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de Freitas STF, Silva FG, Bessa LA, de Souza UJB, Augusto DSS, de Faria GS, Vitorino LC. Low microbial diversity, yeast prevalence, and nematode-trapping fungal presence in fungal colonization and leaf microbiome of Serjania erecta. Sci Rep 2024; 14:15456. [PMID: 38965317 PMCID: PMC11224404 DOI: 10.1038/s41598-024-66161-3] [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: 02/08/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Medicinal plant microbiomes undergo selection due to secondary metabolite presence. Resident endophytic/epiphytic microorganisms directly influence plant's bioactive compound synthesis. Hypothesizing low microbial diversity in Serjania erecta leaves, we assessed leaf colonization by epiphytic and endophytic fungi. Given its traditional medicinal importance, we estimated diversity in the endophytic fungal microbiome. Analyses included scanning electron microscopy (SEM), isolation of cultivable species, and metagenomics. Epiphytic fungi interacted with S. erecta leaf tissues, horizontally transmitted via stomata/trichome bases, expressing traits for nematode trapping. Cultivable endophytic fungi, known for phytopathogenic habits, didn't induce dysbiosis symptoms. This study confirms low leaf microbiome diversity in S. erecta, with a tendency towards more fungal species, likely due to antibacterial secondary metabolite selection. The classification of Halicephalobus sp. sequence corroborated the presence of nematode eggs on the epidermal surface of S. erecta by SEM. In addition, we confirmed the presence of methanogenic archaea and a considerable number of methanotrophs of the genus Methylobacterium. The metagenomic study of endophytic fungi highlighted plant growth-promoting yeasts, mainly Malassezia, Leucosporidium, Meyerozyma, and Hannaella. Studying endophytic fungi and S. erecta microbiomes can elucidate their impact on beneficial bioactive compound production, on the other hand, it is possible that the bioactive compounds produced by this plant can recruit specific microorganisms, impacting the biological system.
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Affiliation(s)
- Samylla Tássia Ferreira de Freitas
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Fabiano Guimarães Silva
- Laboratory of Plant Mineral Nutrition, Instituto Federal Goiano, campus Rio Verde, Rio Verde, Brazil
| | - Layara Alexandre Bessa
- Laboratory of Plant Mineral Nutrition, Instituto Federal Goiano, campus Rio Verde, Rio Verde, Brazil
| | - Ueric José Borges de Souza
- Bioinformatics and Biotechnology Laboratory, Federal University of Tocantins, Campus of Gurupi, Gurupi, TO, 77410-570, Brazil
| | - Damiana Souza Santos Augusto
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Giselle Santos de Faria
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil
| | - Luciana Cristina Vitorino
- Laboratory of Agricultural Microbiology, Instituto Federal Goiano - campus Rio Verde, Highway Sul Goiana, Km 01, Rio Verde, GO, 75901-970, Brazil.
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Kumari P, Deepa N, Trivedi PK, Singh BK, Srivastava V, Singh A. Plants and endophytes interaction: a "secret wedlock" for sustainable biosynthesis of pharmaceutically important secondary metabolites. Microb Cell Fact 2023; 22:226. [PMID: 37925404 PMCID: PMC10625306 DOI: 10.1186/s12934-023-02234-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Many plants possess immense pharmacological properties because of the presence of various therapeutic bioactive secondary metabolites that are of great importance in many pharmaceutical industries. Therefore, to strike a balance between meeting industry demands and conserving natural habitats, medicinal plants are being cultivated on a large scale. However, to enhance the yield and simultaneously manage the various pest infestations, agrochemicals are being routinely used that have a detrimental impact on the whole ecosystem, ranging from biodiversity loss to water pollution, soil degradation, nutrient imbalance and enormous health hazards to both consumers and agricultural workers. To address the challenges, biological eco-friendly alternatives are being looked upon with high hopes where endophytes pitch in as key players due to their tight association with the host plants. The intricate interplay between plants and endophytic microorganisms has emerged as a captivating subject of scientific investigation, with profound implications for the sustainable biosynthesis of pharmaceutically important secondary metabolites. This review delves into the hidden world of the "secret wedlock" between plants and endophytes, elucidating their multifaceted interactions that underpin the synthesis of bioactive compounds with medicinal significance in their plant hosts. Here, we briefly review endophytic diversity association with medicinal plants and highlight the potential role of core endomicrobiome. We also propose that successful implementation of in situ microbiome manipulation through high-end techniques can pave the way towards a more sustainable and pharmaceutically enriched future.
