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Lai Y, Ma J, Zhang X, Xuan X, Zhu F, Ding S, Shang F, Chen Y, Zhao B, Lan C, Unver T, Huo G, Li X, Wang Y, Liu Y, Lu M, Pan X, Yang D, Li M, Zhang B, Zhang D. High-quality chromosome-level genome assembly and multi-omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1833-1847. [PMID: 38363812 PMCID: PMC11182591 DOI: 10.1111/pbi.14305] [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: 03/29/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
High-quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi-C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein-coding genes and 1265 non-coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship with Salvia splendens and Salvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole-genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi-omics (integrated transcriptome and metabolome) analysis showed the tissue-specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up-regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments.
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Affiliation(s)
- Yong Lai
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Jinghua Ma
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | - Xiaobo Xuan
- Key Laboratory of Water Management and Water Security for Yellow River BasinMinistry of Water ResourcesZhengzhouHenanChina
| | - Fengyun Zhu
- School of Biological and Food Processing EngineeringHuanghuai UniversityZhumadianHenanChina
| | - Shen Ding
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Fude Shang
- College of Life ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Yuanyuan Chen
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | - Chen Lan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | | | - George Huo
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Ximei Li
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Yihan Wang
- College of Life ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Yufang Liu
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Mengfei Lu
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Xiaoping Pan
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Deshuang Yang
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Mingwan Li
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Baohong Zhang
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Dangquan Zhang
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
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2
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Yan S, Li J, Zhang Q, Jia S, Zhang Q, Wang R, Ju M, Gu P. Transcriptional Response of Wolfberry to Infestation with the Endophytic Fusarium nematophilum Strain NQ8GII4. PLANT DISEASE 2024; 108:1514-1525. [PMID: 38050402 DOI: 10.1094/pdis-07-23-1397-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Fusarium nematophilum NQ8GII4 is an endophytic fungus isolated from the root of healthy wolfberry (Lycium barbarum). Previous studies have reported that NQ8GII4 could dwell in wolfberry roots and enhance the defense responses in wolfberry against root rot, which is caused by F. oxysporum. To further elucidate the molecular mechanism of wolfberry disease resistance induced by NQ8GII4, in the present study, we adopted RNA sequencing analysis to profile the transcriptome of wolfberry response to NQ8GII4 infestation over a time course of 3 and 7 days postinoculation. Gene ontology enrichment analysis revealed that differentially expressed genes (DEGs) were enriched in biological regulation, response to stimulus, signaling, detoxification, immune system process, transporter activity, electron carrier activity, transcription factor activity, nucleic acid binding transcription factor, and antioxidant activity. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many of these DEGs were enriched in pathways related to plant-pathogen interactions, hormone signal transduction, and the phenylpropanoid biosynthesis pathway in wolfberry. This result suggested that innate immunity, phytohormone signaling, and numerous phenylpropanoid compounds comprise a complex defense network in wolfberry. Chloroplast 50S ribosomal proteins were consistently located at the core position of the response in wolfberry following infestation with NQ8GII4 analyzed by the protein-protein interaction network. This study elucidated the molecular mechanism underlying the interaction between NQ8GII4 and wolfberry, clarified the wolfberry immune response network to endophytic fungi infestation, identified candidate resistance genes in wolfberry, and provided a fundamental date for subsequent work.
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Affiliation(s)
- Siyuan Yan
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Jin Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qingchen Zhang
- Department of Pharmacotherapy and Translational Research, University of Florida, Gainesville, FL 32611, U.S.A
| | - Shuxin Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Qiangqiang Zhang
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Ruotong Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Mingxiu Ju
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
| | - Peiwen Gu
- College of Forestry and Prataculture, Ningxia University, Yinchuan 750021, China
- School of Agriculture, Ningxia University, Yinchuan 750021, China
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3
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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [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: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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4
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Dutta S, Houdinet G, NandaKafle G, Kafle A, Hawkes CV, Garcia K. Agrobacterium tumefaciens-mediated transformation of Nigrospora sp. isolated from switchgrass leaves and antagonistic toward plant pathogens. J Microbiol Methods 2023; 215:106849. [PMID: 37907117 DOI: 10.1016/j.mimet.2023.106849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Nigrospora is a diverse genus of fungi colonizing plants through endophytic, pathogenic, or saprobic interactions. Endophytic isolates can improve growth and development of host plants, as well as their resistance to microbial pathogens, but exactly how they do so remains poorly understood. Developing a reliable transformation method is crucial to investigate these mechanisms, in particular to identify pivotal genes for specific functions that correlate with specific traits. In this study, we identified eight isolates of Nigrospora sp. internally colonizing the leaves of switchgrass plants cultivated in North Carolina. Using an Agrobacterium tumefaciens-mediated transformation approach with control and GFP-expressing vectors, we report the first successful transformation of two Nigrospora isolates. Finally, we demonstrate that wild-type and transgenic isolates both negatively impact the growth of two plant pathogens in co-culture conditions, Bipolaris maydis and Parastagonospora nodorum, responsible for the Southern Leaf Blight and Septoria Nodorum Blotch diseases, respectively. The GFP-transformed strains developed here can therefore serve as accurate reporters of spatial interactions in future studies of Nigrospora and pathogens in the plant. Finally, the transformation method we describe lays the foundation for further genetic research on the Nigrospora genus to expand our mechanistic understanding of plant-endophyte interactions.
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Affiliation(s)
- Summi Dutta
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA; Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695, USA
| | - Gabriella Houdinet
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, USA
| | - Gitanjali NandaKafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Arjun Kafle
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27607, USA
| | - Kevin Garcia
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA.
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5
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Ndinga-Muniania C, Wornson N, Fulcher MR, Borer ET, Seabloom EW, Kinkel L, May G. Cryptic functional diversity within a grass mycobiome. PLoS One 2023; 18:e0287990. [PMID: 37471328 PMCID: PMC10358963 DOI: 10.1371/journal.pone.0287990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/17/2023] [Indexed: 07/22/2023] Open
Abstract
Eukaryotic hosts harbor tremendously diverse microbiomes that affect host fitness and response to environmental challenges. Fungal endophytes are prominent members of plant microbiomes, but we lack information on the diversity in functional traits affecting their interactions with their host and environment. We used two culturing approaches to isolate fungal endophytes associated with the widespread, dominant prairie grass Andropogon gerardii and characterized their taxonomic diversity using rDNA barcode sequencing. A randomly chosen subset of fungi representing the diversity of each leaf was then evaluated for their use of different carbon compound resources and growth on those resources. Applying community phylogenetic analyses, we discovered that these fungal endophyte communities are comprised of phylogenetically distinct assemblages of slow- and fast-growing fungi that differ in their use and growth on differing carbon substrates. Our results demonstrate previously undescribed and cryptic functional diversity in carbon resource use and growth in fungal endophyte communities of A. gerardii.
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Affiliation(s)
- Cedric Ndinga-Muniania
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Nicholas Wornson
- School of Statistics, University of Minnesota, Minneapolis, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Michael R Fulcher
- Foreign Disease-Weed Science Research Unit, United States Department of Agriculture, Frederick, Maryland, United States of America
| | - Elizabeth T Borer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Eric W Seabloom
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Linda Kinkel
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Pathology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Georgiana May
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
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Feng F, Sun X, Jiang W, Ma L, Wang Y, Sheng H, Li Y, Yu X. Stenotrophomonas pavanii DJL-M3 inoculated biochar stabilizes the rhizosphere soil homeostasis of carbendazim-stressed rice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121723. [PMID: 37105458 DOI: 10.1016/j.envpol.2023.121723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Plant-microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3-biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice.
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Affiliation(s)
- Fayun Feng
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xing Sun
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wenqi Jiang
- School of Environment, Nanjing University, Nanjing, 210014, China
| | - Liya Ma
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Ya Wang
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Honjie Sheng
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yong Li
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xiangyang Yu
- Institute of Food Safety and Nutrition, Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Sinha S, Thakuria D, Chaliha C, Uzir P, Hazarika S, Dutta P, Singh AK, Laloo B. Plant growth-promoting traits of culturable seed microbiome of citrus species from Purvanchal Himalaya. FRONTIERS IN PLANT SCIENCE 2023; 14:1104927. [PMID: 37492766 PMCID: PMC10365123 DOI: 10.3389/fpls.2023.1104927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/30/2023] [Indexed: 07/27/2023]
Abstract
Despite Northeastern India being "Treasure House of Citrus Genetic Wealth," genetic erosion of citrus diversity poses severe concern with a corresponding loss in seed microbial diversity. The seed microbiome of citrus species unique to the Purvanchal Himalaya is seldom explored for their use in sustainable orchard management. Isolation and characterization of culturable seed microbiomes of eight citrus species, namely, Citrus reticulata Blanco, C. grandis (L.) Osbeck, C. latipes Tanaka, C. megaloxycarpa Lushaigton, C. jambhiri Lush, C. sinensis (L.) Osbeck, C. macroptera Montr, and C. indica Tanaka collected from NE India were carried out. The isolates were then screened for an array of plant growth-promoting (PGP) traits [indole acetic acid (IAA) production, N2 fixation, phosphate and zinc complex dissolution, siderophores, and Hydrogen Cyanide (HCN) production]. The pure culture isolates of seed microbiomes were capable of dissolving insoluble Ca3(PO4)2 (1.31-4.84 µg Pi ml-1 h-1), Zn3(PO4)2 (2.44-3.16 µg Pi ml-1 h-1), AlPO4 (1.74-3.61 µg Pi ml-1 h-1), and FePO4 (1.54-4.61µg Pi ml-1 h-1), mineralized phytate (12.17-18.00 µg Pi ml-1 h-1) and produced IAA-like substances (4.8-187.29 µg ml-1 h-1). A few isolates of the seed microbiome were also able to fix nitrogen, secrete siderophore-like compounds and HCN, and dissolve ZnSO4 and ZnO. The 16S ribosomal Ribonucleic Acid (rRNA)-based taxonomic findings revealed that Bacillus was the most dominant genus among the isolates across citrus species. Isolates CG2-1, CME6-1, CME6-4, CME6-5, CME6-9, CJ7-1, CMA10-1, CI11-3, and CI11-4 were identified as promising bioinoculants for development of microbial consortium having multifaceted PGP traits for nutritional benefits of nitrogen, phosphorus and zinc, and IAA hormonal benefits to citrus crops for better fitness in acid soils.
