphere in supporting the "cry for help" strategy for plants.
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Affiliation(s)
- Yunxia Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Bin Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Yumei Pan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Siqi Tao
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
| | - Naili Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, Beijing Forestry University, Beijing, People’s Republic of China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan, People’s Republic of China
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15
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Douanla-Meli C, Moll J. Bark-inhabiting fungal communities of European chestnut undergo substantial alteration by canker formation following chestnut blight infection. Front Microbiol 2023; 14:1052031. [PMID: 36778875 PMCID: PMC9911167 DOI: 10.3389/fmicb.2023.1052031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Background Chestnut forests are severely threatened by chestnut blight caused by the fungal pathogen Cryphonectria parasitica and the infected trees exhibit bark canker in the later stage of the disease. European chestnut (Castanea sativa) is further infected by Gnomoniopsis smithogilvyi, another canker-causing fungal pathogen. We explored whether and how chestnut blight is reflected in bark-inhabiting fungal communities of European chestnut and also assessed the co-occurrence of C. parasitica and G. smithogilvyi. Materials and methods We initially investigated the fungal communities of European chestnut bark tissues and further monitored changes in these fungal communities with regard to disease progression from infection to canker formation by analyzing bark samples from asymptomatic trees, asymptomatic trees with latent C. parasitica infection, and infected trees with canker tissues, using amplicon sequencing of the ITS2 region of rDNA. Results The results showed that fungal community composition and diversity differed between the sample types. The fungal community composition was substantially reshaped by canker formation, whereas latent C. parasitica infection and more specifically pre-canker infection period per se had a weak effect. Fungal communities of canker samples was less diverse and more dissimilar to those of other sample types. C. parasitica dominated the mycobiome of canker samples, whereas G. smithogilvyi was found in only 9% of canker samples at very low abundances. However, G. smithogilvyi was a dominant fungus in the bark of healthy plants. Conclusion This study highlights that canker formation is the principal driver of decreasing diversity and altered composition of the mycobiome in bark tissues of European chestnut infected by C. parasitica infection. It additionally emphasizes the scarce co-occurrence of C. parasitica and G. smithogilvyi on European chestnut.
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Affiliation(s)
- Clovis Douanla-Meli
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for National and International Plant Health, Quedlinburg, Germany,*Correspondence: Clovis Douanla-Meli, ✉
| | - Julia Moll
- Department of Soil Ecology, Helmholtz Centre for Environmental Research-UFZ, Halle (Saale), Germany
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16
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Younginger BS, Stewart NU, Balkan MA, Ballhorn DJ. Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favouring a dominant fungus. Mol Ecol 2023; 32:244-257. [PMID: 36218009 DOI: 10.1111/mec.16732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 12/29/2022]
Abstract
Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centred on seed-reproducing hosts, while spore-reproducing plants also host endophytes and may be colonized by unique community members. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we explored endophytes in a single population of ferns, Polystichum munitum, in the Pacific Northwest. Through metabarcoding, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed in vitro competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously undescribed endophyte appears to abundantly colonize the host to the detriment of other microfungi. Competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, and inoculation onto sterile fern gametophytes did not alter growth compared to sterile controls, suggesting its effects are not antagonistic. The presence of this endophyte in the fern population probably demonstrates a case of repeated colonization driving competitive exclusion of other fungal community members.
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Affiliation(s)
| | - Nathan U Stewart
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Mehmet A Balkan
- Department of Biology, Portland State University, Portland, Oregon, USA
| | - Daniel J Ballhorn
- Department of Biology, Portland State University, Portland, Oregon, USA
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17
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Interaction between growth environment and host progeny shape fungal endophytic assemblages in transplanted Fagus sylvatica. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Afridi MS, Javed MA, Ali S, De Medeiros FHV, Ali B, Salam A, Sumaira, Marc RA, Alkhalifah DHM, Selim S, Santoyo G. New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:899464. [PMID: 36186071 PMCID: PMC9524194 DOI: 10.3389/fpls.2022.899464] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 08/08/2022] [Indexed: 07/30/2023]
Abstract
Plant microbiome (or phytomicrobiome) engineering (PME) is an anticipated untapped alternative strategy that could be exploited for plant growth, health and productivity under different environmental conditions. It has been proven that the phytomicrobiome has crucial contributions to plant health, pathogen control and tolerance under drastic environmental (a)biotic constraints. Consistent with plant health and safety, in this article we address the fundamental role of plant microbiome and its insights in plant health and productivity. We also explore the potential of plant microbiome under environmental restrictions and the proposition of improving microbial functions that can be supportive for better plant growth and production. Understanding the crucial role of plant associated microbial communities, we propose how the associated microbial actions could be enhanced to improve plant growth-promoting mechanisms, with a particular emphasis on plant beneficial fungi. Additionally, we suggest the possible plant strategies to adapt to a harsh environment by manipulating plant microbiomes. However, our current understanding of the microbiome is still in its infancy, and the major perturbations, such as anthropocentric actions, are not fully understood. Therefore, this work highlights the importance of manipulating the beneficial plant microbiome to create more sustainable agriculture, particularly under different environmental stressors.
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Affiliation(s)
| | - Muhammad Ammar Javed
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Sher Ali
- Department of Food Engineering, Faculty of Animal Science and Food Engineering, University of São Paulo (USP), São Paulo, Brazil
| | | | - Baber Ali
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Salam
- Zhejiang Key Laboratory of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sumaira
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Romina Alina Marc
- Food Engineering Department, Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
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19
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Roitsch T, Himanen K, Chawade A, Jaakola L, Nehe A, Alexandersson E. Functional phenomics for improved climate resilience in Nordic agriculture. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5111-5127. [PMID: 35727101 PMCID: PMC9440434 DOI: 10.1093/jxb/erac246] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
The five Nordic countries span the most northern region for field cultivation in the world. This presents challenges per se, with short growing seasons, long days, and a need for frost tolerance. Climate change has additionally increased risks for micro-droughts and water logging, as well as pathogens and pests expanding northwards. Thus, Nordic agriculture demands crops that are adapted to the specific Nordic growth conditions and future climate scenarios. A focus on crop varieties and traits important to Nordic agriculture, including the unique resource of nutritious wild crops, can meet these needs. In fact, with a future longer growing season due to climate change, the region could contribute proportionally more to global agricultural production. This also applies to other northern regions, including the Arctic. To address current growth conditions, mitigate impacts of climate change, and meet market demands, the adaptive capacity of crops that both perform well in northern latitudes and are more climate resilient has to be increased, and better crop management systems need to be built. This requires functional phenomics approaches that integrate versatile high-throughput phenotyping, physiology, and bioinformatics. This review stresses key target traits, the opportunities of latitudinal studies, and infrastructure needs for phenotyping to support Nordic agriculture.
