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Moisan MA, Lajoie G, Constant P, Martineau C, Maire V. How tree traits modulate tree methane fluxes: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 940:173730. [PMID: 38839018 DOI: 10.1016/j.scitotenv.2024.173730] [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: 02/11/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/07/2024]
Abstract
Trees can play different roles in the regulation of fluxes of methane (CH4), a greenhouse gas with a warming potential 83 times greater than that of carbon dioxide. Forest soils have the greatest potential for methane uptake compared to other land uses. In addition to their influence on soil CH4 fluxes, trees can act directly as a source or sink of CH4, by transporting CH4 produced in the soil and harbouring the key microorganisms involved in CH4 production and consumption (methanogens and methanotrophs). Tree CH4 fluxes can vary between species characterized by different traits that influence transport and modify the availability of CH4 reaction substrates as well as the habitat for methanogens and methanotrophs. Despite their important role in modulating CH4 fluxes from forest ecosystems, the identity and role of tree traits influencing these fluxes are poorly consolidated in the literature. The objectives of this paper are to 1) Review the functional traits of trees associated with their role in the regulation of CH4 emissions; 2) Assess the importance of inter-specific variability in CH4 fluxes via a global analysis of tree methane fluxes in the literature. Our review highlights that differences in CH4 fluxes between tree species and individuals can be explained by a diversity of traits influencing CH4 transport and microbial production of CH4 such as wood density and secondary metabolites. We propose a functional classification for trees based on the key traits associated with a function in CH4 emissions. We identified the fast-growing species with low wood density, species adapted to flood and species vulnerable to rot as functional groups which can be net sources of CH4 in conditions favorable to CH4 production. The global analysis further demonstrated the importance of taxonomy, with other factors such as land type and season in explaining variability in tree CH4 fluxes.
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Affiliation(s)
- Marie-Ange Moisan
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada; Département des Sciences de l'environnement, Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada; Centre de Recherche sur les Interactions Bassins Versants - Écosystèmes Aquatiques (RIVE), Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada.
| | - Geneviève Lajoie
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke St E, Montréal H1X 2B2, Canada; Jardin Botanique de Montréal, 4101 Sherbrooke St E, Montréal H1X 2B2, Canada
| | - Philippe Constant
- Institut national de la recherche scientifique, Centre Armand-Frappier Santé Biotechnologie, 531 Boul des Prairies, Laval, QC H7V 1B7, Canada
| | - Christine Martineau
- Canadian Forest Service, Natural Resources Canada, Laurentian Forestry Centre, 1055 Rue du Peps, Québec, QC G1V 4C7, Canada
| | - Vincent Maire
- Département des Sciences de l'environnement, Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada; Centre de Recherche sur les Interactions Bassins Versants - Écosystèmes Aquatiques (RIVE), Université du Québec à Trois-Rivières, 3351 Bd des Forges, Trois-Rivières, QC G8Z 4M3, Canada
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2
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Ji K, Wei Y, Lan G. Geographic Location Affects the Bacterial Community Composition and Diversity More than Species Identity for Tropical Tree Species. PLANTS (BASEL, SWITZERLAND) 2024; 13:1565. [PMID: 38891373 PMCID: PMC11175100 DOI: 10.3390/plants13111565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/28/2024] [Accepted: 06/01/2024] [Indexed: 06/21/2024]
Abstract
Microorganisms associated with plants play a crucial role in their growth, development, and overall health. However, much remains unclear regarding the relative significance of tree species identity and spatial variation in shaping the distribution of plant bacterial communities across large tropical regions, as well as how these communities respond to environmental changes. In this study, we aimed to elucidate the characteristics of bacterial community composition in association with two rare and endangered tropical tree species, Dacrydium pectinatum and Vatica mangachapoi, across various geographical locations on Hainan Island. Our findings can be summarized as follows: (1) Significant differences existed in the bacterial composition between D. pectinatum and V. mangachapoi, as observed in the diversity of bacterial populations within the root endosphere. Plant host-related variables, such as nitrogen content, emerged as key drivers influencing leaf bacterial community compositions, underscoring the substantial impact of plant identity on bacterial composition. (2) Environmental factors associated with geographical locations, including temperature and soil pH, predominantly drove changes in both leaf and root-associated bacterial community compositions. These findings underscored the influence of geographical locations on shaping plant-associated bacterial communities. (3) Further analysis revealed that geographical locations exerted a greater influence than tree species identity on bacterial community compositions and diversity. Overall, our study underscores that environmental variables tied to geographical location primarily dictate changes in plant bacterial community composition. These insights contribute to our understanding of microbial biogeography in tropical regions and carry significant implications for the conservation of rare and endangered tropical trees.
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Affiliation(s)
- Kepeng Ji
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
| | - Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- Hainan Danzhou Tropical Agro-Ecosystem National Observation and Research Station, Danzhou 571737, China
| | - Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (K.J.); (Y.W.)