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Affiliation(s)
- Sakshi Sinha
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Dwipendra Thakuria
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Chayanika Chaliha
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Panchali Uzir
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Samarendra Hazarika
- Division of System Research and Engineering, Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Umiam, Meghalaya, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - A. K. Singh
- School of Natural Resource Management, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Bingiala Laloo
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
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Ricks KD, Yannarell AC. Soil moisture incidentally selects for microbes that facilitate locally adaptive plant response. Proc Biol Sci 2023; 290:20230469. [PMID: 37357863 PMCID: PMC10291722 DOI: 10.1098/rspb.2023.0469] [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: 02/24/2023] [Accepted: 06/01/2023] [Indexed: 06/27/2023] Open
Abstract
While a plant's microbiome can facilitate adaptive phenotypes, the plant's role in selecting for these microbes is unclear. Do plants actively recruit microbes beneficial to their current environment, or are beneficial microbes only an incidental by-product of microbial adaptation? We addressed these questions through a multigeneration greenhouse experiment, selecting for either dry- or wet-adapted soil microbial communities, either with or without plants. After three plant generations, we conducted a full reciprocal transplant of each soil community onto wet- and dry-treated plants. We found that plants generally benefited from soil microbes, and this benefit was greater whenever their current watering conditions matched the microbes' historical watering conditions. Principally, the plant's presence was not necessary in the historical treatments for this environmental matching benefit to emerge. Moreover, we found microbes from droughted soils could better tolerate drought stress. Taken together, these results suggest that the moisture environment selects for microbes that benefit plants under those specific moisture conditions, and that these beneficial properties arise as a by-product of microbial adaptation to the watering environment and not as a co-adapting plant-microbe system. This work highlights that understanding the selective agents on these plant-associated microbes will lead to a better understanding of plant adaptation.
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Affiliation(s)
- Kevin D. Ricks
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Anthony C. Yannarell
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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10
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Addison S, Armstrong C, Wigley K, Hartley R, Wakelin S. What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata. ENVIRONMENTAL MICROBIOME 2023; 18:45. [PMID: 37254222 DOI: 10.1186/s40793-023-00507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p < 0.005). Bacterial and fungal phyllosphere microbiome richness was lowest in samples from the top of the canopy, subsequently increasing in the middle and then bottom canopy samples. These differences maybe driven by either by (1) exchange of microbiomes with the forest floor and soil with the lower foliage, (2) strong ecological filtering in the upper canopy via environmental exposure (e.g., UV), (3) canopy density, (4) or combinations of factors. Most taxa present in the top canopy were also present lower in tree; as such, sampling strategies focussing on lower canopy sampling should provide good overall phyllosphere microbiome coverage for the tree. The dominant phyllosphere bacteria were Alpha-proteobacteria (Rhizobiales and Sphingomonas) along with Acidobacteria Gp1. However, the P. radiata phyllosphere microbiome samples were fungal dominated. From the top canopy samples, Arthoniomycetes and Dothideomycetes were highly represented, with abundances of Arthoniomycetes then reducing in lower canopy samples whilst abundances of Ascomycota increased. The most abundant fungal taxa were Phaeococcomyces (14.4% of total reads) and Phaeotheca spp. (10.38%). A second-order effect of canopy sampling direction was evident in bacterial community composition (p = 0.01); these directional influences were not evident for fungal communities. However, sterilisation of needles did impact fungal community composition (p = 0.025), indicating potential for community differences in the endosphere versus leaf surface compartments. Needle age was only important in relation to bacterial communities, but was canopy height dependant (interaction p = 0.008). By building an understanding of the primary and secondary factors related to intra-canopy phyllosphere microbiome variation, we provide a sampling framework to either explicitly minimise or capture variation in needle collection to enable ongoing ecological studies targeted at inter-canopy or other experimental levels.
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Affiliation(s)
| | | | | | | | - Steven Wakelin
- Scion, P.O. Box 29237, Riccarton, Christchurch, 8440, New Zealand.
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11
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Papik J, Strejcek M, Musilova L, Guritz R, Leewis MC, Leigh MB, Uhlik O. Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons. Microbiol Spectr 2023; 11:e0444822. [PMID: 36975310 PMCID: PMC10100700 DOI: 10.1128/spectrum.04448-22] [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: 11/01/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.
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Affiliation(s)
- Jakub Papik
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Michal Strejcek
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Lucie Musilova
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
| | - Rodney Guritz
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Mary-Cathrine Leewis
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Agriculture and Agri-Food Canada, Quebec, Quebec, Canada
| | - Mary Beth Leigh
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, Alaska, USA
- Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, Alaska, USA
| | - Ondrej Uhlik
- University of Chemistry, and Technology, Prague, Faculty of Food and Biochemical Technology, Department of Biochemistry and Microbiology, Prague, Czech Republic
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12
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Macaya-Sanz D, Witzell J, Collada C, Gil L, Martín JA. Core endophytic mycobiome in Ulmus minor and its relation to Dutch elm disease resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1125942. [PMID: 36925756 PMCID: PMC10011445 DOI: 10.3389/fpls.2023.1125942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The core microbiota of plants exerts key effects on plant performance and resilience to stress. The aim of this study was to identify the core endophytic mycobiome in U. minor stems and disentangle associations between its composition and the resistance to Dutch elm disease (DED). We also defined its spatial variation within the tree and among distant tree populations. Stem samples were taken i) from different heights of the crown of a 168-year-old elm tree, ii) from adult elm trees growing in a common garden and representing a gradient of resistance to DED, and iii) from trees growing in two distant natural populations, one of them with varying degrees of vitality. Endophyte composition was profiled by high throughput sequencing of the first internal transcribed spacer region (ITS1) of the ribosomal DNA. Three families of yeasts (Buckleyzymaceae, Trichomeriaceae and Bulleraceae) were associated to DED-resistant hosts. A small proportion (10%) of endophytic OTUs was almost ubiquitous throughout the crown while tree colonization by most fungal taxa followed stochastic patterns. A clear distinction in endophyte composition was found between geographical locations. By combining all surveys, we found evidence of a U. minor core mycobiome, pervasive within the tree and ubiquitous across locations, genotypes and health status.
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Affiliation(s)
- David Macaya-Sanz
- Departamento de Ecología y Genética Forestal, Instituto de Ciencias Forestales (ICIFOR-INIA), CSIC, Madrid, Spain
| | - Johanna Witzell
- Department of Forestry and Wood Technology, Linnaeus University, Växjö, Sweden
| | - Carmen Collada
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería (ETSI) Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Luis Gil
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería (ETSI) Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Juan A. Martín
- Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería (ETSI) Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
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13
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Vivelo S, Alsairafi B, Walsh JT, Bhatnagar JM. Intrinsic growth rate and cellobiohydrolase activity underlie the phylogenetic signal to fungal decomposer succession. FUNGAL ECOL 2023. [DOI: 10.1016/j.funeco.2022.101180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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14
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Bolin LG, Lennon JT, Lau JA. Traits of soil bacteria predict plant responses to soil moisture. Ecology 2023; 104:e3893. [PMID: 36208193 DOI: 10.1002/ecy.3893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/02/2022] [Accepted: 09/09/2022] [Indexed: 02/03/2023]
Abstract
Microorganisms can help plants and animals contend with abiotic stressors, but why they provide such benefits remains unclear. Here we investigated byproduct benefits, which occur when traits that increase the fitness of one species provide incidental benefits to another species with no direct cost to the provider. In a greenhouse experiment, microbial traits predicted plant responses to soil moisture such that bacteria with self-beneficial traits in drought increased plant early growth, size at reproduction, and chlorophyll concentration under drought, while bacteria with self-beneficial traits in well-watered environments increased these same plant traits in well-watered soils. Thus, microbial traits that promote microbial success in different moisture environments also promote plant success in these same environments. Our results demonstrate that byproduct benefits, a concept developed to explain the evolution of cooperation in pairwise mutualisms, can also extend to interactions between plants and nonsymbiotic soil microbes.
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Affiliation(s)
- Lana G Bolin
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Jennifer A Lau
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Environmental Resilience Institute, Indiana University, Bloomington, Indiana, USA
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15
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Nasif SO, Siddique AB, Siddique AB, Islam MM, Hassan O, Deepo DM, Hossain A. Prospects of endophytic fungi as a natural resource for the sustainability of crop production in the modern era of changing climate. Symbiosis 2022. [DOI: 10.1007/s13199-022-00879-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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16
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Bastías DA, Balestrini R, Pollmann S, Gundel PE. Environmental interference of plant-microbe interactions. PLANT, CELL & ENVIRONMENT 2022; 45:3387-3398. [PMID: 36180415 PMCID: PMC9828629 DOI: 10.1111/pce.14455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Environmental stresses can compromise the interactions of plants with beneficial microbes. In the present review, experimental results showing that stresses negatively affect the abundance and/or functionality of plant beneficial microbes are summarized. It is proposed that the environmental interference of these plant-microbe interactions is explained by the stress-mediated induction of plant signalling pathways associated with defence hormones and reactive oxygen species. These plant responses are recognized to regulate beneficial microbes within plants. The direct negative effect of stresses on microbes may also contribute to the environmental regulation of these plant mutualisms. It is also posited that, in stress situations, beneficial microbes harbour mechanisms that contribute to maintain the mutualistic associations. Beneficial microbes produce effector proteins and increase the antioxidant levels in plants that counteract the detrimental effects of plant stress responses on them. In addition, they deliver specific stress-protective mechanisms that assist to their plant hosts to mitigate the negative effects of stresses. Our study contributes to understanding how environmental stresses affect plant-microbe interactions and highlights why beneficial microbes can still deliver benefits to plants in stressful environments.