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Affiliation(s)
- Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
- Department of Adaptive Biotechnologies, Global Change Research Institute, Czech Academy of Sciences, Brno, Czechia
| | - Kristiina Himanen
- National Plant Phenotyping Infrastructure, HiLIFE, University of Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Finland
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Laura Jaakola
- Climate laboratory Holt, Department of Arctic and Marine Biology, UiT the Arctic University of Norway, Tromsø, Norway
- NIBIO, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Ajit Nehe
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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20
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Amplicon Sequencing Reveals Novel Fungal Species Responsible for a Controversial Tea Disease. J Fungi (Basel) 2022; 8:jof8080782. [PMID: 35893150 PMCID: PMC9394346 DOI: 10.3390/jof8080782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/22/2022] [Accepted: 07/24/2022] [Indexed: 12/10/2022] Open
Abstract
Amplicon sequencing is a powerful tool for analyzing the fungal composition inside plants, whereas its application for the identification of etiology for plant diseases remains undetermined. Here, we utilize this strategy to clarify the etiology responsible for tea leaf brown-black spot disease (LBSD), a noticeable disease infecting tea plants etiology that remains controversial. Based on the ITS-based amplicon sequencing analysis, Didymella species were identified as separate from Pestalotiopsis spp. and Cercospora sp., which are concluded as the etiological agents. This was further confirmed by the fungal isolation and their specific pathogenicity on diverse tea varieties. Based on the morphologies and phylogenetic analysis constructed with multi-loci (ITS, LSU, tub2, and rpb2), two novel Didymella species—tentatively named D. theae and D. theifolia as reference to their host plants—were proposed and characterized. Here, we present an integrated approach of ITS-based amplicon sequencing in combination with fungal isolation and fulfillment of Koch’s postulates for etiological identification of tea plant disease, revealing new etiology for LBSD. This contributes useful information for further etiological identification of plant disease based on amplicon sequencing, as well as understanding, prevention, and management of this economically important disease.
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21
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Epstein B, Burghardt LT, Heath KD, Grillo MA, Kostanecki A, Hämälä T, Young ND, Tiffin P. Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis. Mol Ecol 2022. [PMID: 35793264 DOI: 10.1111/mec.16602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.
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Affiliation(s)
- Brendan Epstein
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Liana T Burghardt
- Department of Plant Sciences, The University of Pennsylvania, University Park, Pennsylvania, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Adam Kostanecki
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
| | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Nevin D Young
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA.,Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, USA
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22
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Adnan M, Islam W, Gang L, Chen HYH. Advanced research tools for fungal diversity and its impact on forest ecosystem. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:45044-45062. [PMID: 35460003 DOI: 10.1007/s11356-022-20317-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.
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Affiliation(s)
- Muhammad Adnan
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Waqar Islam
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liu Gang
- College of Life Sciences and Oceanography, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Han Y H Chen
- Faculty of Forestry and the Forest Environment, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada.
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23
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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24
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Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris). FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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First Report of Fungal Endophyte Communities and Non-Defensive Phytochemistry of Biocontrol-Inoculated Whitebark Pine Seedlings in a Restoration Planting. FORESTS 2022. [DOI: 10.3390/f13060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Plant endosymbionts (endophytes) influence host plant health and express genotype-dependent ecological relationships with plant hosts. A fungal species intended to confer host plant resistance to a forest pathogen was used as inoculum to test for effects of inoculation on disease resistance, microbiomes, and phytochemistry of a threatened pine species planted in a restoration setting. Correlations of inoculation presence/absence, phytochemistry, spatial location of seedlings, maternal seed sources, and fungal endophytic communities in the foliage of six-year-old whitebark pine (Pinus albicaulis) seedlings were assessed five years after an experimental inoculation of seedlings with foliar endophytic fungi cultured from whitebark pine trees at Crater Lake National Park, including Paramyrothecium roridum. We hypothesized that P. roridum would modify host microbiomes in a manner that combats white pine blister rust disease. Our assessment of seedlings in the field five years after inoculation allowed us to consider whether inoculation stimulated long-lasting changes in microbiome communities and whether effects varied by seedling genetic family. Tests for effects of endophyte inoculation on disease resistance were inconclusive due to current low levels of rust infection observed at the field site. Foliar fungal endophyte richness and Shannon diversity varied with maternal seed sources. Isotopic stoichiometry and phytochemistry did not vary with seedling spatial proximity, inoculation treatment, or maternal seed family. However, endophyte community composition varied with both seedling spatial proximity and maternal seed sources. Endophytic communities did not vary with the inoculation treatment, and the hypothesized biocontrol was not detected in inoculated seedlings. We draw three conclusions from this work: (1) fungal microbiomes of whitebark pine seedlings across our study site did not vary with host phytochemical signatures of ecophysiological status, (2) the inoculation of P. albicaulis seedlings with a mixture of fungal endophytes did not lead to persistent systemic changes in seedling foliar microbiomes, and (3) in correspondence with other studies, our data suggest that maternal seed source and spatial patterns influence fungal endophyte community composition.