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Affiliation(s)
- Poonam Kumari
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Nikky Deepa
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Prabodh Kumar Trivedi
- Division of Plant Biotechnology, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2753, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden.
| | - Akanksha Singh
- Division of Crop Production and Protection, Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Islam SU, Mangral ZA, Hussain K, Tariq L, Bhat BA, Khuroo AA, Hassan Dar TU. Unravelling diversity, drivers, and indicators of soil microbiome of Trillium govanianum, an endangered plant species of the Himalaya. ENVIRONMENTAL RESEARCH 2023; 227:115819. [PMID: 37011799 DOI: 10.1016/j.envres.2023.115819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/19/2023] [Accepted: 03/30/2023] [Indexed: 05/08/2023]
Abstract
In an era of global environmental change, conservation of threatened biodiversity and ecosystem restoration are formidable ecological challenges. The forest understory strata and the belowground soil environment including rhizospheric microbial communities, which are crucial for ecosystem functioning and overall forest biodiversity maintenance, have remained understudied. Here, we investigate the soil microbiome of Trillium govanianum - an endangered Himalayan Forest herb, to unravel the underground diversity, drivers, and potential indicators of the microbial community. We collected rhizospheric and bulk soil samples for microbiome and physicochemical analysis at three sites along an elevation gradient (2500-3300 m) in Kashmir Himalaya. Amplicon sequencing of 16 S rRNA and ITS was used to identify the bacterial and fungal soil microorganisms. We found significant differences in the structure and diversity of microbial community (bacterial and fungal) between the rhizosphere and bulk soil along the altitudinal gradient, and noticeable shifts in the nutrient level in dominant microbial phyla associated with T. govanianum. A significant difference between soil physicochemical parameters and increasing altitude suggests that microbial community structure is determined by altitude and soil type. Similarly, the microbial communities showed a significant (P < 0.05) correlation with soil physicochemical variables along the altitudinal gradient. The moisture content in bacterial and total organic carbon in fungal communities showed the most substantial impact on the physiochemical drivers. We also identify potential bacterial and fungal plant growth promoter indicator species in the soil microbiome of T. govanianum. Overall, our findings provide novel research insights that can be pivotal in designing integrated species recovery programs and long-term restoration plans for T. govanianum, with learnings for biodiversity conservation elsewhere.
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Affiliation(s)
- Shahid Ul Islam
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Zahid Ahmed Mangral
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Khalid Hussain
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Lubna Tariq
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, School of Biological Sciences, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Anzar Ahmad Khuroo
- Centre for Biodiversity and Taxonomy, Department of Botany, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Tanvir Ul Hassan Dar
- Department of Biotechnology, School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, Jammu and Kashmir, India.