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Affiliation(s)
- Daniel A. Bastías
- AgResearch LimitedGrasslands Research CentrePalmerston NorthNew Zealand
| | | | - Stephan Pollmann
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentación (INIA/CSIC)Campus de MontegancedoMadridSpain
- Departamento de Biotecnología‐Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de BiosistemasUniversidad Politécnica de Madrid (UPM)MadridSpain
| | - Pedro E. Gundel
- IFEVA, CONICET, Universidad de Buenos AiresFacultad de AgronomíaBuenos AiresArgentina
- Centro de Ecología Integrativa, Instituto de Ciencias BiológicasUniversidad de TalcaTalcaChile
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17
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Colón Carrión N, Troche CL, Arnold AE. Communities of endophytic fungi in a Puerto Rican rainforest vary along a gradient of disturbance due to Hurricane Maria. Ecol Evol 2022; 12:e9618. [PMID: 36532133 PMCID: PMC9750846 DOI: 10.1002/ece3.9618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/18/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
Increases in the frequency and intensity of hurricanes influence the structure, function, and resilience of Caribbean forests. Trees in such forests harbor diverse fungal endophytes within leaves and roots. Fungal endophytes often are important for plant health and stress responses, but how their communities are impacted by hurricanes is not well known. We measured forest disturbance in Carite State Forest in Puerto Rico ca. 16 months after the passage of Hurricane Maria, a Category 4 storm. In three sites, each comprising three plots representing a local gradient of hurricane disturbance, we evaluated soil chemistry and used culture-free analyses to measure richness, phylogenetic diversity, and composition of endophyte communities in leaves and roots. We found that endophyte richness did not vary significantly among plant families or as a function of soil chemistry. Instead, leaf endophytes peaked in richness and decreased in phylogenetic diversity at intermediate levels of disturbance. Root endophytes did not show such variation, but both leaf- and root endophyte communities differed in species composition as a function of disturbance across the forest. Locations with less disturbance typically hosted distinctive assemblages of foliar endophytes, whereas more disturbed locations had more regionally homogeneous endophyte communities. Together, our results show that changes in endophyte richness and phylogenetic diversity can be detected in aboveground tissues more than a year after major storms. In turn, pervasive shifts in endophyte community composition both aboveground and belowground suggest a subtle and lasting effect of hurricanes that merits further study, potentially contributing to the promotion of spatially heterogeneous endophyte assemblages at a landscape scale in these diverse island forests.
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Affiliation(s)
| | | | - A. Elizabeth Arnold
- School of Plant SciencesUniversity of ArizonaTucsonArizonaUSA
- Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
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18
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Chang CH, Lee YC, Hsiao G, Chang LK, Chi WC, Cheng YC, Huang SJ, Wang TC, Lu YS, Lee TH. Anti-Epstein-Barr Viral Agents from the Medicinal Herb-Derived Fungus Alternaria alstroemeriae Km2286. JOURNAL OF NATURAL PRODUCTS 2022; 85:2667-2674. [PMID: 36346918 DOI: 10.1021/acs.jnatprod.2c00783] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chromatographic separation on the liquid-state fermented products produced by the fungal strain Alternaria alstroemeriae Km2286 isolated from the littoral medicinal herb Atriplex maximowicziana Makino resulted in the isolation of compounds 1-9. Structures were determined by spectroscopic analysis as four undescribed perylenequinones, altertromins A-D (1-4), along with altertoxin IV (5), altertoxin VIII (6), stemphyperylenol (7), tenuazonic acid (8), and allo-tenuazonic acid (9). Compounds 1-6 exhibited antiviral activities against Epstein-Barr virus (EBV) with EC50 values ranging from 0.17 ± 0.07 to 3.13 ± 0.31 μM and selectivity indices higher than 10. In an anti-neuroinflammatory assay, compounds 1-4, 6, and 7 showed inhibitory activity of nitric oxide production in lipopolysaccharide-induced microglial BV-2 cells, with IC50 values ranging from 0.33 ± 0.04 to 4.08 ± 0.53 μM without significant cytotoxicity. This is the first report to describe perylenequinone-type compounds with potent anti-EBV and anti-neuroinflammatory activities.
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Affiliation(s)
- Chia-Hao Chang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Chieh Lee
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | - George Hsiao
- Department of Pharmacology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Li-Kwan Chang
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Wei-Chiung Chi
- Department of Food Science, National Quemoy University, Kinmen 89250, Taiwan
| | - Yuan-Chung Cheng
- Department of Chemistry and Center for Quantum Science and Engineering, National Taiwan University, Taipei 10617, Taiwan
| | - Shu-Jung Huang
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tai-Chou Wang
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Yi-Shan Lu
- Department of Biochemical Science and Technology, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Tzong-Huei Lee
- Institute of Fisheries Science, National Taiwan University, Taipei 10617, Taiwan
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19
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Wang Z, Liu J, White JF, Li C. Epichloë bromicola from wild barley improves salt-tolerance of cultivated barley by altering physiological responses to salt stress. Front Microbiol 2022; 13:1044735. [PMID: 36504776 PMCID: PMC9730248 DOI: 10.3389/fmicb.2022.1044735] [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: 09/15/2022] [Accepted: 11/02/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Epichloë bromicola is a cultivable fungal endophyte that lives in symbiosis with wild barley (Hordeum brevisubulatum) to which it confers salt tolerance. This study tested the hypothesis that E. bromicola derived from wild barley has the potential to increase salt tolerance in cultivated barley under salt stress. Methods To test this hypothesis, the growth response, physiological parameters, and metabolic profiles of barley plants inoculated with E. bromicola (E+) and those not inoculated with E. bromicola (E-) were compared under salt stress. Results Compared with E- barley plants, E+ barley plants had significantly increased plant height, shoot biomass, total biomass, chlorophyll content, osmotic synthesis, and accumulation of stress adaptation metabolites. E. bromicola increased the salt stress tolerance of cultivated barley, and the positive effects correlated with different salt stress conditions. Discussion These results suggest that E. bromicola has promising potential for enhancing the salt tolerance of barley. New insights into the mechanisms underlying this barley-fungal endophyte association are provided, and interesting questions regarding the role of E. bromicola in fungus-enhanced tolerance to salt stress in this symbiosis are raised.
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Affiliation(s)
- Zhengfeng Wang
- Economic Crops and Malt Barley Research Institute, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Jing Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, Gansu Tech Innovation Center of Western China Grassland Industry, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - James F. White
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, United States
| | - Chunjie Li
- Grassland Research Center of National Forestry and Grassland Administration, Chinese Academy of Forestry Sciences, Beijing, China,*Correspondence: Chunjie Li
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Kumari M, Qureshi KA, Jaremko M, White J, Singh SK, Sharma VK, Singh KK, Santoyo G, Puopolo G, Kumar A. Deciphering the role of endophytic microbiome in postharvest diseases management of fruits: Opportunity areas in commercial up-scale production. FRONTIERS IN PLANT SCIENCE 2022; 13:1026575. [PMID: 36466226 PMCID: PMC9716317 DOI: 10.3389/fpls.2022.1026575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
As endophytes are widely distributed in the plant's internal compartments and despite having enormous potential as a biocontrol agent against postharvest diseases of fruits, the fruit-endophyte-pathogen interactions have not been studied detail. Therefore, this review aims to briefly discuss the colonization patterns of endophytes and pathogens in the host tissue, the diversity and distribution patterns of endophytes in the carposphere of fruits, and host-endophyte-pathogen interactions and the molecular mechanism of the endophytic microbiome in postharvest disease management in fruits. Postharvest loss management is one of the major concerns of the current century. It is considered a critical challenge to food security for the rising global population. However, to manage the postharvest loss, still, a large population relies on chemical fungicides, which affect food quality and are hazardous to health and the surrounding environment. However, the scientific community has searched for alternatives for the last two decades. In this context, endophytic microorganisms have emerged as an economical, sustainable, and viable option to manage postharvest pathogens with integral colonization properties and eliciting a defense response against pathogens. This review extensively summarizes recent developments in endophytic interactions with harvested fruits and pathogens-the multiple biocontrol traits of endophytes and colonization and diversity patterns of endophytes. In addition, the upscale commercial production of endophytes for postharvest disease treatment is discussed.
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Affiliation(s)
- Madhuree Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kamal A. Qureshi
- Department of Pharmaceutics, Unaizah College of Pharmacy, Qassim University, Unaizah, Saudi Arabia
| | - Mariusz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (R.S.R.C.), Division of Biological and Environmental Sciences and Engineering (B.E.S.E.), King Abdullah University of Science and Technology (K.A.U.S.T.), Thuwal, Saudi Arabia
| | - James White
- Department of Plant Biology, Rutgers University, The State University of New Jersey, New Brunswick, NJ, United States
| | - Sandeep Kumar Singh
- Division of Microbiology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Vijay Kumar Sharma
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mexico
| | - Gerardo Puopolo
- Center Agriculture Food Environment, University of Trento, Trentino, TN, Italy
| | - Ajay Kumar
- Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India
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21
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Tran T, French E, Iyer-Pascuzzi AS. In vitro functional characterization predicts the impact of bacterial root endophytes on plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5758-5772. [PMID: 35596672 DOI: 10.1093/jxb/erac228] [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: 12/15/2021] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Utilizing beneficial microbes for crop improvement is one strategy to achieve sustainable agriculture. However, identifying microbial isolates that promote crop growth is challenging, in part because using bacterial taxonomy to predict an isolate's effect on plant growth may not be reliable. The overall aim of this work was to determine whether in vitro functional traits of bacteria were predictive of their in planta impact. We isolated 183 bacterial endophytes from field-grown roots of two tomato species, Solanum lycopersicum and S. pimpinellifolium. Sixty isolates were screened for six in vitro functional traits: auxin production, siderophore production, phosphate solubilization, antagonism to a soilborne pathogen, and the presence of two antimicrobial metabolite synthesis genes. Hierarchical clustering of the isolates based on the in vitro functional traits identified several groups of isolates sharing similar traits. We called these groups 'functional groups'. To understand how in vitro functional traits of bacteria relate to their impact on plants, we inoculated three isolates from each of the functional groups on tomato seedlings. Isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy. Together, our results demonstrate the importance of examining root endophyte functions for improving crop production.