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26
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Liu B, Ju Y, Xia C, Zhong R, Christensen MJ, Zhang X, Nan Z. The effect of Epichloë endophyte on phyllosphere microbes and leaf metabolites in Achnatherum inebrians. iScience 2022; 25:104144. [PMID: 35402863 PMCID: PMC8991375 DOI: 10.1016/j.isci.2022.104144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 01/09/2022] [Accepted: 03/21/2022] [Indexed: 11/21/2022] Open
Abstract
Upon exposure to the prevailing environment, leaves become increasingly colonized by fungi and bacteria located on the surface (epiphytic) or within (endophytic) the leaves. Many cool season grasses, including Achnatherum inebrians, host a seed-borne, intercellular, mutualistic Epichloë fungal endophyte, the growth of which is synchronized with the host grass. A study utilizing illumina sequencing was used to examine the epiphytic and endophytic microbial communities in Epichloë endophyte-infected and endophyte-free A. inebrians plants growing under hot dry field conditions. The presence of Epichloë endophyte increased the Shannon and decreased Simpson diversity of bacterial and fungal communities. Sphingomonas and Hymenobacter bacteria and Filobasidium and Mycosphaerella fungi were growing largely epiphytically, whereas Methylobacterium, Escherichia-Shigella, and the fungus Blumeria were mostly found within leaves with the location of colonization influenced by the Epichloë endophyte. In addition, leaf metabolites in Epichloë-infected and Epichloë-free leaves were examined using LC/MS. Epichloë was significantly correlated with 132 metabolites. Epichloë altered the composition and diversity of phyllosphere microbial communities 414 detected metabolites were annotated, of which the 132 differential metabolites There were 229 significant correlations between metabolites and microbial phyla
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Affiliation(s)
- Bowen Liu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Yawen Ju
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Chao Xia
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Rui Zhong
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | | | - Xingxu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiome, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, People's Republic of China
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27
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Soil Origin and Plant Genotype Modulate Switchgrass Aboveground Productivity and Root Microbiome Assembly. mBio 2022; 13:e0007922. [PMID: 35384699 PMCID: PMC9040762 DOI: 10.1128/mbio.00079-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Switchgrass (Panicum virgatum) is a model perennial grass for bioenergy production that can be productive in agricultural lands that are not suitable for food production. There is growing interest in whether its associated microbiome may be adaptive in low- or no-input cultivation systems. However, the relative impact of plant genotype and soil factors on plant microbiome and biomass are a challenge to decouple. To address this, a common garden greenhouse experiment was carried out using six common switchgrass genotypes, which were each grown in four different marginal soils collected from long-term bioenergy research sites in Michigan and Wisconsin. We characterized the fungal and bacterial root communities with high-throughput amplicon sequencing of the ITS and 16S rDNA markers, and collected phenological plant traits during plant growth, as well as soil chemical traits. At harvest, we measured the total plant aerial dry biomass. Significant differences in richness and Shannon diversity across soils but not between plant genotypes were found. Generalized linear models showed an interaction between soil and genotype for fungal richness but not for bacterial richness. Community structure was also strongly shaped by soil origin and soil origin × plant genotype interactions. Overall, plant genotype effects were significant but low. Random Forest models indicate that important factors impacting switchgrass biomass included NO3−, Ca2+, PO43−, and microbial biodiversity. We identified 54 fungal and 52 bacterial predictors of plant aerial biomass, which included several operational taxonomic units belonging to Glomeraceae and Rhizobiaceae, fungal and bacterial lineages that are involved in provisioning nutrients to plants.
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28
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Redondo MA, Oliva J, Elfstrand M, Boberg J, Capador-Barreto HD, Karlsson B, Berlin A. Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce. Environ Microbiol 2022; 24:3640-3654. [PMID: 35315253 PMCID: PMC9544151 DOI: 10.1111/1462-2920.15974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/28/2022]
Abstract
The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
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Affiliation(s)
- Miguel A Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Jonàs Oliva
- Department of Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, Lleida, 25198, Spain.,Joint Research Unit CTFC-AGROTECNIO, Alcalde Rovira Roure 191, Lleida, 25198, Spain
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Johanna Boberg
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Hernán D Capador-Barreto
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
| | - Bo Karlsson
- Skogforsk, Svalöv, Ekebo 2250, 268 90, Sweden
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Box 7026, 750 07, Sweden
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29
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Perreault R, Laforest-Lapointe I. Plant-microbe interactions in the phyllosphere: facing challenges of the anthropocene. THE ISME JOURNAL 2022; 16:339-345. [PMID: 34522008 PMCID: PMC8776876 DOI: 10.1038/s41396-021-01109-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
Global change is a defining feature of the Anthropocene, the current human-dominated epoch, and poses imminent threats to ecosystem dynamics and services such as plant productivity, biodiversity, and environmental regulation. In this era, terrestrial ecosystems are experiencing perturbations linked to direct habitat modifications as well as indirect effects of global change on species distribution and extreme abiotic conditions. Microorganisms represent an important reservoir of biodiversity that can influence macro-organisms as they face habitat loss, rising atmospheric CO2 concentration, pollution, global warming, and increased frequency of drought. Plant-microbe interactions in the phyllosphere have been shown to support plant growth and increase host resistance to biotic and abiotic stresses. Here, we review how plant-microbe interactions in the phyllosphere can influence host survival and fitness in the context of global change. We highlight evidence that plant-microbe interactions (1) improve urban pollution remediation through the degradation of pollutants such as ultrafine particulate matter, black carbon, and atmospheric hydrocarbons, (2) have contrasting impacts on plant species range shifts through the loss of symbionts or pathogens, and (3) drive plant host adaptation to drought and warming. Finally, we discuss how key community ecology processes could drive plant-microbe interactions facing challenges of the Anthropocene.