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Shao Q, Dong C, Hu H, Huang J, Zou X, Liang Z, Han Y. Effects of Medicinal Plants on Fungal Community Structure and Function in Hospital Grassplot Soil. Curr Microbiol 2022; 79:377. [DOI: 10.1007/s00284-022-03083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
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Liu L, Wang X, Chen S, Liu D, Song C, Yi S, Zhu F, Wang W, Wang F, Wang G, Song X, Jia B, Chen C, Peng H, Guo L, Han B. Fungal isolates influence the quality of Peucedanum praeruptorum Dunn. FRONTIERS IN PLANT SCIENCE 2022; 13:1011001. [PMID: 36352875 PMCID: PMC9638934 DOI: 10.3389/fpls.2022.1011001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The symbiotic relationship between beneficial microorganisms and plants plays a vital role in natural and agricultural ecosystems. Although Peucedanum praeruptorum Dunn is widely distributed, its development is greatly limited by early bolting. The reason for early bolting in P. praeruptorum remains poorly characterized. We focus on the plant related microorganisms, including endophytes and rhizosphere microorganisms, by combining the traditional isolation and culture method with metagenomic sequencing technology. We found that the OTUs of endophytes and rhizosphere microorganisms showed a positive correlation in the whole growth stage of P. praeruptorum. Meanwhile, the community diversity of endophytic and rhizosphere fungi showed an opposite change trend, and bacteria showed a similar change trend. Besides, the microbial communities differed during the pre- and post-bolting stages of P. praeruptorum. Beneficial bacterial taxa, such as Pseudomonas and Burkholderia, and fungal taxa, such as Didymella and Fusarium, were abundant in the roots in the pre-bolting stage. Further, a strain belonging to Didymella was obtained by traditional culture and was found to contain praeruptorin A, praeruptorin B, praeruptorin E. In addition, we showed that the fungus could affect its effective components when it was inoculated into P. praeruptorum. This work provided a research reference for the similar biological characteristics of perennial one-time flowering plants, such as Saposhnikovia divaricate, Angelica sinensis and Angelica dahurica.
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Affiliation(s)
- Li Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Xuejun Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shaotong Chen
- College of Life Science, South China Agricultural University, Guangzhou, China
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Shanyong Yi
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Wei Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Guanglin Wang
- Analytical and Testing Center, West Anhui University, Lu’an, China
| | - Xiangwen Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Bin Jia
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Cunwu Chen
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
| | - Huasheng Peng
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Engineering Research Center for Eco-agriculture of Traditional Chinese Medicine, West Anhui University, Lu’an, China
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Yun T, Jing T, Zhou D, Zhang M, Zhao Y, Li K, Zang X, Zhang L, Xie J, Wang W. Potential Biological Control of Endophytic Streptomyces sp. 5-4 Against Fusarium Wilt of Banana Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4. PHYTOPATHOLOGY 2022; 112:1877-1885. [PMID: 35471064 DOI: 10.1094/phyto-11-21-0464-r] [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] [Indexed: 06/14/2023]
Abstract
Fusarium wilt of banana caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) is one of the most disastrous fungal diseases. Biological control is a promising strategy for controlling Fusarium wilt of banana. To explore endophytic actinomycetes as biocontrol resources against Foc TR4, antagonistic strains were isolated from different tissues of medicinal plants. Here, a total of 144 actinomycetes were isolated and belonged to Nonomuraea, Kitasatospora, and Streptomyces. Forty-three isolates exhibited antifungal activities against Foc TR4. The strain labeled with 5-4 isolated from roots of Piper austrosinense had a broad-spectrum antifungal activity by the production of chitinase and β-1,3-glucanase and was identified as Streptomyces hygroscopicus subsp. hygroscopicus 5-4. Furthermore, disease index of banana wilt was significantly reduced by application of strain 5-4 in comparison with application of Foc TR4 alone. Exogenous application of strain 5-4 increased the expression levels of defense genes such as (PAL), peroxidase (POD), pathogenesis-related protein 1 (PR-1), hydrolytic enzymes (β-1,3-glucanase), lysin motif receptor kinase 1 (LYK-1), and mitogen-activated protein kinase 1 (MPK-1). The antifungal mechanism assay demonstrated that extracts of strain 5-4 inhibited spore gemination and hyphal growth of Foc TR4, and caused abnormally swollen, deformity, and rupture of Foc TR4 hypha. Thus, S. hygroscopicus subsp. hygroscopicus 5-4 could be used as a potential biological agent for controlling Fusarium wilt of banana.