- Hainan Danzhou Tropical Agro-Ecosystem National Observation and Research Station, Danzhou 571737, China
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3
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Kończak B, Wiesner-Sękala M, Ziembińska-Buczyńska A. The European trees phyllosphere characteristics and its potential in air bioremediation. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 349:123977. [PMID: 38621454 DOI: 10.1016/j.envpol.2024.123977] [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: 01/17/2024] [Revised: 03/08/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.
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Affiliation(s)
- B Kończak
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - M Wiesner-Sękala
- Department of Water Protection, Central Mining Institute - National Research Institute, Plac Gwarków 1, 40-166, Katowice, Poland.
| | - A Ziembińska-Buczyńska
- Department of Environmental Biotechnology, Faculty of Power and Environmental Engineering, Silesian University of Technology, str. Akademicka 2, 44-100, Gliwice, Poland.
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4
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Chen X, Li L, He Y. Epiphytic and endophytic bacteria on Camellia oleifera phyllosphere: exploring region and cultivar effect. BMC Ecol Evol 2024; 24:62. [PMID: 38735962 PMCID: PMC11089727 DOI: 10.1186/s12862-024-02240-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/10/2024] [Indexed: 05/14/2024] Open
Abstract
The epiphytic and endophytic bacteria play an important role in the healthy growth of plants. Both plant species and growth environmental influence the bacterial population diversity, yet it is inconclusive whether it is the former or the latter that has a greater impact. To explore the communities of the epiphytic and endophytic microbes in Camellia oleifera, this study assessed three representative C. oleifera cultivars from three areas in Hunan, China by Illumina high-throughput sequencing. The results showed that the diversity and species richness of endophytic microbial community in leaves were significantly higher than those of microbial community in the epiphytic. The diversity and species richness of epiphytic and endophytic microbes are complex when the same cultivar was grown in different areas. The C. oleifera cultivars grown in Youxian had the highest diversity of epiphytic microbial community, but the lowest abundance, while the cultivars grown in Changsha had the highest diversity and species richness of endophytic microbes in leaves. It was concluded that the dominant phylum mainly included Proteobacteria, Actinobacteriota and Firmicutes through the analysis of the epiphytic and endophytic microbial communities of C. oleifera. The species and relative abundances of epiphytic and endophytic microbial community were extremely different at the genus level. The analysis of NMDS map and PERMANOVA shows that the species richness and diversity of microbial communities in epiphytes are greatly influenced by region. However, the community structure of endophytic microorganisms in leaves is influenced by region and cultivated varieties, but the influence of cultivars is more significant. Molecular ecological network analysis showed that the symbiotic interaction of epiphytic microbial community was more complex.
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Affiliation(s)
- Xiaolin Chen
- Key Laboratory of National Forestry and Grassland Administration On Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Ordos Forestry and Grassland Development Center, Ordos, China
| | - Lili Li
- Key Laboratory of National Forestry and Grassland Administration On Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yuanhao He
- Key Laboratory of National Forestry and Grassland Administration On Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-Wood Forest Cultivation and Conservation of Ministry of Education, Key Laboratory of Forest Bio-Resources and Integrated Pest Management for Higher Education in Hunan Province, College of Forestry, Central South University of Forestry and Technology, Changsha, China.
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5
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Park J, Yoon SG, Lee H, An J, Nam K. Effects of in situ Fe oxide precipitation on As stabilization and soil ecological resilience under salt stress. JOURNAL OF HAZARDOUS MATERIALS 2024; 462:132629. [PMID: 37832440 DOI: 10.1016/j.jhazmat.2023.132629] [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: 06/08/2023] [Revised: 09/04/2023] [Accepted: 09/23/2023] [Indexed: 10/15/2023]
Abstract
Iron (Fe) oxide precipitation is a promising method for stabilizing arsenic (As) in contaminated soils; however, the addition of salts during the process can negatively affect soil functions. This study investigated the effects of in situ Fe oxide precipitation on As stabilization and the impact of salt stress on soil functions and microbial communities. Fe oxide precipitation reduced the concentration of bioaccessible As by 84% in the stabilized soil, resulting in the formation of ferrihydrite and lepidocrocite, as confirmed by XANES. Nevertheless, an increase in salt stress reduced barley development, microbial enzyme activities, and microbial diversity compared to those in the original soil. Despite this, the stabilized soil exhibited natural resilience and potential for enhanced microbial adaptations, with increased retention of salt-tolerant bacteria. Washing the stabilized soil with water restored EC1:5 to the level of the original soil, resulting in increased barley growth rates and enzyme activities after 5-d and 20-week incubation periods, suggesting soil function recovery. 16 S rRNA sequencing revealed the retention of salt-tolerant bacteria in the stabilized soil, while salt-removed soil exhibited an increase in Proteobacteria, which could facilitate ecological functions. Overall, Fe oxide precipitation effectively stabilized soil As and exhibited potential for restoring the natural resilience and ecological functions of soils through microbial adaptations and salt removal.