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Affiliation(s)
- Rosaëlle Perreault
- grid.86715.3d0000 0000 9064 6198Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada
| | - Isabelle Laforest-Lapointe
- grid.86715.3d0000 0000 9064 6198Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada ,grid.86715.3d0000 0000 9064 6198Centre Sève, Université de Sherbrooke, Sherbrooke, QC J1K 2R1 Canada
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30
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Bai HY, Zhang AY, Mei Y, Xu M, Lu XL, Dai CC, Jia Y. Effects of ectomycorrhizal fungus bolete identity on the community assemblages of endofungal bacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:852-861. [PMID: 34494716 DOI: 10.1111/1758-2229.13007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Ectomycorrhiza-associated bacteria, especially endofungal bacterial microbiota (EBM) in the fruiting body, play important roles in driving the establishment and function of ectomycorrhizae. However, the influence of ectomycorrhizal fungus bolete identity on their EBM is still unclear. We analysed the EBM of three different bolete fruiting body species on Thousand Island Lake, including Tylopilus felleus, Tylopilus areolatus and Boletus queletii, and compared them with their corresponding mycosphere soil bacterial microbiota by high-throughput sequencing. The EBM was classified into Bacillus, Pseudomonas, Burkholderia and Stenotrophomonas genera. Proteobacteria, Bacteroidetes and Acidobacteria were predominant in the EBM of bolete fruiting bodies as well as their mycosphere soil, while Firmicutes was significantly higher in the EBM. Moreover, the core microbiome (342 operational taxonomic units) of the EBM was shared among the three bolete fungal species. The relative abundances of gene families related to cell cycle control and nucleotide, coenzyme and lipid metabolism were significantly higher in the EBM than in the corresponding mycosphere soil bacterial microbiota, but there was no difference among the three different boletes. The results suggested that the host identity of ectomycorrhizal fungus boletes could affect the EBM, which might be mainly due to the selection of host fungi for the different functional EBM needed.
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Affiliation(s)
- Hong-Yan Bai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yan Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Man Xu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiao-Lin Lu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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31
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Faticov M, Abdelfattah A, Roslin T, Vacher C, Hambäck P, Blanchet FG, Lindahl BD, Tack AJM. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. THE NEW PHYTOLOGIST 2021; 231:1770-1783. [PMID: 33960441 DOI: 10.1111/nph.17434] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/15/2021] [Indexed: 05/13/2023]
Abstract
Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood. We used a multifactorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak Quercus robur across one growing season. Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially at the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming × genotype interactions on species richness and community composition. Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.
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Affiliation(s)
- Maria Faticov
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, A-8010, Austria
| | - Tomas Roslin
- Department of Ecology, Swedish University of Agricultural Sciences, PO Box 7044, Uppsala, SE-756 51, Sweden
| | | | - Peter Hambäck
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - F Guillaume Blanchet
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département de Mathématique, Faculté des Sciences, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke, QC, J1K 2R1, Canada
- Département des Sciences de la Santé Communautaire, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, QC, J1H 5N4, Canada
| | - Björn D Lindahl
- Department of Soil and Environment, Swedish University of Agricultural Sciences, PO Box 7014, Uppsala, SE-750 07, Sweden
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
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32
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O'Keeffe KR, Halliday FW, Jones CD, Carbone I, Mitchell CE. Parasites, niche modification and the host microbiome: A field survey of multiple parasites. Mol Ecol 2021; 30:2404-2416. [PMID: 33740826 DOI: 10.1111/mec.15892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 02/04/2021] [Accepted: 03/15/2021] [Indexed: 01/04/2023]
Abstract
Parasites can affect and be affected by the host's microbiome, with consequences for host susceptibility, parasite transmission, and host and parasite fitness. Yet, two aspects of the relationship between parasite infection and host microbiota remain little understood: the nature of the relationship under field conditions, and how the relationship varies among parasites. To overcome these limitations, we performed a field survey of the within-leaf fungal community in a tall fescue population. We investigated how diversity and composition of the fungal microbiome associate with natural infection by fungal parasites with different feeding strategies. A parasite's feeding strategy affects both parasite requirements of the host environment and parasite impacts on the host environment. We hypothesized that parasites that more strongly modify niches available within a host will be associated with greater changes in microbiome diversity and composition. Parasites with a feeding strategy that creates necrotic tissue to extract resources (necrotrophs) may not only have different niche requirements, but also act as particularly strong niche modifiers. Barcoded amplicon sequencing of the fungal ITS region revealed that leaf segments symptomatic of necrotrophs had lower fungal diversity and distinct composition compared to segments that were asymptomatic or symptomatic of other parasites. There were no clear differences in fungal diversity or composition between leaf segments that were asymptomatic and segments symptomatic of other parasite feeding strategies. Our results motivate future experimental work to test how the relationship between the microbiome and parasite infection is impacted by parasite feeding strategy and highlight the potential importance of parasite traits.
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Affiliation(s)
- Kayleigh R O'Keeffe
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Fletcher W Halliday
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Corbin D Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
| | - Charles E Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Environment, Ecology and Energy Program, University of North Carolina, Chapel Hill, NC, USA
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33
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Establishment of Regional Phytoremediation Buffer Systems for Ecological Restoration in the Great Lakes Basin, USA. I. Genotype × Environment Interactions. FORESTS 2021. [DOI: 10.3390/f12040430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Poplar remediation systems are ideal for reducing runoff, cleaning groundwater, and delivering ecosystem services to the North American Great Lakes and globally. We used phyto-recurrent selection (PRS) to establish sixteen phytoremediation buffer systems (phyto buffers) (buffer groups: 2017 × 6; 2018 × 5; 2019 × 5) throughout the Lake Superior and Lake Michigan watersheds comprised of twelve PRS-selected clones each year. We tested for differences in genotypes, environments, and their interactions for health, height, diameter, and volume from ages one to four years. All trees had optimal health. Mean first-, second-, and third-year volume ranged from 71 ± 26 to 132 ± 39 cm3; 1440 ± 575 to 5765 ± 1132 cm3; and 8826 ± 2646 to 10,530 ± 2110 cm3, respectively. Fourth-year mean annual increment of 2017 buffer group trees ranged from 1.1 ± 0.7 to 7.8 ± 0.5 Mg ha−1 yr−1. We identified generalist varieties with superior establishment across a broad range of buffers (‘DM114’, ‘NC14106’, ‘99038022’, ‘99059016’) and specialist clones uniquely adapted to local soil and climate conditions (‘7300502’, ‘DN5’, ‘DN34’, ‘DN177’, ‘NM2’, ‘NM5’, ‘NM6’). Using generalists and specialists enhances the potential for phytoremediation best management practices that are geographically robust, being regionally designed yet globally relevant.