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Affiliation(s)
- Tri Tran
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Elizabeth French
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Anjali S Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA
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22
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Byregowda R, Prasad SR, Oelmüller R, Nataraja KN, Prasanna Kumar MK. Is Endophytic Colonization of Host Plants a Method of Alleviating Drought Stress? Conceptualizing the Hidden World of Endophytes. Int J Mol Sci 2022; 23:ijms23169194. [PMID: 36012460 PMCID: PMC9408852 DOI: 10.3390/ijms23169194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/13/2022] [Indexed: 11/16/2022] Open
Abstract
In the wake of changing climatic conditions, plants are frequently exposed to a wide range of biotic and abiotic stresses at various stages of their development, all of which negatively affect their growth, development, and productivity. Drought is one of the most devastating abiotic stresses for most cultivated crops, particularly in arid and semiarid environments. Conventional breeding and biotechnological approaches are used to generate drought-tolerant crop plants. However, these techniques are costly and time-consuming. Plant-colonizing microbes, notably, endophytic fungi, have received increasing attention in recent years since they can boost plant growth and yield and can strengthen plant responses to abiotic stress. In this review, we describe these microorganisms and their relationship with host plants, summarize the current knowledge on how they “reprogram” the plants to promote their growth, productivity, and drought tolerance, and explain why they are promising agents in modern agriculture.
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Affiliation(s)
- Roopashree Byregowda
- Department of Seed Science and Technology, University of Agricultural Sciences, Bangalore 560065, India
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
| | | | - Ralf Oelmüller
- Department of Plant Physiology, Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich-Schiller-University, 07743 Jena, Germany
- Correspondence:
| | - Karaba N. Nataraja
- Department of Crop Physiology, University of Agricultural Sciences, Bangalore 560065, India
| | - M. K. Prasanna Kumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore 560065, India
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Rivera-Vega LJ, Zhou W, Buchman LW, Valencia CU, Jack ALH, Castillo Lopez D, Sword GA. Plant-associated fungi affect above- and belowground pest responses to soybean plants. J Appl Microbiol 2022; 133:422-435. [PMID: 35352442 DOI: 10.1111/jam.15554] [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: 11/30/2021] [Revised: 02/22/2022] [Accepted: 03/26/2022] [Indexed: 11/28/2022]
Abstract
AIM The objective of this research was to screen fungal isolates originally isolated from cotton plants and measure their effects on the interactions between soybean and two aboveground pests (cabbage looper; Trichoplusia ni and soybean looper; Chrysodeixis includens) as well as a belowground pest (soybean cyst nematode; Heterodera glycines). METHODS AND RESULTS For aboveground pests, we measured the leaf area consumed and larval weight. For our belowground pest tests, we measured shoot height, shoot fresh weight, root fresh weight and number of cysts. Out of the 50 fungal isolates tested, we tested 30 fungi in the interaction with cabbage looper, 36 for soybean looper, 41 for soybean cyst nematode. We tested 23 isolates against all pests and identified multiple isolates that significantly changed the response of pests on inoculated soybean plants versus controls. CONCLUSIONS We identified three fungal isolates that significantly reduced both leaf area consumed aboveground by caterpillars and number of cysts produced belowground by nematodes. These isolates were an Epicoccum italicum, a Chaetomium undulatum and a Stemphylium majusculum. SIGNIFICANCE AND IMPACT OF STUDY Overall, this study provides important insights into plant-fungal interactions and their effect on both above- and belowground pests. This study also highlights an important first step towards harnessing the potential of microbial inoculates as a tool for integrated pest management in soybeans.
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Affiliation(s)
- Loren J Rivera-Vega
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Wenqing Zhou
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Leah W Buchman
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Cesar U Valencia
- Department of Entomology, Texas A&M University, College Station, Texas, USA
| | - Allison L H Jack
- Indigo Ag Inc, Boston, Massachusetts, USA
- New Leaf Symbiotics, St. Louis., Missouri, USA
| | | | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, Texas, USA
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24
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Whitaker BK, Giauque H, Timmerman C, Birk N, Hawkes CV. Local Plants, Not Soils, Are the Primary Source of Foliar Fungal Community Assembly in a C4 Grass. MICROBIAL ECOLOGY 2022; 84:122-130. [PMID: 34405252 DOI: 10.1007/s00248-021-01836-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities, like their macro-organismal counterparts, assemble from multiple source populations and by processes acting at multiple spatial scales. However, the relative importance of different sources to the plant microbiome and the spatial scale at which assembly occurs remains debated. In this study, we analyzed how source contributions to the foliar fungal microbiome of a C4 grass differed between locally abundant plants and soils across an abiotic gradient at different spatial scales. Specifically, we used source-sink analysis to assess the likelihood that fungi in leaves from Panicum hallii came from three putative sources: two plant functional groups (C4 grasses and dicots) and soil. We expected that physiologically similar C4 grasses would be more important sources to P. hallii than dicots. We tested this at ten sites in central Texas spanning a steep precipitation gradient. We also examined source contributions at three spatial scales: individual sites (local), local plus adjacent sites (regional), or all sites (gradient-wide). We found that plants were substantially more important sources than soils, but contributions from the two plant functional groups were similar. Plant contributions overall declined and unexplained variation increased as mean annual precipitation increased. This source-sink analysis, combined with partitioning of beta-diversity into nestedness and turnover components, indicated high dispersal limitation and/or strong environmental filtering. Overall, our results suggest that the source-sink dynamics of foliar fungi are primarily local, that foliar fungi spread from plant-to-plant, and that the abiotic environment may affect fungal community sourcing both directly and via changes to host plant communities.
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Affiliation(s)
- Briana K Whitaker
- Department of Plant and Microbial Biology, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention & Applied Microbiology Unit, 1815 N University St, Peoria, IL, 61604, USA
| | - Hannah Giauque
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Corey Timmerman
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Nicolas Birk
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA
| | - Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, 112 Derieux Place, Raleigh, NC, 27607, USA.
- Department of Integrative Biology, University of Texas Austin, Austin, TX, USA.
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25
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Redman RS, Anderson JA, Biaggi TM, Malmberg KEL, Rienstra MN, Weaver JL, Rodriguez RJ. Symbiotic Modulation as a Driver of Niche Expansion of Coastal Plants in the San Juan Archipelago of Washington State. Front Microbiol 2022; 13:868081. [PMID: 35814642 PMCID: PMC9260653 DOI: 10.3389/fmicb.2022.868081] [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: 02/02/2022] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
Modern evolutionary theory and population genetics posit that adaptation and habitat expansion of plants result from processes exclusive to their genomes. Here, we present studies showing that plants can grow across complex habitat gradients by modulating symbiotic associations with Class 2 fungal endophytes. Endophyte analysis of three native (Leymus mollis, Distichlis spicata, and Salicornia pacifica) and one invasive (Spartina anglica) plant growing across adjacent microhabitats in the San Juan Archipelago altered associations with Class 2 fungal endophytes in response to soil salinity levels. At the microhabitat interfaces where the gradation of salinity varied, the plants were colonized by endophytes from both microhabitats. A reciprocal transplant study along a salt gradient demonstrated that Leymus mollis (dunegrass) required endophytes indigenous to each microhabitat for optimal fitness and/or survival. In contrast, when dunegrass and Grindelia integrifolia (gumweed) were found growing in low salinity, but high drought habitats, these plant species had their own unique dominant endophyte association regardless of geographic proximity and conferred drought but not high salt stress tolerance. Modulation of endophyte abundance occurred in planta based on the ability of the symbiont to confer tolerance to the stress imposed on plants. The ability of an endophyte to confer appropriate stress tolerance resulted in a significant increase of in planta fungal abundance. Conversely, the inability of an endophyte to confer stress tolerance resulted in a decrease of in planta fungal abundance. Our studies indicate that Class 2 fungal endophytes can provide a symbiotic mechanism for niche expansion and phenotypic plasticity across environmental gradients.
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26
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Sandy M, Bui TI, Abá KS, Ruiz N, Paszalek J, Connor EW, Hawkes CV. Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02057-x. [PMID: 35713682 DOI: 10.1007/s00248-022-02057-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Fungal symbionts living inside plant leaves ("endophytes") can vary from beneficial to parasitic, but the mechanisms by which the fungi affect the plant host phenotype remain poorly understood. Chemical interactions are likely the proximal mechanism of interaction between foliar endophytes and the plant, as individual fungal strains are often exploited for their diverse secondary metabolite production. Here, we go beyond single strains to examine commonalities in how 16 fungal endophytes shift plant phenotypic traits such as growth and physiology, and how those relate to plant metabolomics profiles. We inoculated individual fungi on switchgrass, Panicum virgatum L. This created a limited range of plant growth and physiology (2-370% of fungus-free controls on average), but effects of most fungi overlapped, indicating functional similarities in unstressed conditions. Overall plant metabolomics profiles included almost 2000 metabolites, which were broadly correlated with plant traits across all the fungal treatments. Terpenoid-rich samples were associated with larger, more physiologically active plants and phenolic-rich samples were associated with smaller, less active plants. Only 47 metabolites were enriched in plants inoculated with fungi relative to fungus-free controls, and of these, Lasso regression identified 12 metabolites that explained from 14 to 43% of plant trait variation. Fungal long-chain fatty acids and sterol precursors were positively associated with plant photosynthesis, conductance, and shoot biomass, but negatively associated with survival. The phytohormone gibberellin, in contrast, was negatively associated with plant physiology and biomass. These results can inform ongoing efforts to develop metabolites as crop management tools, either by direct application or via breeding, by identifying how associations with more beneficial components of the microbiome may be affected.