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Affiliation(s)
- Jinhee Park
- Department of Civil & Environmental Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Sang-Gyu Yoon
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea
| | - Hosub Lee
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
| | - Jinsung An
- Department of Smart City Engineering, Hanyang University, Ansan 15588, South Korea; Department of Civil & Environmental Engineering, Hanyang University, Ansan 15588, South Korea.
| | - Kyoungphile Nam
- Department of Civil & Environmental Engineering, Seoul National University, Seoul 08826, South Korea
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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7
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Likar M, Grašič M, Stres B, Regvar M, Gaberščik A. Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community. Sci Rep 2023; 13:21741. [PMID: 38066117 PMCID: PMC10709317 DOI: 10.1038/s41598-023-49044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.
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Affiliation(s)
- Matevž Likar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia.
| | - Mateja Grašič
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Blaž Stres
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, Ljubljana, Slovenia
- Biocybernetics and Robotics, Department of Automation, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Marjana Regvar
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Alenka Gaberščik
- Biotechnical Faculty, Department of Biology, University of Ljubljana, Večna Pot 111, 1000, Ljubljana, Slovenia
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8
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He C, Meng D, Li W, Li X, He X. Dynamics of Endophytic Fungal Communities Associated with Cultivated Medicinal Plants in Farmland Ecosystem. J Fungi (Basel) 2023; 9:1165. [PMID: 38132766 PMCID: PMC10744690 DOI: 10.3390/jof9121165] [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: 10/06/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
Microorganisms are an important component of global biodiversity and play an important role in plant growth and development and the protection of host plants from various biotic and abiotic stresses. However, little is known about the identities and communities of endophytic fungi inhabiting cultivated medicinal plants in the farmland ecosystem. The diversity and community composition of the endophytic fungi of cultivated medicinal plants in different hosts, tissue niches, and seasonal effects in the farmland of Northern China were examined using the next-generation sequencing technique. In addition, the ecological functions of the endophytic fungal communities were investigated by combining the sequence classification information and fungal taxonomic function annotation. A total of 1025 operational taxonomic units (OTUs) of endophytic fungi were obtained at a 97% sequence similarity level; they were dominated by Dothideomycetes and Pleosporales. Host factors (species identities and tissue niches) and season had significant effects on the community composition of endophytic fungi, and endophytic fungi assembly was shaped more strongly by host than by season. In summer, endophytic fungal diversity was higher in the root than in the leaf, whereas opposite trends were observed in winter. Network analysis showed that network connectivity was more complex in the leaf than in the root, and the interspecific relationship between endophytic fungal OTUs in the network structure was mainly positive rather than negative. The functional predications of fungi revealed that the pathotrophic types of endophytic fungi decreased and the saprotrophic types increased from summer to winter in the root, while both pathotrophic and saprotrophic types of endophytic fungi increased in the leaf. This study improves our understanding of the community composition and ecological distribution of endophytic fungi inhabiting scattered niches in the farmland ecosystem. In addition, the study provides insight into the biodiversity assessment and management of cultivated medicinal plants.
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Affiliation(s)
- Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China;
| | - Deyao Meng
- College of Life Sciences, Hebei University, Baoding 071002, China; (D.M.); (W.L.)
| | - Wanyun Li
- College of Life Sciences, Hebei University, Baoding 071002, China; (D.M.); (W.L.)
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China;
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding 071002, China; (D.M.); (W.L.)
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9
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Shang H, Tan BZ, Dakwa V, D'Agnese E, Stanley RA, Sassi H, Lai YW, Deaker R, Bowman JP. Effect of pre-harvest sanitizer treatments on Listeria survival, sensory quality and bacterial community dynamics on leafy green vegetables grown under commercial conditions. Food Res Int 2023; 173:113341. [PMID: 37803650 DOI: 10.1016/j.foodres.2023.113341] [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: 03/23/2023] [Revised: 07/19/2023] [Accepted: 07/31/2023] [Indexed: 10/08/2023]
Abstract
Leafy green vegetables (LGVs) have large surface areas and can be colonized by various microorganisms including pathogens. In this study, we investigated the effect of pre-harvest sanitizer treatments on the survival of inoculated proxy pathogen Listeria innocua ATCC 33090 and the natural microbial community of mizuna, rocket (arugula), red chard and spinach grown under commercial conditions. Electrolyzed water (e-water), peracetic acid (PAA), and 1-bromo-3-chloro-5-dimethylhydantoin (BCDMH) were tested against water controls. We also observed the subsequent sensorial changes of harvested, bagged LGV leaves over a period of 12 days within chill storage alongside the growth, diversity and structure of bacterial populations determined using 16S rRNA gene amplicon sequencing and total viable counts (TVC). Treatment with PAA resulted in the highest reductions of L. innocua (2.4-5.5 log units) compared to the other treatments (0.25-2.5 log units). On day 0 (24 h after sanitizer application), the TVC on sanitizer treated LGVs were significantly reduced compared to water controls, except for rocket. During storage at 4.5 (±0.5)°C sanitisers only hindered microbial growth on LGVs initially and did not influence final bacterial population levels, growth rates or changes in LGV sample colour, decay, odour and texture compared to water controls. Shelf-life was not extended nor was it reduced. The community structure on LGV types differed though a core set of bacterial amplicon sequence variants (ASV) were present across all samples. No significant differences were observed in bacterial diversity between sanitizer treatments, however sanitizer treated LGV samples had initially reduced diversity compared to water treated samples. The bacterial compositions observed at the end point of storage considerably differed from what was observed at initial point owing to the increase in abundance of specific bacterial taxa, mainly Pseudomonas spp., the abundance and growth responses differing between LGV types studied. This study provides a better understanding on the microbiology and sensory impact of pre-harvest applied sanitiser treatments on different LGVs destined for commercial food use.