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Bernard J, Wall CB, Costantini MS, Rollins RL, Atkins ML, Cabrera FP, Cetraro ND, Feliciano CKJ, Greene AL, Kitamura PK, Olmedo-Velarde A, Sirimalwatta VNS, Sung HW, Thompson LPM, Vu HT, Wilhite CJ, Amend AS. Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. THE ISME JOURNAL 2021; 15:999-1009. [PMID: 33188299 PMCID: PMC8115680 DOI: 10.1038/s41396-020-00826-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023]
Abstract
Plant microbiomes are shaped by forces working at different spatial scales. Environmental factors determine a pool of potential symbionts while host physiochemical factors influence how those microbes associate with distinct plant tissues. These scales are seldom considered simultaneously, despite their potential to interact. Here, we analyze epiphytic microbes from nine Hibiscus tiliaceus trees across a steep, but short, environmental gradient within a single Hawaiian watershed. At each location, we sampled eight microhabitats: leaves, petioles, axils, stems, roots, and litter from the plant, as well as surrounding air and soil. The composition of bacterial communities is better explained by microhabitat, while location better predicted compositional variance for fungi. Fungal community compositional dissimilarity increased more rapidly along the gradient than did bacterial composition. Additionally, the rates of fungal community compositional dissimilarity along the gradient differed among plant parts, and these differences influenced the distribution patterns and range size of individual taxa. Within plants, microbes were compositionally nested such that aboveground communities contained a subset of the diversity found belowground. Our findings indicate that both environmental context and microhabitat contribute to microbial compositional variance in our study, but that these contributions are influenced by the domain of microbe and the specific microhabitat in question, suggesting a complicated and potentially interacting dynamic.
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Affiliation(s)
- Jared Bernard
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christopher B. Wall
- grid.410445.00000 0001 2188 0957Hawai’i Institute of Marine Biology, University of Hawai’i–Mānoa, 46-007 Lilipuna Road, Kāneʻohe, HI 96744 USA ,grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Maria S. Costantini
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Randi L. Rollins
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA ,grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Melissa L. Atkins
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Feresa P. Cabrera
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Nicolas D. Cetraro
- grid.410445.00000 0001 2188 0957Pacific Biosciences Research Center, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Christian K. J. Feliciano
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Austin L. Greene
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Philip K. Kitamura
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Alejandro Olmedo-Velarde
- grid.410445.00000 0001 2188 0957Department of Plant and Environmental Protection Sciences, University of Hawai’i–Mānoa, 3050 Maile Way, Honolulu, HI 96822 USA
| | - Vithanage N. S. Sirimalwatta
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Helen W. Sung
- grid.410445.00000 0001 2188 0957Department of Biology, University of Hawai’i–Mānoa, 2538 McCarthy Mall, Honolulu, HI 96822 USA
| | - Leah P. M. Thompson
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
| | - Huong T. Vu
- grid.410445.00000 0001 2188 0957Department of Molecular Biosciences and Bioengineering, University of Hawai’i–Mānoa, 1955 East-West Road, Honolulu, HI 96822 USA
| | - Chad J. Wilhite
- grid.410445.00000 0001 2188 0957Department of Natural Resources and Environmental Management, University of Hawai’i–Mānoa, 1910 East-West Road, Honolulu, HI 96822 USA
| | - Anthony S. Amend
- grid.410445.00000 0001 2188 0957Department of Botany, University of Hawai’i–Mānoa, 3190 Maile Way, Honolulu, HI 96822 USA
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Host plant environmental filtering drives foliar fungal community assembly in symptomatic leaves. Oecologia 2021; 195:737-749. [PMID: 33582871 DOI: 10.1007/s00442-021-04849-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/03/2021] [Indexed: 12/21/2022]
Abstract
Foliar fungi (defined as all fungal species in leaves after surface sterilization; hereafter, 'FF') are of great importance to host plant growth and health, and can also affect ecosystem functioning. Despite this importance, few studies have explicitly examined the role of host filtering in shaping local FF communities, and we know little about the differences of FF community assembly between symptomatic (caused by fungal pathogens) and asymptomatic leaves, and whether there is phylogenetic congruence between host plants and FF. We examined FF communities from 25 host plant species (for each species, symptomatic and asymptomatic leaves, respectively) in an alpine meadow of the Tibetan Plateau using MiSeq sequencing of ITS1 gene biomarkers. We evaluated the phylogenetic congruence of FF-plant interactions based on cophylogenetic analysis, and examined α- and β-phylogenetic diversity indices of the FF communities. We found strong support for phylogenetic congruence between host plants and FF for both asymptomatic and symptomatic leaves, and a host-caused filter appears to play a major role in shaping FF communities. Most importantly, we provided independent lines of evidence that host environmental filtering (caused by fungal infections) outweighs competitive exclusion in driving FF community assembly in symptomatic leaves. Our results help strengthen the foundation of FF community assembly by demonstrating the importance of host environmental filtering in driving FF community assembly.
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Farner JE, Spear ER, Mordecai EA. Habitat type and interannual variation shape unique fungal pathogen communities on a California native bunchgrass. FUNGAL ECOL 2021; 48. [PMID: 33408755 DOI: 10.1016/j.funeco.2020.100983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The role of infectious disease in regulating host populations is increasingly recognized, but how environmental conditions affect pathogen communities and infection levels remains poorly understood. Over 3 y, we compared foliar disease burden, fungal pathogen community composition, and foliar chemistry in the perennial bunchgrass Stipa pulchra occurring in adjacent serpentine and nonserpentine grassland habitats with distinct soil types and plant communities. We found that serpentine and nonserpentine S. pulchra experienced consistent, low disease pressure associated with distinct fungal pathogen communities with high interannual species turnover. Additionally, plant chemistry differed with habitat type. The results indicate that this species experiences minimal foliar disease associated with diverse fungal communities that are structured across landscapes by spatially and temporally variable conditions. Distinct fungal communities associated with different growing conditions may shield S. pulchra from large disease outbreaks, contributing to the low disease burden observed on this and other Mediterranean grassland species.