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Affiliation(s)
- Tianyan Yun
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Tao Jing
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Dengbo Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Miaoyi Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Yankun Zhao
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Kai Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Xiaoping Zang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Lu Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Jianghui Xie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
| | - Wei Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, 571101, China
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Succession of Bacterial and Fungal Communities during Fermentation of Medicinal Plants. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8080383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The fermentation of medicinal plants has been studied very little, as compared to the fermentation of food and beverages. One approach applies fermentation by single bacterial or fungal strains and targets the production of specific compounds or preservation of the fermented material. Spontaneous fermentation by an autochthonous starter community may lead to a more diverse blend of fermentation products because co-occurring microbes may activate the biosynthetic potentials and formation of compounds not produced in single strain approaches. We applied the community approach and studied the fermentation of four medicinal plants (Achillea millefolium, Taraxacum officinale, Mercurialis perennis, and Euphrasia officinalis), according to a standardized pharmaceutical fermentation method. It is based on the spontaneous fermentation by plant-specific bacterial and fungal communities under a distinct temperature regime, with a recurrent cooling during the first week and further fermentation for at least six months. The results revealed both general and plant-specific patterns in the composition and succession of microbial communities during fermentation. Lactic acid bacteria increasingly dominated in all preparations, whereas the fungal communities retained more plant-specific features. Three distinct fermentation phases with characteristic bacterial communities were identified, i.e., early, middle, and late phases. Co-occurrence network analyses revealed the plant-specific features of the microbial communities.
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Bill M, Gokul JK, Viljoen F, Korsten L. Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions. J Appl Microbiol 2022; 133:1905-1918. [PMID: 35776004 DOI: 10.1111/jam.15693] [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: 03/24/2022] [Revised: 05/27/2022] [Accepted: 06/26/2022] [Indexed: 11/27/2022]
Abstract
AIM OF THE STUDY To characterise the baseline microbial population of the avocado carposphere and understand shifts in community structure from the harvest to ready-to-eat stages. METHODS AND RESULTS The changes in surface or stem-end fungal microbiomes at the postharvest stage of avocado fruit were studied using next-generation sequencing of the internal transcribed spacer (ITS) region. Avocado fructoplane and stem-end pulp fungal richness differed significantly between postharvest stages with a decline following prochloraz dip treatments. Known postharvest decay-causing genera, Colletotrichum, Fusarium, Alternaria, Epicoccum, Penicillium and Neofusicoccum were detected, with Papiliotrema, Meyerozyma and Aureobasidium confirmed as the most dominant potentially beneficial genera. Postharvest interventions such as prochloraz had a negative non-target effect on the presence of Papiliotrema flavescens on the avocado fructoplane. CONCLUSION Our findings reveal a core community of beneficial and pathogenic taxa in the avocado fructoplane, and further highlights the reduction of pathogenic fungi as a consequence of fungicide use. SIGNIFICANCE AND IMPACT OF THE STUDY The current study provides important baseline data for further exploration of fungal population shifts in avocado fruit driven by chemical (fungicide) as well as physical (cold storage) interventions.
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Affiliation(s)
- Malick Bill
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | | | - Francois Viljoen
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield 0028, South Africa
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Dong C, Shao Q, Ren Y, Ge W, Yao T, Hu H, Huang J, Liang Z, Han Y. Assembly, Core Microbiota, and Function of the Rhizosphere Soil and Bark Microbiota in Eucommia ulmoides. Front Microbiol 2022; 13:855317. [PMID: 35591983 PMCID: PMC9110929 DOI: 10.3389/fmicb.2022.855317] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022] Open
Abstract
Medicinal plants are inhabited by diverse microbes in every compartment, and which play an essential role in host growth and development, nutrient absorption, synthesis of secondary metabolites, and resistance to biological and abiotic stress. However, the ecological processes that manage microbiota assembly and the phenotypic and metabolic characteristics of the core microbiota of Eucommia ulmoides remain poorly explored. Here, we systematically evaluated the effects of genotypes, compartment niches, and environmental conditions (climate, soil nutrition, and secondary metabolites) on the assembly of rhizosphere soil and bark associated bacterial communities. In addition, phenotypic and metabolic characteristics of E. ulmoides core microbiota, and their relationship with dominant taxa, rare taxa, and pharmacologically active compounds were deciphered. Results suggested that microbiota assembly along the two compartments were predominantly shaped by the environment (especially pH, relative humidity, and geniposide acid) and not by host genotype or compartment niche. There were 690 shared genera in the rhizosphere soil and bark, and the bark microbiota was mainly derived from rhizosphere soil. Core microbiota of E. ulmoides was a highly interactive “hub” microbes connecting dominant and rare taxa, and its phenotypic characteristics had a selective effect on compartment niches. Metabolic functions of the core microbiota included ammonia oxidation, nitrogen fixation, and polyhydroxybutyrate storage, which are closely related to plant growth or metabolism. Moreover, some core taxa were also significantly correlated with three active compounds. These findings provide an important scientific basis for sustainable agricultural management based on the precise regulation of the rhizosphere soil and bark microbiota of E. ulmoides.