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Affiliation(s)
- Hongshan Shang
- School of Life and Environmental Sciences, F22 - LEES Building, The University of Sydney, NSW 2006, Australia; Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Bi Zheng Tan
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Vongai Dakwa
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Erin D'Agnese
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Roger A Stanley
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia
| | - Hannah Sassi
- School of Life and Environmental Sciences, F22 - LEES Building, The University of Sydney, NSW 2006, Australia
| | - Yu-Wen Lai
- School of Life and Environmental Sciences, F22 - LEES Building, The University of Sydney, NSW 2006, Australia
| | - Rosalind Deaker
- School of Life and Environmental Sciences, F22 - LEES Building, The University of Sydney, NSW 2006, Australia
| | - John P Bowman
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Sandy Bay, Tasmania 7005, Australia.
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10
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Sun Z, Zhang W, Liu Y, Ding C, Zhu W. The Changes of Phyllosphere Fungal Communities among Three Different Populus spp. Microorganisms 2023; 11:2479. [PMID: 37894137 PMCID: PMC10609125 DOI: 10.3390/microorganisms11102479] [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: 08/28/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves' physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely-P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves' chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.
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Affiliation(s)
- Zhuo Sun
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling 110161, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China;
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100083, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang 110000, China; (Z.S.); (Y.L.)
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling 110161, China
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11
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Gao L, Kantar MB, Moxley D, Ortiz-Barrientos D, Rieseberg LH. Crop adaptation to climate change: An evolutionary perspective. MOLECULAR PLANT 2023; 16:1518-1546. [PMID: 37515323 DOI: 10.1016/j.molp.2023.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/20/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023]
Abstract
The disciplines of evolutionary biology and plant and animal breeding have been intertwined throughout their development, with responses to artificial selection yielding insights into the action of natural selection and evolutionary biology providing statistical and conceptual guidance for modern breeding. Here we offer an evolutionary perspective on a grand challenge of the 21st century: feeding humanity in the face of climate change. We first highlight promising strategies currently under way to adapt crops to current and future climate change. These include methods to match crop varieties with current and predicted environments and to optimize breeding goals, management practices, and crop microbiomes to enhance yield and sustainable production. We also describe the promise of crop wild relatives and recent technological innovations such as speed breeding, genomic selection, and genome editing for improving environmental resilience of existing crop varieties or for developing new crops. Next, we discuss how methods and theory from evolutionary biology can enhance these existing strategies and suggest novel approaches. We focus initially on methods for reconstructing the evolutionary history of crops and their pests and symbionts, because such historical information provides an overall framework for crop-improvement efforts. We then describe how evolutionary approaches can be used to detect and mitigate the accumulation of deleterious mutations in crop genomes, identify alleles and mutations that underlie adaptation (and maladaptation) to agricultural environments, mitigate evolutionary trade-offs, and improve critical proteins. Continuing feedback between the evolution and crop biology communities will ensure optimal design of strategies for adapting crops to climate change.
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Affiliation(s)
- Lexuan Gao
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Michael B Kantar
- Department of Tropical Plant & Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Dylan Moxley
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Daniel Ortiz-Barrientos
- School of Biological Sciences and Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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12
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Kolackova I, Smolkova B, Skladanka J, Kouril P, Hrudova E. Epiphytic microflora and mycotoxin content in meadows-Is plant biodiversity affecting fungal contamination? PLoS One 2023; 18:e0288397. [PMID: 37708181 PMCID: PMC10501618 DOI: 10.1371/journal.pone.0288397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/23/2023] [Indexed: 09/16/2023] Open
Abstract
Ecosystem services are an important aspect of grasslands utilization; however, they are often contradictory to their main purpose, which is a production of good quality and safe feed. In this study, we evaluated the difference between grass monocultures and species-rich mixtures in terms of epiphytic microflora and mycotoxin contamination levels. We hypothesized that higher species diversity would lead to higher microbial counts, which could lead to higher mycotoxin contamination risk. Differences in epiphytic fungal, yeast and total amount of microorganisms (CFU g -1) depending on the species diversity in the field has been evaluated by cultivation method. Concentration of deoxynivalenol (DON), zearalenone (ZEN) and aflatoxin B1 (AFB1) was measured by ELISA. Results are suggesting that higher total amount of microorganisms were found in monocultures, however, fungal and yeast counts were higher in species-rich mixtures. Higher species diversity of grasses was related to higher total microbial count (TMC) and yeast colonization of phyllosphere. Our results suggest higher risk of fungal phyllosphere colonization of species-rich mixtures with higher biodiversity and therefore higher risk of mycotoxin contamination of such feed.