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Affiliation(s)
- Johannah E Farner
- Biology Department, Stanford University, Stanford, California 94305 USA
| | - Erin R Spear
- Biology Department, Stanford University, Stanford, California 94305 USA.,Smithsonian Tropical Research Institute, Panama City, Panama, Republic of Panama
| | - Erin A Mordecai
- Biology Department, Stanford University, Stanford, California 94305 USA
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Barroso-Bergadà D, Pauvert C, Vallance J, Delière L, Bohan DA, Buée M, Vacher C. Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: Strengths and pitfalls. Mol Ecol Resour 2020; 21:762-780. [PMID: 33245839 DOI: 10.1111/1755-0998.13302] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/13/2020] [Indexed: 01/04/2023]
Abstract
Environmental DNA contains information on the species interaction networks that support ecosystem functions and services. Next-generation biomonitoring proposes the use of this data to reconstruct ecological networks in real time and then compute network-level properties to assess ecosystem change. We investigated the relevance of this proposal by assessing: (i) the replicability of DNA-based networks in the absence of ecosystem change, and (ii) the benefits and shortcomings of community- and network-level properties for monitoring change. We selected crop-associated microbial networks as a case study because they support disease regulation services in agroecosystems and analysed their response to change in agricultural practice between organic and conventional systems. Using two statistical methods of network inference, we showed that network-level properties, especially β-properties, could detect change. Moreover, consensus networks revealed robust signals of interactions between the most abundant species, which differed between agricultural systems. These findings complemented those obtained with community-level data that showed, in particular, a greater microbial diversity in the organic system. The limitations of network-level data included (i) the very high variability of network replicates within each system; (ii) the low number of network replicates per system, due to the large number of samples needed to build each network; and (iii) the difficulty in interpreting links of inferred networks. Tools and frameworks developed over the last decade to infer and compare microbial networks are therefore relevant to biomonitoring, provided that the DNA metabarcoding data sets are large enough to build many network replicates and progress is made to increase network replicability and interpretation.
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Affiliation(s)
- Didac Barroso-Bergadà
- INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
| | | | - Jessica Vallance
- INRAE, ISVV, SAVE, Villenave d'Ornon, France.,Bordeaux Sciences Agro, Univ. Bordeaux, SAVE, Gradignan, France
| | - Laurent Delière
- INRAE, ISVV, SAVE, Villenave d'Ornon, France.,INRAE, Vigne Bordeaux, Villenave d'Ornon, France
| | - David A Bohan
- INRAE, Université Bourgogne, Université Bourgogne Franche-Comté, Agroécologie, Dijon, France
| | - Marc Buée
- INRAE, Université de Lorraine, IAM, Champenoux, France
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Whitaker BK, Christian N, Chai Q, Clay K. Foliar fungal endophyte community structure is independent of phylogenetic relatedness in an Asteraceae common garden. Ecol Evol 2020; 10:13895-13912. [PMID: 33391689 PMCID: PMC7771118 DOI: 10.1002/ece3.6983] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 09/28/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Phylogenetic distance among host species represents a proxy for host traits that act as biotic filters to shape host-associated microbiome community structure. However, teasing apart potential biotic assembly mechanisms, such as host specificity or local species interactions, from abiotic factors, such as environmental specificity or dispersal barriers, in hyperdiverse, horizontally transmitted microbiomes remains a challenge. In this study, we tested whether host phylogenetic relatedness among 18 native Asteraceae plant species and spatial distance between replicated plots in a common garden affects foliar fungal endophyte (FFE) community structure. We found that FFE community structure varied significantly among host species, as well as host tribes, but not among host subfamilies. However, FFE community dissimilarity between host individuals was not significantly correlated with phylogenetic distance between host species. There was a significant effect of spatial distance among host individuals on FFE community dissimilarity within the common garden. The significant differences in FFE community structure among host species, but lack of a significant host phylogenetic effect, suggest functional differences among host species not accounted for by host phylogenetic distance, such as metabolic traits or phenology, may drive FFE community dissimilarity. Overall, our results indicate that host species identity and the spatial distance between plants can determine the similarity of their microbiomes, even across a single experimental field, but that host phylogeny is not closely tied to FFE community divergence in native Asteraceae.
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Affiliation(s)
| | - Natalie Christian
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Department of BiologyUniversity of LouisvilleLouisvilleKYUSA
| | - Qing Chai
- Department of BiologyIndiana UniversityBloomingtonINUSA
- School of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Keith Clay
- Department of BiologyIndiana UniversityBloomingtonINUSA
- Department of Ecology and Evolutionary BiologyTulane UniversityNew OrleansLAUSA
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39
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Katsoula A, Vasileiadis S, Sapountzi M, Karpouzas DG. The response of soil and phyllosphere microbial communities to repeated application of the fungicide iprodione: accelerated biodegradation or toxicity? FEMS Microbiol Ecol 2020; 96:5813261. [PMID: 32221586 DOI: 10.1093/femsec/fiaa056] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/23/2020] [Indexed: 12/30/2022] Open
Abstract
Pesticides interact with microorganisms in various ways with the outcome being negative or positive for the soil microbiota. Pesticides' effects on soil microorganisms have been studied extensively in soil but not in other pesticides-exposed microbial habitats like the phyllosphere. We tested the hypothesis that soil and phyllosphere support distinct microbial communities, but exhibit a similar response (accelerated biodegradation or toxicity) to repeated exposure to the fungicide iprodione. Pepper plants received four repeated foliage or soil applications of iprodione, which accelerated its degradation in soil (DT50_1st = 1.23 and DT50_4th = 0.48 days) and on plant leaves (DT50_1st > 365 and DT50_4th = 5.95 days). The composition of the epiphytic and soil bacterial and fungal communities, determined by amplicon sequencing, was significantly altered by iprodione. The archaeal epiphytic and soil communities responded differently; the former showed no response to iprodione. Three iprodione-degrading Paenarthrobacter strains were isolated from soil and phyllosphere. They hydrolyzed iprodione to 3,5-dichloraniline via the formation of 3,5-dichlorophenyl-carboxiamide and 3,5-dichlorophenylurea-acetate, a pathway shared by other soil-derived arthrobacters implying a phylogenetic specialization in iprodione biotransformation. Our results suggest that iprodione-repeated application could affect soil and epiphytic microbial communities with implications for the homeostasis of the plant-soil system and agricultural production.