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Affiliation(s)
- Moriah Sandy
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Tina I Bui
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Kenia Segura Abá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Nestor Ruiz
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - John Paszalek
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Elise W Connor
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Biology, College of Western Idaho, Nampa, ID, 83687, USA
| | - Christine V Hawkes
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27607, USA.
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27
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Carrell AA, Lawrence TJ, Cabugao KGM, Carper DL, Pelletier DA, Lee JH, Jawdy SS, Grimwood J, Schmutz J, Hanson PJ, Shaw AJ, Weston DJ. Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming. THE NEW PHYTOLOGIST 2022; 234:2111-2125. [PMID: 35266150 PMCID: PMC9310625 DOI: 10.1111/nph.18072] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Travis J. Lawrence
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Kristine Grace M. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee1502 Cumberland Ave.KnoxvilleTN37996USA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Dale A. Pelletier
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jun Hyung Lee
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | | | - David J. Weston
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
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28
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Angulo V, Beriot N, Garcia-Hernandez E, Li E, Masteling R, Lau JA. Plant-microbe eco-evolutionary dynamics in a changing world. THE NEW PHYTOLOGIST 2022; 234:1919-1928. [PMID: 35114015 DOI: 10.1111/nph.18015] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Both plants and their associated microbiomes can respond strongly to anthropogenic environmental changes. These responses can be both ecological (e.g. a global change affecting plant demography or microbial community composition) and evolutionary (e.g. a global change altering natural selection on plant or microbial populations). As a result, global changes can catalyse eco-evolutionary feedbacks. Here, we take a plant-focused perspective to discuss how microbes mediate plant ecological responses to global change and how these ecological effects can influence plant evolutionary response to global change. We argue that the strong and functionally important relationships between plants and their associated microbes are particularly likely to result in eco-evolutionary feedbacks when perturbed by global changes and discuss how improved understanding of plant-microbe eco-evolutionary dynamics could inform conservation or even agriculture.
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Affiliation(s)
- Violeta Angulo
- Ecology and Biodiversity Group, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Nicolas Beriot
- Soil Physics and Land Management Group, Wageningen University & Research, PO Box 47, Wageningen, 6700AA, the Netherlands
- Sustainable Use, Management and Reclamation of Soil and Water Research Group, Universidad Politécnica de Cartagena, Paseo Alfonso XIII, 48, Cartagena, 30203, Spain
| | - Edisa Garcia-Hernandez
- Microbial Community Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, 9700 CC, the Netherlands
| | - Erqin Li
- Plant-Microbe Interactions Group, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
- Institut für Biologie, Freie Universität Berlin, Berlin, 14195, Germany
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
| | - Raul Masteling
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, Wageningen, 6708 PB, the Netherlands
- Institute of Biology, Leiden University, Leiden, 2333 BE, the Netherlands
| | - Jennifer A Lau
- Biology Department and the Environmental Resilience Institute, Indiana University, 1001 East 3rd St., Bloomington, IN, 47405, USA
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29
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Barge EG, Leopold DR, Rojas A, Vilgalys R, Busby PE. Phylogenetic conservatism of mycoparasitism and its contribution to pathogen antagonism. Mol Ecol 2022; 31:3018-3030. [DOI: 10.1111/mec.16436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Edward G. Barge
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Devin R. Leopold
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology University of Arkansas Fayetteville AR 72701 USA
| | - Rytas Vilgalys
- Department of Biology Duke University Durham NC 27708 USA
| | - Posy E. Busby
- Department of Botany and Plant Pathology Oregon State University Corvallis OR 97331 USA
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30
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Evans S, Allison S, Hawkes C. Microbes, memory, and moisture: predicting microbial moisture responses and their impact on carbon cycling. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Evans
- W.K. Kellogg Biological Station, Ecology and Evolutionary Biology Program Department of Integrative Biology Michigan State University Hickory Corners MI 49083 USA
| | - Steve Allison
- Department of Ecology and Evolutionary Biology Department of Earth System Science University of California Irvine California 92697 USA
| | - Christine Hawkes
- Department of Plant and Microbial Biology North Carolina State University Raleigh NC 27607 USA
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31
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Garnica S, Liao Z, Hamard S, Waller F, Parepa M, Bossdorf O. Environmental stress determines the colonization and impact of an endophytic fungus on invasive knotweed. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02749-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThere is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed (Reynoutria ssp.) in Europe, but their effects on the invaders are unknown. We used the recently isolated Sebacinales root endophyte Serendipita herbamans to experimentally inoculate invasive knotweed and study root colonisation and effects on knotweed growth under different environmental conditions. We verified the inoculation success and fungal colonisation through immunofluorescence microscopy and qPCR. We found that S. herbamans strongly colonized invasive knotweed in low-nutrient and shade environments, but much less under drought or benign conditions. At low nutrients, the endophyte had a positive effect on plant growth, whereas the opposite was true under shaded conditions. Our study demonstrates that the root endophyte S. herbamans has the potential to colonize invasive knotweed fine roots and impact its growth, and it could thus also play a role in natural populations. Our results also show that effects of fungal endophytes on plants can be strongly environment-dependent, and may only be visible under stressful environmental conditions.
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32
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The Role of Plant Growth-Promoting Rhizobacteria (PGPR) in Mitigating Plant’s Environmental Stresses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12031231] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoremediation is a cost-effective and sustainable technology used to clean up pollutants from soils and waters through the use of plant species. Indeed, plants are naturally capable of absorbing metals and degrading organic molecules. However, in several cases, the presence of contaminants causes plant suffering and limited growth. In such situations, thanks to the production of specific root exudates, plants can engage the most suitable bacteria able to support their growth according to the particular environmental stress. These plant growth-promoting rhizobacteria (PGPR) may facilitate plant growth and development with several beneficial effects, even more evident when plants are grown in critical environmental conditions, such as the presence of toxic contaminants. For instance, PGPR may alleviate metal phytotoxicity by altering metal bioavailability in soil and increasing metal translocation within the plant. Since many of the PGPR are also hydrocarbon oxidizers, they are also able to support and enhance plant biodegradation activity. Besides, PGPR in agriculture can be an excellent support to counter the devastating effects of abiotic stress, such as excessive salinity and drought, replacing expensive inorganic fertilizers that hurt the environment. A better and in-depth understanding of the function and interactions of plants and associated microorganisms directly in the matrix of interest, especially in the presence of persistent contamination, could provide new opportunities for phytoremediation.
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González-Teuber M, Contreras RA, Zúñiga GE, Barrera D, Bascuñán-Godoy L. Synergistic Association With Root Endophytic Fungi Improves Morpho-Physiological and Biochemical Responses of Chenopodium quinoa to Salt Stress. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.787318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Symbiotic associations with microbes can contribute to mitigating abiotic environmental stress in plants. In this study, we investigated individual and interactive effects of two root endophytic fungal species on physiological and biochemical mechanisms of the crop Chenopodium quinoa in response to salinity. Fungal endophytes (FE) Talaromyces minioluteus and Penicillium murcianum, isolated from quinoa plants that occur naturally in the Atacama Desert, were used for endophyte inoculation. A greenhouse experiment was developed using four plant groups: (1) plants inoculated with T. minioluteus (E1+), (2) plants inoculated with P. murcianum (E2+), (3) plants inoculated with both fungal species (E1E2+), and (4) non-inoculated plants (E-). Plants from each group were then assigned to either salt (300 mM) or control (no salt) treatments. Differences in morphological traits, photosynthesis, stomatal conductance, transpiration, superoxide dismutase (SOD), ascorbate peroxidase (APX), peroxidase, (POD), phenylalanine ammonia-lyase (PAL), phenolic content, and lipid peroxidation between plant groups under each treatment were examined. We found that both endophyte species significantly improved morphological and physiological traits, including plant height, number of shoots, photosynthesis, stomatal conductance, and transpiration, in C. quinoa in response to salt, but optimal physiological responses were observed in E1E2+ plants. Under saline conditions, endophyte inoculation improved SOD, APX, and POD activity by over 50%, and phenolic content by approximately 30%, with optimal enzymatic responses again observed in E1E2+ plants. Lipid peroxidation was significantly lower in inoculated plants than in non-inoculated plants. Results demonstrate that both endophyte species enhanced the ability of C. quinoa to cope with salt stress by improving antioxidative enzyme and non-enzyme systems. In general, both FE species interacting in tandem yielded better morphological, physiological, and biochemical responses to salinity in quinoa than inoculation by a single species in isolation. Our study highlights the importance of stress-adapted FE as a biological agent for mitigating abiotic stress in crop plants.