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Affiliation(s)
- Ivana Kolackova
- Department of Animal Nutrition and Forage Production, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Barbora Smolkova
- Department of Animal Nutrition and Forage Production, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Jiri Skladanka
- Department of Animal Nutrition and Forage Production, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Petr Kouril
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Eva Hrudova
- Department of Crop Science, Breeding and Plant Medicine, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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13
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Demarquest G, Lajoie G. Bacterial endophytes of sugar maple leaves vary more idiosyncratically than epiphytes across a large geographic area. FEMS Microbiol Ecol 2023; 99:fiad079. [PMID: 37442613 DOI: 10.1093/femsec/fiad079] [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: 04/17/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/15/2023] Open
Abstract
Bacteria from the leaf surface and the leaf tissue have been attributed with several beneficial properties for their plant host. Though physically connected, the microbial ecology of these compartments has mostly been studied separately such that we lack an integrated understanding of the processes shaping their assembly. We sampled leaf epiphytes and endophytes from the same individuals of sugar maple across the northern portion of its range to evaluate if their community composition was driven by similar processes within and across populations differing in plant traits and overall abiotic environment. Leaf compartment explained most of the variation in community diversity and composition across samples. Leaf epiphytic communities were driven more by host and site characteristics than endophytic communities, whose community composition was more idiosyncratic across samples. Our results suggest a greater importance of priority effects and opportunistic colonization in driving community assembly of leaf endophytes. Understanding the comparative assembly of bacterial communities at the surface and inside plant leaves may be particularly useful for leveraging their respective potential for improving the health of plants in natural and anthropized ecosystems.
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Affiliation(s)
- Garance Demarquest
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Université de Rennes, Agro-Campus Ouest, 65 Rue de Saint-Brieuc, 35042 Rennes, France
| | - Geneviève Lajoie
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
- Jardin Botanique de Montréal, 4101 rue Sherbrooke E, H1X 2B2 Montréal, Canada
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14
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Luo K, Zhao G, Chen M, Tian X. Effects of maize resistance and leaf chemical substances on the structure of phyllosphere fungal communities. FRONTIERS IN PLANT SCIENCE 2023; 14:1241055. [PMID: 37645458 PMCID: PMC10461017 DOI: 10.3389/fpls.2023.1241055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
It is well known that plant genotype can regulate phyllosphere fungi at the species level. However, little is known about how plant varieties shape the fungal communities in the phyllosphere. In this study, four types of maize varieties with various levels of resistances to Exserohilum turcicum were subjected to high-throughput sequencing to reveal the properties that influences the composition of phyllosphere fungal communities. The dominant fungi genera for all four maize varieties were Alternaria at different relative abundances, followed by Nigrospora. Hierarchical clustering analysis, non-metric multidimensional scaling and similarity analysis confirmed that the fungal communities in the phyllosphere of the four varieties were significantly different and clustered into the respective maize variety they inhabited. The findings from Redundancy Analysis (RDA) indicated that both maize resistance and leaf chemical constituents, including nitrogen, phosphorus, tannins, and flavonoids, were the major drivers in determining the composition of phyllosphere fungal communities. Among these factors, maize resistance was found to be the most influential, followed by phosphorus. The co-occurrence network of the fungal communities in the phyllosphere of highly resistant variety had higher complexity, integrity and stability compared to others maize varieties. In a conclusion, maize variety resistance and leaf chemical constituents play a major role in shaping the phyllosphere fungal community. The work proposes a link between the assembled fungal communities within the phyllosphere with maize variety that is resistant to pathogenic fungi infection.
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Affiliation(s)
- Kun Luo
- Hunan Agricultural University, Changsha, Hunan, China
| | - Gonghua Zhao
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mengfei Chen
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xueliang Tian
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
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15
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Huang S, Zha X, Fu G. Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2891. [PMID: 37631103 PMCID: PMC10458011 DOI: 10.3390/plants12162891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.