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Affiliation(s)
- A Katsoula
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - S Vasileiadis
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - M Sapountzi
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
| | - Dimitrios G Karpouzas
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis 41500, Larissa, Greece
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40
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Küngas K, Bahram M, Põldmaa K. Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest. FEMS Microbiol Ecol 2020; 96:5673485. [PMID: 31825516 DOI: 10.1093/femsec/fiz199] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/10/2019] [Indexed: 01/21/2023] Open
Abstract
Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.
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Affiliation(s)
- Kati Küngas
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., EE51005 Tartu, Estonia
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
| | - Kadri Põldmaa
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St., EE51005 Tartu, Estonia
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41
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Chen J, Akutse KS, Saqib HSA, Wu X, Yang F, Xia X, Wang L, Goettel MS, You M, Gurr GM. Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors. Front Microbiol 2020; 11:1519. [PMID: 32760366 PMCID: PMC7373767 DOI: 10.3389/fmicb.2020.01519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
Endophytic fungi are important in diverse plant functions but knowledge of the factors that shape assemblages of these symbionts is lacking. Here, using a culture-dependent approach, we report 4,178 endophytic fungal isolates representing 16 orders isolated from stems, roots and leaves of three cruciferous plant species, Chinese cabbage (Brassica rapa L.), radish (Raphanus sativus L.) and white cabbage (B. olerocea L.), collected from 21 focal fields with different landscape contexts and pesticide uses during four seasons (summer, autumn, winter and spring). The colonization rate of fungi was found to be most strongly affected by season, plant identity and plant tissue. The colonization was highest during autumn, followed by summer, spring and lowest during winter. The colonization was highest in B. olerocea (53.2%), followed by B. rapa (42.6%), and lowest in R. sativus (35.0%). The colonization was highest in stems (51.9%) in all plant types, followed by leaves (42.4%) and roots (37.5%). Hypocreales was the dominant order (33.3% of all the isolates), followed by Glomerellales (26.5%), Eurotiales (12.1%), Pleosporales (9.8%) and Capnodiales (6.0%). Fungal endophyte abundance (number of isolates) followed the same pattern as colonization rate, while species richness varied with season and host plant tissue. Ordination analyses showed that the abundance and richness of Hypocreales, Eurotiales and Sordariales were associated with plant roots, while Capnodiales, Pleosporales and Trichosphaeriales were associated with spring. Other environmental factors, elevation, and the proportions of grassland, forest, orchard and waterbodies in the surrounding landscape also exerted effects within some categories of other main effects or for certain fungal taxa. Our results indicate that while fungal endophyte communities of crucifer crops vary strongly with the season, they are also strongly structured by plant identity and plant tissue, to a lesser extent by pesticide use and only weakly by landscape composition. The understanding of the ecological roles of fungal endophytes could contribute to habitat management and consequently improve crop pest management.
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Affiliation(s)
- Junhui Chen
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | | | - Hafiz Sohaib Ahmed Saqib
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Xiaolu Wu
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Feiying Yang
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Xiaofeng Xia
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Liande Wang
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Mark S. Goettel
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
| | - Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Graham Centre, Charles Sturt University, Orange, NSW, Australia
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42
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Mainland and island populations of Mussaenda kwangtungensis differ in their phyllosphere fungal community composition and network structure. Sci Rep 2020; 10:952. [PMID: 31969602 PMCID: PMC6976661 DOI: 10.1038/s41598-020-57622-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 01/03/2020] [Indexed: 01/12/2023] Open
Abstract
We compared community composition and co-occurrence patterns of phyllosphere fungi between island and mainland populations within a single plant species (Mussaenda kwangtungensis) using high-throughput sequencing technology. We then used 11 microsatellite loci for host genotyping. The island populations differed significantly from their mainland counterparts in phyllosphere fungal community structure. Topological features of co-occurrence network showed geographic patterns wherein fungal assemblages were less complex, but more modular in island regions than mainland ones. Moreover, fungal interactions and community composition were strongly influenced by the genetic differentiation of host plants. This study may advance our understanding of assembly principles and ecological interactions of phyllosphere fungal communities, as well as improve our ability to optimize fungal utilization for the benefit of people.
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Nilsson RH, Anslan S, Bahram M, Wurzbacher C, Baldrian P, Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat Rev Microbiol 2020; 17:95-109. [PMID: 30442909 DOI: 10.1038/s41579-018-0116-y] [Citation(s) in RCA: 404] [Impact Index Per Article: 101.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Fungi are major ecological players in both terrestrial and aquatic environments by cycling organic matter and channelling nutrients across trophic levels. High-throughput sequencing (HTS) studies of fungal communities are redrawing the map of the fungal kingdom by hinting at its enormous - and largely uncharted - taxonomic and functional diversity. However, HTS approaches come with a range of pitfalls and potential biases, cautioning against unwary application and interpretation of HTS technologies and results. In this Review, we provide an overview and practical recommendations for aspects of HTS studies ranging from sampling and laboratory practices to data processing and analysis. We also discuss upcoming trends and techniques in the field and summarize recent and noteworthy results from HTS studies targeting fungal communities and guilds. Our Review highlights the need for reproducibility and public data availability in the study of fungal communities. If the associated challenges and conceptual barriers are overcome, HTS offers immense possibilities in mycology and elsewhere.