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Affiliation(s)
- Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Yulian Ren
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Ting Yao
- Analysis and Test Center, Huangshan University, Huangshan, China
| | - Haiyan Hu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, China
| | - Jianzhong Huang
- Engineering Research Centre of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Zongqi Liang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, China.,Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, China
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10
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Wang N, Chen S, Xie L, Wang L, Feng Y, Lv T, Fang Y, Ding H. The complete chloroplast genomes of three Hamamelidaceae species: Comparative and phylogenetic analyses. Ecol Evol 2022; 12:e8637. [PMID: 35222983 PMCID: PMC8848467 DOI: 10.1002/ece3.8637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/10/2022] [Accepted: 01/27/2022] [Indexed: 11/07/2022] Open
Abstract
Hamamelidaceae is an important group that represents the origin and early evolution of angiosperms. Its plants have many uses, such as timber, medical, spice, and ornamental uses. In this study, the complete chloroplast genomes of Loropetalum chinense (R. Br.) Oliver, Corylopsis glandulifera Hemsl., and Corylopsis velutina Hand.‐Mazz. were sequenced using the Illumina NovaSeq 6000 platform. The sizes of the three chloroplast genomes were 159,402 bp (C. glandulifera), 159,414 bp (C. velutina), and 159,444 bp (L. chinense), respectively. These chloroplast genomes contained typical quadripartite structures with a pair of inverted repeat (IR) regions (26,283, 26,283, and 26,257 bp), a large single‐copy (LSC) region (88,134, 88,146, and 88,160 bp), and a small single‐copy (SSC) region (18,702, 18,702, and 18,770 bp). The chloroplast genomes encoded 132–133 genes, including 85–87 protein‐coding genes, 37–38 tRNA genes, and 8 rRNA genes. The coding regions were composed of 26,797, 26,574, and 26,415 codons, respectively, most of which ended in A/U. A total of 37–43 long repeats and 175–178 simple sequence repeats (SSRs) were identified, and the SSRs contained a higher number of A + T than G + C bases. The genome comparison showed that the IR regions were more conserved than the LSC or SSC regions, while the noncoding regions contained higher variability than the gene coding regions. Phylogenetic analyses revealed that species in the same genus tended to cluster together. Chunia Hung T. Chang, Mytilaria Lecomte, and Disanthus Maxim. may have diverged early and Corylopsis Siebold & Zucc. was closely related to Loropetalum R. Br. This study provides valuable information for further species identification, evolution, and phylogenetic studies of Hamamelidaceae plants.
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Affiliation(s)
- NingJie Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - ShuiFei Chen
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
| | - Lei Xie
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Lu Wang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YueYao Feng
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Ting Lv
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - YanMing Fang
- Co‐Innovation Center for Sustainable Forestry in Southern China College of Biology and the Environment Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation Nanjing Forestry University Nanjing China
| | - Hui Ding
- Research Center for Nature Conservation and Biodiversity State Environmental Protection Scientific Observation and Research Station for Ecology and Environment of Wuyi Mountains State Environmental Protection Key Laboratory on Biosafety Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment Nanjing China
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