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Affiliation(s)
- Shaolin Huang
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xinjie Zha
- Xi’an University of Finance and Economics, Xi’an 710100, China;
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
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16
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Vadillo Gonzalez S, Vranken S, Coleman MA, Wernberg T, Steinberg PD, Marzinelli EM. Host genotype and microbiome associations in co-occurring clonal and non-clonal kelp, Ecklonia radiata. Mol Ecol 2023; 32:4584-4598. [PMID: 37332135 DOI: 10.1111/mec.17056] [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: 10/25/2022] [Revised: 04/21/2023] [Accepted: 06/09/2023] [Indexed: 06/20/2023]
Abstract
A fundamental question in holobiont biology is the extent to which microbiomes are determined by host characteristics regulated by their genotype. Studies on the interactions of host genotype and microbiomes are emerging but disentangling the role that host genotype has in shaping microbiomes remains challenging in natural settings. Host genotypes tend to be segregated in space and affected by different environments. Here we overcome this challenge by studying an unusual situation where host asexual (5 clonal lineages) and sexual genotypes (15 non-clonal lineages) of the same species co-occur under the same environment. This allowed us to partition the influence of morphological traits and genotype in shaping host-associated bacterial communities. Lamina-associated bacteria of co-occurring kelp sexual non-clonal (Ecklonia radiata) and asexual clonal (E. brevipes) morphs were compared to test whether host genotype influences microbiomes beyond morphology. Similarity of bacterial composition and predicted functions were evaluated among individuals within a single clonal genotype or among non-clonal genotypes of each morph. Higher similarity in bacterial composition and inferred functions were found among identical clones of E. brevipes compared to other clonal genotypes or unique non-clonal E. radiata genotypes. Additionally, bacterial diversity and composition differed significantly between the two morphs and were related with one morphological trait in E. brevipes (haptera). Thus, factors regulated by the host genotype (e.g. secondary metabolite production) likely drive differences in microbial communities between morphs. The strong association of genotype and microbiome found here highlights the importance of genetic relatedness of hosts in determining variability in their bacterial symbionts.
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Affiliation(s)
- Sebastian Vadillo Gonzalez
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
| | - Sofie Vranken
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
| | - Melinda A Coleman
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- New South Wales Fisheries, Department of Primary Industries, National Marine Science Centre, Coffs Harbour, New South Wales, Australia
| | - Thomas Wernberg
- UWA Oceans Institute & School of Biological Sciences, University of Western Australia, Crowley, Western Australia, Australia
- Institute of Marine Research, Floedevigen Research Station, His, Norway
| | - Peter D Steinberg
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ezequiel M Marzinelli
- The University of Sydney, School of Life and Environmental Sciences, Sydney, New South Wales, Australia
- Sydney Institute of Marine Science, Mosman, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore City, Singapore
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17
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Lin T, Tang J, Li S, Li S, Han S, Liu Y, Yang C, Chen G, Chen L, Zhu T. Drought stress-mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:1100-1113. [PMID: 37177875 DOI: 10.1111/tpj.16283] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/04/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Phyllosphere-associated microbes play a crucial role in plant-pathogen interactions while their composition and diversity are strongly influenced by drought stress. As dioecious plant species exhibited secondary dimorphism between the two sexes in response to drought stress, whether such difference will lead to sex-specific differences in phyllosphere microbiome and associated pathogen resistance between male and female conspecifics is still unknown. In this study, we subjected female and male full siblings of a dioecious poplar species to a short period of drought treatment followed by artificial infection of a leaf pathogenic fungus. Our results showed that male plants grew better than females with or without drought stress. Female control plants had more leaf lesion area than males after pathogen infection, whereas drought stress reversed such a difference. Further correlation and in vitro toxicity tests suggested that drought-mediated sexual differences in pathogen resistance between the two plant sexes could be attributed to the shifts in structure and function of phyllosphere-associated microbiome rather than the amount of leaf main defensive chemicals contained in plant leaves. Supportively, the microbiome analysis through high-throughput sequencing indicated that female phyllosphere enriched a higher abundance of ecologically beneficial microbes that serve as biological plant protectants, while males harbored abundant phytopathogens under drought-stressed conditions. The results could provide potential implications for the selection of suitable poplar sex to plants in drought or semi-drought habitats.
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Affiliation(s)
- Tiantian Lin
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China and Centre of Invasion Biology, Institute of Biodiversity, Yunnan University, 650504, Kunming, China
| | - Jiayao Tang
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shuying Li
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shujiang Li
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Shan Han
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yinggao Liu
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Chunlin Yang
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Gang Chen
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Lianghua Chen
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tianhui Zhu
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, Key Laboratory of Forest Protection of Sichuan Education Department, College of Forestry, Sichuan Agricultural University, 611130, Chengdu, China
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18
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Gao J, Uwiringiyimana E, Zhang D. Microbial composition and diversity of the tobacco leaf phyllosphere during plant development. Front Microbiol 2023; 14:1199241. [PMID: 37502406 PMCID: PMC10368876 DOI: 10.3389/fmicb.2023.1199241] [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: 04/03/2023] [Accepted: 06/06/2023] [Indexed: 07/29/2023] Open
Abstract
Phyllosphere-associated microorganisms affect host plant's nutrients availability, its growth and ecological functions. Tobacco leaves provide a wide-area habitat for microbial life. Previous studies have mainly focused on phyllosphere microbiota at one time point of tobacco growth process, but more is unknown about dynamic changes in phyllospheric microbial composition from earlier to the late stage of plant development. In the current study, we had determined the bacterial and fungal communities succession of tobacco growth stages (i.e., seedling, squaring, and maturing) by using both 16S rRNA sequencing for bacterial and ITS sequencing for fungi. Our results demonstrated that among tobacco growth stages, the phyllospheric bacterial communities went through more distinct succession than the fungal communities did. Proteobacteria and Actinobacteria exerted the most influence in tobacco development from seedling to squaring stages. At maturing stage, Proteobacteria and Actinobacteria dominance was gradually replaced by Firmicutes and Bacteroidetes. Network analysis revealed that Proteobacteria, as the core phyllospheric microbia, played essential role in stabilizing the whole bacterial network during tobacco development, and consequently rendered it to more profound ecological functions. During tobacco development, the contents of leaf sugar, nicotine, nitrogen and potassium were significantly correlated with either bacterial or fungal communities, and these abiotic factors accounted for 39.3 and 51.5% of the total variation, respectively. We overall evinced that the development of tobacco phyllosphere is accompanied by variant dynamics of phyllospheric microbial community.