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Rawal R, Scheerens JC, Fenstemaker SM, Francis DM, Miller SA, Benitez MS. Novel Trichoderma Isolates Alleviate Water Deficit Stress in Susceptible Tomato Genotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:869090. [PMID: 35586213 PMCID: PMC9108677 DOI: 10.3389/fpls.2022.869090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/01/2022] [Indexed: 05/15/2023]
Abstract
Symbiotic fungi in the genus Trichoderma can induce abiotic stress tolerance in crops. The beneficial effects of Trichoderma on water deficit stress are poorly understood and may be isolate-specific. Our objective was to evaluate a collection of Nepalese Trichoderma isolates and their efficacy to improve tomato (Solanum lycopersicum) growth under water deficit. Variable growth in low moisture environments was observed among Trichoderma isolates from Nepal, Ohio, and commercial sources using in vitro assays. The overall performance of the population decreased when cultured under conditions of decreasing matric water potential (0.0, -2.8, -4.8, and -8.5 Ψ). Twelve isolates were selected for evaluation for their potential to elicit drought tolerance in greenhouse-grown 'Roma Organic' tomatoes. Plants treated with T. asperelloides-NT33 had higher shoot weight than the non-inoculated control (T0) under water deficit stress conditions. Further, the stress-reducing efficacy of isolates T. asperelloides-NT33, T. asperellum-NT16, T. asperelloides-NT3, and commercial T. harzianum-T22 were tested on tomato genotypes with differing tolerance to drought ['Roma Organic,' 'Jaune Flamme,' and 'Punta Banda']. The water deficit susceptible genotypes 'Roma Organic' and 'Jaune Flamme' inoculated with isolate NT33 had significantly higher shoot weight (37 and 30% respectively; p < 0.05) compared to the non-inoculated control under water deficit stress conditions. In drought tolerant 'Punta Banda,' shoot weight was also significantly greater in NT33 inoculated plants under water deficit stress conditions, but with lower magnitude difference (8%; p < 0.05). Our results demonstrate differences in the ability of Trichoderma isolates to confer tolerance to water deficit in tomato with NT33 potentially relieving stress. Tomato genotypes also play a role in the outcome of interactions with the Trichoderma isolates we tested.
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Affiliation(s)
- Ranjana Rawal
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Joseph C. Scheerens
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Sean M. Fenstemaker
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - David M. Francis
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Sally A. Miller
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Maria-Soledad Benitez
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
- *Correspondence: Maria-Soledad Benitez,
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35
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Jochems LW, Lau JA, Brudvig LA, Grman E. Do southern seed or soil microbes mitigate the effects of warming on establishing prairie plant communities? ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e02487. [PMID: 34679217 DOI: 10.1002/eap.2487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Restoration in this era of climate change comes with a new challenge: anticipating how best to restore populations to persist under future climate conditions. Specifically, it remains unknown whether locally adapted or warm-adapted seeds best promote native plant community restoration in the warmer conditions predicted in the future and whether local or warm-adapted soil microbial communities could mitigate plant responses to warming. This may be especially relevant for biomes spanning large climatic gradients, such as the North American tallgrass prairie. Here, we used a short-term mesocosm experiment to evaluate how seed provenances (Local Northern region, Non-local Northern region, Non-local Southern region) of 10 native tallgrass prairie plants (four forbs, two legumes, and four grasses) responded to warmer conditions predicted in the future and how soil microbial communities from those three regions influenced these responses. Warming and seed provenance affected plant community composition and warming decreased plant diversity for all three seed provenances. Plant species varied in their individual responses to warming, and across species, we detected no consistent differences among the three provenances in terms of biomass response to warming and few strong effects of soil provenance. Our work provides evidence that warming, in part, may reduce plant diversity and affect restored prairie composition. Because the southern provenance did not consistently outperform others under warming and we found little support for the "local is best" paradigm currently dominating restoration practice, identifying appropriate seed provenances to promote restoration success both now and in future warmer environments may be challenging. Due to the idiosyncratic responses across species, we recommend that land managers compare seeds from different regions for each species to determine which seed provenance performs best under warming and in restoration for tallgrass prairies.
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Affiliation(s)
- Louis W Jochems
- Department of Biology, Eastern Michigan University, 441 Mark Jefferson Hall, Ypsilanti, Michigan, 48197, USA
| | - Jennifer A Lau
- Department of Biology and the Environmental Resilience Institute, Indiana University, Bloomington, Indiana, 47405, USA
| | - Lars A Brudvig
- Department of Plant Biology and Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Emily Grman
- Department of Biology, Eastern Michigan University, 441 Mark Jefferson Hall, Ypsilanti, Michigan, 48197, USA
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36
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Cong W, Yu J, Feng K, Deng Y, Zhang Y. The Coexistence Relationship Between Plants and Soil Bacteria Based on Interdomain Ecological Network Analysis. Front Microbiol 2021; 12:745582. [PMID: 34950114 PMCID: PMC8689066 DOI: 10.3389/fmicb.2021.745582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
The relationship between plants and their associated soil microbial communities plays a crucial role in maintaining ecosystem processes and function. However, identifying these complex relationships is challenging. In this study, we constructed an interdomain ecology network (IDEN) of plant–bacteria based on SparCC pairwise associations using synchronous aboveground plant surveys and belowground microbial 16S rRNA sequencing among four different natural forest types along the climate zones in China. The results found that a total of 48 plants were associated with soil bacteria among these four sites, and soil microbial group associations with specific plant species existed within the observed plant–bacteria coexistence network. Only 0.54% of operational taxonomy units (OTUs) was shared by the four sites, and the proportion of unique OTUs for each site ranged from 43.08 to 76.28%, which occupied a large proportion of soil bacterial community composition. The plant–bacteria network had a distinct modular structure (p < 0.001). The tree Acer tetramerum was identified as the network hubs in the warm temperate coniferous and broad-leaved mixed forests coexistence network and indicates that it may play a key role in stabilizing of the community structure of these forest ecosystems. Therefore, IDEN of plant–bacteria provides a novel perspective for exploring the relationships of interdomain species, and this study provides valuable insights into understanding coexistence between above-ground plants and below-ground microorganisms.
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Affiliation(s)
- Wei Cong
- Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Jingjing Yu
- Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuguang Zhang
- Key Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
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Impact of Harvest on Switchgrass Leaf Microbial Communities. Genes (Basel) 2021; 13:genes13010022. [PMID: 35052362 PMCID: PMC8774549 DOI: 10.3390/genes13010022] [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: 10/21/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 11/21/2022] Open
Abstract
Switchgrass is a promising feedstock for biofuel production, with potential for leveraging its native microbial community to increase productivity and resilience to environmental stress. Here, we characterized the bacterial, archaeal and fungal diversity of the leaf microbial community associated with four switchgrass (Panicum virgatum) genotypes, subjected to two harvest treatments (annual harvest and unharvested control), and two fertilization levels (fertilized and unfertilized control), based on 16S rRNA gene and internal transcribed spacer (ITS) region amplicon sequencing. Leaf surface and leaf endosphere bacterial communities were significantly different with Alphaproteobacteria enriched in the leaf surface and Gammaproteobacteria and Bacilli enriched in the leaf endosphere. Harvest treatment significantly shifted presence/absence and abundances of bacterial and fungal leaf surface community members: Gammaproteobacteria were significantly enriched in harvested and Alphaproteobacteria were significantly enriched in unharvested leaf surface communities. These shifts were most prominent in the upland genotype DAC where the leaf surface showed the highest enrichment of Gammaproteobacteria, including taxa with 100% identity to those previously shown to have phytopathogenic function. Fertilization did not have any significant impact on bacterial or fungal communities. We also identified bacterial and fungal taxa present in both the leaf surface and leaf endosphere across all genotypes and treatments. These core taxa were dominated by Methylobacterium, Enterobacteriaceae, and Curtobacterium, in addition to Aureobasidium, Cladosporium, Alternaria and Dothideales. Local core leaf bacterial and fungal taxa represent promising targets for plant microbe engineering and manipulation across various genotypes and harvest treatments. Our study showcases, for the first time, the significant impact that harvest treatment can have on bacterial and fungal taxa inhabiting switchgrass leaves and the need to include this factor in future plant microbial community studies.
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38
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Bowman EA, Arnold AE. Drivers and implications of distance decay differ for ectomycorrhizal and foliar endophytic fungi across an anciently fragmented landscape. THE ISME JOURNAL 2021; 15:3437-3454. [PMID: 34099878 PMCID: PMC8630060 DOI: 10.1038/s41396-021-01006-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 07/30/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023]
Abstract
Fungal communities associated with plants often decrease in similarity as the distance between sampling sites increases (i.e., they demonstrate distance decay). In the southwestern USA, forests occur in highlands separated from one another by warmer, drier biomes with plant and fungal communities that differ from those at higher elevations. These disjunct forests are broadly similar in climate to one another, offering an opportunity to examine drivers of distance decay in plant-associated fungi across multiple ecologically similar yet geographically disparate landscapes. We examined ectomycorrhizal and foliar endophytic fungi associated with a dominant forest tree (Pinus ponderosa) in forests across ca. 550 km of geographic distance from northwestern to southeastern Arizona (USA). Both guilds of fungi showed distance decay, but drivers differed for each: ectomycorrhizal fungi are constrained primarily by dispersal limitation, whereas foliar endophytes are constrained by specific environmental conditions. Most ectomycorrhizal fungi were found in only a single forested area, as were many endophytic fungi. Such regional-scale perspectives are needed for baseline estimates of fungal diversity associated with forest trees at a landscape scale, with attention to the sensitivity of different guilds of fungal symbionts to decreasing areas of suitable habitat, increasing disturbance, and related impacts of climate change.