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Affiliation(s)
- R Henrik Nilsson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
| | - Sten Anslan
- Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christian Wurzbacher
- Chair of Urban Water Systems Engineering, Technical University of Munich, Garching, Germany
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czech Republic
| | - Leho Tedersoo
- Natural History Museum of Tartu University, Tartu, Estonia
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44
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Maggi E, Bongiorni L, Fontanini D, Capocchi A, Dal Bello M, Giacomelli A, Benedetti‐Cecchi L. Artificial light at night erases positive interactions across trophic levels. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13485] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Elena Maggi
- Dip. di Biologia, CoNISMa Università di Pisa Pisa Italy
| | | | | | | | - Martina Dal Bello
- Physics of Living Systems Group Department of Physics Massachusetts Institute of Technology Cambridge MA USA
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45
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Fernandez-Conradi P, Fort T, Castagneyrol B, Jactel H, Robin C. Fungal endophyte communities differ between chestnut galls and surrounding foliar tissues. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.100876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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46
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Pellitier PT, Zak DR, Salley SO. Environmental filtering structures fungal endophyte communities in tree bark. Mol Ecol 2019; 28:5188-5198. [DOI: 10.1111/mec.15237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Peter T. Pellitier
- School for Environment and Sustainability University of Michigan Ann Arbor MI USA
| | - Donald R. Zak
- School for Environment and Sustainability University of Michigan Ann Arbor MI USA
- Department of Ecology & Evolutionary Biology University of Michigan Ann Arbor MI USA
| | - Sydney O. Salley
- School for Environment and Sustainability University of Michigan Ann Arbor MI USA
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Rainfall homogenizes while fruiting increases diversity of spore deposition in Mediterranean conditions. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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The needle mycobiome of Picea glauca – A dynamic system reflecting surrounding environment and tree phenological traits. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.05.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Bani A, Borruso L, Matthews Nicholass KJ, Bardelli T, Polo A, Pioli S, Gómez-Brandón M, Insam H, Dumbrell AJ, Brusetti L. Site-Specific Microbial Decomposer Communities Do Not Imply Faster Decomposition: Results from a Litter Transplantation Experiment. Microorganisms 2019; 7:microorganisms7090349. [PMID: 31547404 PMCID: PMC6780308 DOI: 10.3390/microorganisms7090349] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 12/28/2022] Open
Abstract
Microbes drive leaf litter decomposition, and their communities are adapted to the local vegetation providing that litter. However, whether these local microbial communities confer a significant home-field advantage in litter decomposition remains unclear, with contrasting results being published. Here, we focus on a litter transplantation experiment from oak forests (home site) to two away sites without oak in South Tyrol (Italy). We aimed to produce an in-depth analysis of the fungal and bacterial decomposer communities using Illumina sequencing and qPCR, to understand whether local adaptation occurs and whether this was associated with litter mass loss dynamics. Temporal shifts in the decomposer community occurred, reflecting changes in litter chemistry over time. Fungal community composition was site dependent, while bacterial composition did not differ across sites. Total litter mass loss and rates of litter decomposition did not change across sites. Litter quality influenced the microbial community through the availability of different carbon sources. Additively, our results do not support the hypothesis that locally adapted microbial decomposers lead to a greater or faster mass loss. It is likely that high functional redundancy within decomposer communities regulated the decomposition, and thus greater future research attention should be given to trophic guilds rather than taxonomic composition.
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Affiliation(s)
- Alessia Bani
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | | | - Tommaso Bardelli
- Department of Agrifood and Environmental Science, University of Florence, Piazzale delle Cascine 18, 50144 Florence, Italy.
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Andrea Polo
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - Silvia Pioli
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
| | - María Gómez-Brandón
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, E-36310 Vigo, Spain.
| | - Heribert Insam
- Institute of Microbiology, University of Innsbruck, Technikerstraβe 25d, 6020 Innsbruck, Austria.
| | - Alex J Dumbrell
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK.
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen/Bolzano, Piazza Università 5, 39100 Bolzano, Italy.
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Ricks KD, Koide RT. The role of inoculum dispersal and plant species identity in the assembly of leaf endophytic fungal communities. PLoS One 2019; 14:e0219832. [PMID: 31310633 PMCID: PMC6640817 DOI: 10.1371/journal.pone.0219832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/03/2019] [Indexed: 01/15/2023] Open
Abstract
Because of disturbance and plant species loss at the local level, many arid ecosystems in the western USA benefit from revegetation. There is a growing interest in improving revegetation success by purposefully inoculating revegetation plants with mutualistic endophytic fungi that increase plant stress tolerance. However, inoculant fungi must compete against fungi that indigenous to the habitat, many of which may not be mutualistic. Our overall goal, therefore, is to learn how to efficiently colonize revegetation plants using endophytic fungal inoculum. The goal will be facilitated by understanding the factors that limit colonization of plants by endophytic fungi, including inoculum dispersal and host compatibility. We analyzed endophytic fungal communities in leaves of Bromus tectorum and Elymus elymoides (Poaceae), Chrysothamnus depressus and Artemisia tridentata (Asteraceae), Alyssum alyssoides (Brassicaceae) and Atriplex canescens (Amaranthaceae), each occurring in each of 18 field plots. We found that dispersal limitation was significant for endophytic fungal communities of Atriplex canescens and Bromus tectorum, accounting for 9 and 17%, respectively, of the variation in endophytic fungal community structure, even though the maximum distance between plots was only 350 m. Plant species identity accounted for 33% of the variation in endophytic fungal community structure. These results indicate that the communities of endophytic fungi assembling in these plant species depend significantly on proximity to inoculum source as well as the identity of the plant species. Therefore, if endophytic fungi are to be used to facilitate revegetation by these plant species, land managers may find it profitable to consider both the proximity of inoculum to revegetation plants and the suitability of the inoculum to targeted host plant species.
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Affiliation(s)
- Kevin D. Ricks
- Department of Biology, Brigham Young University, Provo, UT, United States of America
| | - Roger T. Koide
- Department of Biology, Brigham Young University, Provo, UT, United States of America
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