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Affiliation(s)
- Jianing Gao
- College of Tourism and Geographical Science, Leshan Normal University, Leshan, China
| | - Ernest Uwiringiyimana
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dan Zhang
- Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
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19
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Sánchez-Salazar AM, Taparia T, Olesen AK, Acuña JJ, Sørensen SJ, Jorquera MA. An overview of plasmid transfer in the plant microbiome. Plasmid 2023; 127:102695. [PMID: 37295540 DOI: 10.1016/j.plasmid.2023.102695] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023]
Abstract
Plant microbiomes are pivotal for healthy plant physiological development. Microbes live in complex co-association with plant hosts, and interactions within these microbial communities vary with plant genotype, plant compartment, phenological stage, and soil properties, among others. Plant microbiomes also harbor a substantial and diverse pool of mobile genes encoded on plasmids. Several plasmid functions attributed to plant-associated bacteria are relatively poorly understood. Additionally, the role of plasmids in disseminating genetic traits within plant compartments is not well known. Here, we present the current knowledge on the occurrence, diversity, function, and transfer of plasmids in plant microbiomes, emphasizing the factors that could modulate gene transfer in-planta. We also describe the role of the plant microbiome as a plasmid reservoir and the dissemination of its genetic material. We include a brief discussion on the current methodological limitations in studying plasmid transfer within plant microbiomes. This information could be useful to elucidate the dynamics of the bacterial gene pools, the adaptations different organisms have made, and variations in bacterial populations that might have never been described before, particularly in complex microbial communities associated with plants in natural and anthropogenic impacted environments.
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Affiliation(s)
- Angela M Sánchez-Salazar
- Programa de Doctorado en Ciencias de Recursos Naturales, Facultad de Ingeniería y Ciencia, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Tanvi Taparia
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Asmus K Olesen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark
| | - Jacquelinne J Acuña
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile
| | - Søren J Sørensen
- Section for Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15 Bldg 1, 2100 Copenhagen, Denmark.
| | - Milko A Jorquera
- Laboratorio de Ecología Microbiana Aplicada, Departamento de Ciencias Químicas y Recursos Naturales, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile; The Network for Extreme Environment Research (NEXER), Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Av. Francisco Salazar, 01145 Temuco, Chile.
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20
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Punja ZK, Ni L, Lung S, Buirs L. Total yeast and mold levels in high THC-containing cannabis ( Cannabis sativa L.) inflorescences are influenced by genotype, environment, and pre-and post-harvest handling practices. Front Microbiol 2023; 14:1192035. [PMID: 37383630 PMCID: PMC10294073 DOI: 10.3389/fmicb.2023.1192035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/10/2023] [Indexed: 06/30/2023] Open
Abstract
Total yeast and mold (TYM) levels in inflorescences of high THC-containing Cannabis sativa (cannabis) are regulated to ensure that medicinal and recreational users, especially those with immunocompromised systems, are not exposed to potentially harmful levels. In North America, the limits imposed range from 1,000-10,000 cfu/g of dried product to 50,000-100,000 cfu/g, depending on the jurisdiction. Factors affecting a build-up of TYM in cannabis inflorescences have not been previously researched. In this study, >2,000 fresh and dried samples were assayed for TYM over a 3-year period (2019-2022) to identify specific factors which can contribute to TYM levels. Greenhouse-grown inflorescences were sampled before and after commercial harvest, homogenized for 30 s, and plated onto potato dextrose agar (PDA) with 140 mg/L streptomycin sulfate. Colony-forming-units (cfu) were rated after 5 days of incubation at 23°C under 10-14 h light. PDA provided more consistent counts of cfu compared to Sabouraud dextrose and tryptic soy agars. The predominant fungal genera identified by PCR of the ITS1-5.8S-ITS2 region of rDNA were Penicillium, Aspergillus, Cladosporium, and Fusarium. In addition, four yeast genera were recovered. In total, 21 species of fungi and yeasts constituted the total cfu present in the inflorescences. The variables that significantly (p < 0.05) increased these TYM levels in inflorescences were: the genotype (strain) grown, presence of leaf litter in the greenhouse, harvesting activity by workers, genotypes with a higher abundance of stigmatic tissues and inflorescence leaves, higher temperature and relative humidity within the inflorescence microclimate, time of year (May-October), method of drying buds after harvest, and inadequate drying of buds. The variables which significantly (p < 0.05) decreased TYM in samples were: genotypes with lower numbers of inflorescence leaves, air circulation achieved by fans during inflorescence maturation, harvesting during November-April, hang-drying of entire inflorescence stems, and drying to a moisture content of 12-14% (water activity of 0.65-0.7) or lower which was inversely correlated with cfu levels. Under these conditions, the majority of dried commercial cannabis samples contained <1,000-5,000 cfu/g. Our findings indicate that TYM in cannabis inflorescences are the result of a dynamic interaction between genotype, environment, and post-harvest handling methods. Some of these factors may be altered by cannabis producers to reduce the potential build-up of these microbes. Among the 21 fungal and yeast species recovered from greenhouse-grown cannabis inflorescences, a few could pose a potential threat to human health, while many do not and they could provide beneficial interactions within the cannabis plant. The currently recommended plating methods onto agar media and enumeration of total cfu are unable to distinguish between these two groups.