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Affiliation(s)
- Elizabeth A. Bowman
- grid.134563.60000 0001 2168 186XSchool of Plant Sciences, The University of Arizona, Tucson, AZ USA
| | - A. Elizabeth Arnold
- grid.134563.60000 0001 2168 186XSchool of Plant Sciences, The University of Arizona, Tucson, AZ USA ,grid.134563.60000 0001 2168 186XDepartment of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ USA
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39
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Zaret MM, Bauer JT, Clay K, Whitaker BK. Conspecific leaf litter induces negative feedbacks in Asteraceae seedlings. Ecology 2021; 102:e03557. [PMID: 34625950 DOI: 10.1002/ecy.3557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 07/07/2021] [Accepted: 07/23/2021] [Indexed: 11/07/2022]
Abstract
The plant soil feedback (PSF) framework has been instrumental in understanding the impacts of soil microbes on plant fitness and species coexistence. PSFs develop when soil microbial communities are altered due to the identity and density of a particular plant species, which can then enhance or inhibit the local survival and growth of that plant species as well as different plant species. The recent extension of the PSF framework to aboveground microbiota, termed here as plant phyllosphere feedbacks (PPFs), can also help to determine the impact of aboveground microbes on plant fitness and species interactions. However, experimental tests of PPFs during early plant growth are nascent and the prevalence of PPFs across diverse plant species remains unknown. Additionally, it is unclear whether plant host characteristics, such as functional traits or phylogenetic distance, may help to predict the strength and direction of PPFs. To test for the prevalence of litter-mediated PPFs, recently senesced plant litter from 10 native Asteraceae species spanning a range of life history strategies was used to inoculate seedlings of both conspecific and heterospecific species. We found that exposure to conspecific litter significantly reduced the growth of four species relative to exposure to heterospecific litter (i.e., significant negative PPFs), three species experienced marginally significant negative PPFs, and the PPF estimates for all 10 species were negative. However, neither plant functional traits, nor phylogenetic distance were predictive of litter feedbacks across plant species pairs, suggesting that other mechanisms or traits not measured may be driving conspecific negative PPFs. Our results indicate that negative, litter-mediated PPFs are common among native Asteraceae species and that they may have substantial impacts on plant growth and plant species interactions, particularly during early plant growth.
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Affiliation(s)
- Max M Zaret
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, Minnesota, USA
| | - Jonathan T Bauer
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Biology, Miami University, Oxford, Ohio, USA.,Institute for the Environment and Sustainability, Miami University, Oxford, Ohio, USA
| | - Keith Clay
- Department of Biology, Indiana University, Bloomington, Indiana, USA.,Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Briana K Whitaker
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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40
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Christian N, Espino Basurto B, Toussaint A, Xu X, Ainsworth EA, Busby PE, Heath KD. Elevated carbon dioxide reduces a common soybean leaf endophyte. GLOBAL CHANGE BIOLOGY 2021; 27:4154-4168. [PMID: 34022078 DOI: 10.1111/gcb.15716] [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: 12/01/2020] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2 ] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2 ] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.
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Affiliation(s)
- Natalie Christian
- Department of Biology, University of Louisville, Louisville, KY, USA
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Baldemar Espino Basurto
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Amber Toussaint
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Xinyan Xu
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
| | - Elizabeth A Ainsworth
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
| | - Posy E Busby
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Katy D Heath
- Department of Plant Biology, School of Integrative Biology, University of Illinois, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, USA
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41
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Lu H, Wei T, Lou H, Shu X, Chen Q. A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses. J Fungi (Basel) 2021; 7:719. [PMID: 34575757 PMCID: PMC8466524 DOI: 10.3390/jof7090719] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
Endophytic fungi infect plant tissues by evading the immune response, potentially stimulating stress-tolerant plant growth. The plant selectively allows microbial colonization to carve endophyte structures through phenotypic genes and metabolic signals. Correspondingly, fungi develop various adaptations through symbiotic signal transduction to thrive in mycorrhiza. Over the past decade, the regulatory mechanism of plant-endophyte interaction has been uncovered. Currently, great progress has been made on plant endosphere, especially in endophytic fungi. Here, we systematically summarize the current understanding of endophytic fungi colonization, molecular recognition signal pathways, and immune evasion mechanisms to clarify the transboundary communication that allows endophytic fungi colonization and homeostatic phytobiome. In this work, we focus on immune signaling and recognition mechanisms, summarizing current research progress in plant-endophyte communication that converge to improve our understanding of endophytic fungi.
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Affiliation(s)
- Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Tianyu Wei
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Hanghang Lou
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Xiaoli Shu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
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42
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Bell-Dereske LP, Evans SE. Contributions of environmental and maternal transmission to the assembly of leaf fungal endophyte communities. Proc Biol Sci 2021; 288:20210621. [PMID: 34375558 DOI: 10.1098/rspb.2021.0621] [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: 01/16/2023] Open
Abstract
Leaf fungal endophytes (LFEs) contribute to plant growth and responses to stress. Fungi colonize leaves through maternal transmission, e.g. via the seed, and through environmental transmission, e.g. via aerial dispersal. The relative importance of these two pathways in assembly and function of the LFE community is poorly understood. We used amplicon sequencing to track switchgrass (Panicum virgatum) LFEs in a greenhouse and field experiment as communities assembled from seed endophytes and rain fungi (integration of wet and dry aerial dispersal) in germinating seeds, seedlings, and adult plants. Rain fungi varied temporally and hosted a greater portion of switchgrass LFE richness (greater than 65%) than were found in seed endophytes (greater than 25%). Exposure of germinating seeds to rain inoculum increased dissimilarity between LFE communities and seed endophytes, increasing the abundance of rain-derived taxa, but did not change diversity. In the field, seedling LFE composition changed more over time, with a decline in seed-derived taxa and an increase in richness, in response to environmental transmission than LFEs of adult plants. We show that environmental transmission is an important driver of LFE assembly, and likely plant growth, but its influence depends on both the conditions at the time of colonization and plant life stage.
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Affiliation(s)
- Lukas P Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Sarah E Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA.,Department of Integrative Biology, Michigan State University, East Lansing, MI 48824, USA.,Ecology and Evolutionary Biology Program, Michigan State University, East Lansing, MI 48824, USA
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43
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Feng F, Zhan H, Wan Q, Wang Y, Li Y, Ge J, Sun X, Zhu H, Yu X. Rice recruits Sphingomonas strain HJY-rfp via root exudate regulation to increase chlorpyrifos tolerance and boost residual catabolism. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5673-5686. [PMID: 33987653 DOI: 10.1093/jxb/erab210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Inoculation with pollution-degrading endophytes boosts the catabolism of residual contaminants and promotes the pollution adaptation of host plants. We investigated the interaction pattern between Sphingomonas strain HJY-rfp, a chlorpyrifos-degrading endophytic bacterium, and rice (Oryza sativa) under pesticide stress using hydroponic cultivation. We observed a notable trend of endophytic root colonization in rice plants treated with 10 mg l-1 chlorpyrifos solution, and after 24 h the migration of HJY-rfp enhanced the chlorpyrifos degradation rate in leaves and stems by 53.36% and 40.81%, respectively. Critically, the rice root exudate profile (organic acids and amino acids) changed under chlorpyrifos stress, and variations in the contents of several components affected the chemotactic behaviour of HJY-rfp. HJY-rfp colonization dramatically activated defensive enzymes, which enabled efficient scavenging of reactive oxygen species, and led to 9.8%, 22.5%, and 41.9% increases in shoot length, fresh weight, and accumulation of total chlorophyll, respectively, in rice suffering from oxidative damage by chlorpyrifos. Endophytic colonization caused up-regulation of detoxification genes that have shown a significant positive correlation with chlorpyrifos degradation in vivo. Collectively, our results demonstrate that agrochemical stress causes plants to actively recruit specific symbiotic microbes to detoxify contaminants and survive better under pollution conditions.
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Affiliation(s)
- Fayun Feng
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing, China
| | - Honglin Zhan
- Department of Biotechnology, Qingdao University of Science &Technology, Qingdao, China
| | - Qun Wan
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ya Wang
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yong Li
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jing Ge
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xing Sun
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hong Zhu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiangyang Yu
- Institute of Agricultural Resources and Environment, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Ministry of Science and Technology/Key Laboratory of Control Technology and Standard for Agro-product Safety and Quality, Ministry of Agriculture, Nanjing, China
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44
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Pei D, Zhang Q, Zhu X, Han S. Endophytic Bacillus subtilis P10 from Prunus cerasifera as a biocontrol agent against tomato Verticillium wilt. BRAZ J BIOL 2021; 83:e244261. [PMID: 34287505 DOI: 10.1590/1519-6984.244261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/25/2021] [Indexed: 11/21/2022] Open
Abstract
Endophytic bacteria serve key roles in the maintenance of plant health and growth. Few studies to date, however, have explored the antagonistic and plant growth-promoting (PGP) properties of Prunus cerasifera endophytes. To that end, we isolated endophytic bacteria from P. cerasifera tissue samples and used a dual culture plate assay to screen these microbes for antagonistic activity against Verticillium dahliae, Botryosphaeria dothidea, Fusarium oxysporum, F. graminearum, and F. moniliforme. Of the 36 strains of isolated bacteria, four (strains P1, P10, P16, and P20) exhibited antagonistic effects against all five model pathogens, and the P10 strain exhibited the strongest antagonistic to five pathogens. This P10 strain was then characterized in-depth via phenotypic assessments, physiological analyses, and 16s rDNA sequencing, revealing it to be a strain of Bacillus subtilis. Application of a P10 cell suspension (1×108 CFU/mL) significantly enhanced the seed germination and seedling growth of tomato in a greenhouse setting. This P10 strain further significantly suppressed tomato Verticillium wilt with much lower disease incidence and disease index scores being observed following P10 treatment relative to untreated plants in pot-based experiments. Tomato plants that had been treated with strain P10 also enhanced defense-related enzymes, peroxidase, superoxide dismutase, and catalase activity upon V. dahliae challenge relative to plants that had not been treated with this endophytic bacterium. The results revealed that the P10 bacterial strain has potential value as a biocontrol agent for use in the prevention of tomato Verticillium wilt.
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Affiliation(s)
- D Pei
- Shangqiu Normal University, Henan Provincial Engineering Research Center for Development and Appllication of Characteristic Microorganism Resources, College of Biology and Food, Key Laboratory of Plant-Microbe Interactions, Shangqiu, China
| | - Q Zhang
- Shangqiu Normal University, Henan Provincial Engineering Research Center for Development and Appllication of Characteristic Microorganism Resources, College of Biology and Food, Key Laboratory of Plant-Microbe Interactions, Shangqiu, China
| | - X Zhu
- Shangqiu Normal University, Henan Provincial Engineering Research Center for Development and Appllication of Characteristic Microorganism Resources, College of Biology and Food, Key Laboratory of Plant-Microbe Interactions, Shangqiu, China
| | - S Han
- Shangqiu Normal University, Henan Provincial Engineering Research Center for Development and Appllication of Characteristic Microorganism Resources, College of Biology and Food, Key Laboratory of Plant-Microbe Interactions, Shangqiu, China
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45
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Abstract
AbstractAnalyses of species functional traits are suitable to better understand the coexistence of species in a given environment. Trait information can be applied to investigate diversity patterns along environmental gradients and subsequently to predict and mitigate threats associated with climate change and land use. Species traits are used to calculate community trait means, which can be related to environmental gradients. However, while species traits can provide insights into the mechanisms underlying community assembly, they can lead to erroneous inferences if mean trait values are used. An alternative is to incorporate intraspecific trait variability (ITV) into calculating the community trait means. This approach gains increasing acceptance in plant studies. For macrofungi, functional traits have recently been applied to examine their community ecology but, to our knowledge, ITV has yet to be incorporated within the framework of community trait means. Here, we present a conceptual summary of the use of ITV to investigate the community ecology of macrofungi, including the underlying ecological theory. Inferences regarding community trait means with or without the inclusion of ITV along environmental gradients are compared. Finally, an existing study is reconsidered to highlight the variety of possible outcomes when ITV is considered. We hope this Opinion will increase awareness of the potential for within-species trait variability and its importance for statistical inferences, interpretations, and predictions of the mechanisms structuring communities of macro- and other fungi.
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46
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Hawkes CV, Kjøller R, Raaijmakers JM, Riber L, Christensen S, Rasmussen S, Christensen JH, Dahl AB, Westergaard JC, Nielsen M, Brown-Guedira G, Hestbjerg Hansen L. Extension of Plant Phenotypes by the Foliar Microbiome. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:823-846. [PMID: 34143648 DOI: 10.1146/annurev-arplant-080620-114342] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The foliar microbiome can extend the host plant phenotype by expanding its genomic and metabolic capabilities. Despite increasing recognition of the importance of the foliar microbiome for plant fitness, stress physiology, and yield, the diversity, function, and contribution of foliar microbiomes to plant phenotypic traits remain largely elusive. The recent adoption of high-throughput technologies is helping to unravel the diversityand spatiotemporal dynamics of foliar microbiomes, but we have yet to resolve their functional importance for plant growth, development, and ecology. Here, we focus on the processes that govern the assembly of the foliar microbiome and the potential mechanisms involved in extended plant phenotypes. We highlight knowledge gaps and provide suggestions for new research directions that can propel the field forward. These efforts will be instrumental in maximizing the functional potential of the foliar microbiome for sustainable crop production.
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Affiliation(s)
- Christine V Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Rasmus Kjøller
- Department of Biology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, 6708 PB Wageningen, The Netherlands;
| | - Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Svend Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark;
| | - Jan H Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Jesper Cairo Westergaard
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
| | - Mads Nielsen
- Department of Computer Science, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Gina Brown-Guedira
- Plant Science Research Unit, USDA Agricultural Research Service and Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA;
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark; , , , ,
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47
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Petipas RH, Geber MA, Lau JA. Microbe-mediated adaptation in plants. Ecol Lett 2021; 24:1302-1317. [PMID: 33913572 DOI: 10.1111/ele.13755] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/07/2021] [Accepted: 03/17/2021] [Indexed: 12/30/2022]
Abstract
Interactions with microbial symbionts have yielded great macroevolutionary innovations across the tree of life, like the origins of chloroplasts and the mitochondrial powerhouses of eukaryotic cells. There is also increasing evidence that host-associated microbiomes influence patterns of microevolutionary adaptation in plants and animals. Here we describe how microbes can facilitate adaptation in plants and how to test for and differentiate between the two main mechanisms by which microbes can produce adaptive responses in higher organisms: microbe-mediated local adaptation and microbe-mediated adaptive plasticity. Microbe-mediated local adaptation is when local plant genotypes have higher fitness than foreign genotypes because of a genotype-specific affiliation with locally beneficial microbes. Microbe-mediated adaptive plasticity occurs when local plant phenotypes, elicited by either the microbial community or the non-microbial environment, have higher fitness than foreign phenotypes as a result of interactions with locally beneficial microbes. These microbial effects on adaptation can be difficult to differentiate from traditional modes of adaptation but may be prevalent. Ignoring microbial effects may lead to erroneous conclusions about the traits and mechanisms underlying adaptation, hindering management decisions in conservation, restoration, and agriculture.
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Affiliation(s)
- Renee H Petipas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Monica A Geber
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jennifer A Lau
- Department of Biology, Indiana University, Bloomington, IN, USA.,The Environmental Resilience Institute, Indiana University, Bloomington, IN, USA
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Henning JA, Kinkel L, May G, Lumibao CY, Seabloom EW, Borer ET. Plant diversity and litter accumulation mediate the loss of foliar endophyte fungal richness following nutrient addition. Ecology 2020; 102:e03210. [PMID: 32981067 DOI: 10.1002/ecy.3210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/22/2020] [Accepted: 08/06/2020] [Indexed: 01/20/2023]
Abstract
Foliar fungal endophytes are ubiquitous plant symbionts that can affect plant growth and reproduction via their roles in pathogen and stress tolerance, as well as plant hormonal signaling. Despite their importance, we have a limited understanding of how foliar fungal endophytes respond to varying environmental conditions such as nutrient inputs. The responses of foliar fungal endophyte communities to increased nutrient deposition may be mediated by the simultaneous effects on within-host competition as well as the indirect impacts of altered host population size, plant productivity, and plant community diversity and composition. Here, we leveraged a 7-yr experiment manipulating nitrogen, phosphorus, potassium, and micronutrients to investigate how nutrient-induced changes to plant diversity, plant productivity, and plant community composition relate to changes in foliar fungal endophyte diversity and richness in a focal native grass host, Andropogon gerardii. We found limited evidence of direct effects of nutrients on endophyte diversity. Instead, the effects of nutrients on endophyte diversity appeared to be mediated by accumulation of plant litter and plant diversity loss. Specifically, nitrogen addition is associated with a 40% decrease in plant diversity and an 11% decrease in endophyte richness. Although nitrogen, phosphorus, and potassium addition increased aboveground live biomass and decreased relative Andropogon cover, endophyte diversity did not covary with live plant biomass or Andropogon cover. Our results suggest that fungal endophyte diversity within this focal host is determined in part by the diversity of the surrounding plant community and its potential impact on immigrant propagules and dispersal dynamics. Our results suggest that elemental nutrients reduce endophyte diversity indirectly via impacts on the local plant community, not direct response to nutrient addition. Thus, the effects of global change drivers, such as nutrient deposition, on characteristics of host populations and the diversity of their local communities are important for predicting the response of symbiont communities in a changing global environment.
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Affiliation(s)
- Jeremiah A Henning
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA.,Department of Biology, University of South Alabama, 5871 USA Drive N., Room 124, Mobile, Alabama, 36688, USA
| | - Linda Kinkel
- Department of Plant Pathology, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Georgiana May
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Candice Y Lumibao
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA.,Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Eric W Seabloom
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
| | - Elizabeth T Borer
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St Paul, Minnesota, 55108, USA
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Wandrag EM, Bates SE, Barrett LG, Catford JA, Thrall PH, van der Putten WH, Duncan RP. Phylogenetic signals and predictability in plant-soil feedbacks. THE NEW PHYTOLOGIST 2020; 228:1440-1449. [PMID: 32619298 PMCID: PMC7689780 DOI: 10.1111/nph.16768] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/12/2020] [Indexed: 05/28/2023]
Abstract
There is strong evidence for a phylogenetic signal in the degree to which species share co-evolved biotic partners and in the outcomes of biotic interactions. This implies there should be a phylogenetic signal in the outcome of feedbacks between plants and the soil microbiota they cultivate. However, attempts to identify a phylogenetic signal in plant-soil feedbacks have produced mixed results. Here we clarify how phylogenetic signals could arise in plant-soil feedbacks and use a recent compilation of data from feedback experiments to identify: whether there is a phylogenetic signal in the outcome of plant-soil feedbacks; and whether any signal arises through directional or divergent changes in feedback outcomes with evolutionary time. We find strong evidence for a divergent phylogenetic signal in feedback outcomes. Distantly related plant species show more divergent responses to each other's soil microbiota compared with closely related plant species. The pattern of divergence implies occasional co-evolutionary shifts in how plants interact with soil microbiota, with strongly contrasting feedback responses among some plant lineages. Our results highlight that it is difficult to predict feedback outcomes from phylogeny alone, other than to say that more closely related species tend to have more similar responses.
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Affiliation(s)
- Elizabeth M. Wandrag
- Institute for Applied EcologyUniversity of CanberraCanberraACT2617Australia
- School of Environmental and Rural ScienceUniversity of New EnglandArmidaleNSW2350Australia
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)PO Box 50Wageningen6700 ABthe Netherlands
| | - Sarah E. Bates
- Institute for Applied EcologyUniversity of CanberraCanberraACT2617Australia
| | | | - Jane A. Catford
- Department of GeographyKing’s College LondonLondonWC2B 4BGUK
- School of BioSciencesUniversity of MelbourneMelbourneVic.3010Australia
| | | | - Wim H. van der Putten
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)PO Box 50Wageningen6700 ABthe Netherlands
- Laboratory of NematologyWageningen UniversityPO Box 8123Wageningen6700 ESthe Netherlands
| | - Richard P. Duncan
- Institute for Applied EcologyUniversity of CanberraCanberraACT2617Australia
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Ye S, Bhattacharjee M, Siemann E. Stress tolerance alteration in the freshwater cnidarian green hydra (Hydra viridissima) via symbiotic algae mutagenesis. Symbiosis 2020. [DOI: 10.1007/s13199-020-00712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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