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Fan X, Su J, Zhou S, An X, Li H. Plant cultivar determined bacterial community and potential risk of antibiotic resistance gene spread in the phyllosphere. J Environ Sci (China) 2023; 127:508-518. [PMID: 36522081 DOI: 10.1016/j.jes.2022.06.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 06/17/2023]
Abstract
The global increased antibiotic resistance level in pathogenic microbes has posed a significant threat to human health. Fresh vegetables have been recognized to be an important vehicle of antibiotic resistance genes (ARGs) from environments to human beings. Phyllosphere ARGs have been indicated to be changed with plant species, yet the influence of plant cultivar on the phyllospheric resistome is still unclear. Here, we detected the ARGs and bacterial communities in the phyllosphere of two cultivars of cilantros and their corresponding soils using high-throughput quantitative PCR technique and bacterial 16S rRNA gene-based high-throughput sequencing, respectively. We further identified the potential bacterial pathogens and analyzed the effects of plant cultivar on ARGs, mobile genetic elements (MGEs), microbiome and potential bacterial pathogens. The results showed that the cultivars did not affect the ARG abundance and composition, but significantly shaped the abundance of MGEs and the composition structure of bacteria in the phyllosphere. The relative abundance of potential bacterial pathogens was significantly higher in the phyllosphere than that in soils. Mantel test showed that the ARG patterns were significantly correlated to the patterns of potential bacterial pathogens. Our results suggested that the horizontal gene transfer of ARGs in the phyllosphere might be different between the two cultivars of cilantro and highlighted the higher risk of phyllospheric microorganisms compared with those in soils. These findings extend our knowledge on the vegetable microbiomes, ARGs, and potential pathogens, suggesting more agricultural and hygiene protocols are needed to control the risk of foodborne ARGs.
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Affiliation(s)
- Xiaoting Fan
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianqiang Su
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyidan Zhou
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinli An
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Zhu C, Lin Y, Wang Z, Luo W, Zhang Y, Chu C. Community assembly and network structure of epiphytic and endophytic phyllosphere fungi in a subtropical mangrove ecosystem. Front Microbiol 2023; 14:1147285. [PMID: 37007520 PMCID: PMC10064055 DOI: 10.3389/fmicb.2023.1147285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Microorganisms can influence plant growth and health, ecosystem functioning, and stability. Community and network structures of mangrove phyllosphere fungi have rarely been studied although mangroves have very important ecological and economical values. Here, we used high throughput sequencing of the internal transcribed spacer 2 (ITS2) to assess epiphytic and endophytic phyllosphere fungal communities of six true mangrove species and five mangrove associates. Totally, we obtained 1,391 fungal operational taxonomic units (OTUs), including 596 specific epiphytic fungi, 600 specific endophytic fungi, and 195 shared fungi. The richness and community composition differed significantly for epiphytes and endophytes. Phylogeny of the host plant had a significant constraint on epiphytes but not endophytes. Network analyses showed that plant–epiphyte and plant–endophyte networks exhibited strong specialization and modularity but low connectance and anti-nestedness. Compared to plant–endophyte network, plant–epiphyte network showed stronger specialization, modularity, and robustness but lower connectance and anti-nestedness. These differences in community and network structures of epiphytes and endophytes may be caused by spatial niche partitioning, indicating their underlying ecological and environmental drivers are inconsistent. We highlight the important role of plant phylogeny in the assembly of epiphytic but not endophytic fungal communities in mangrove ecosystems.
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Affiliation(s)
- Chunchao Zhu
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
- *Correspondence: Chunchao Zhu,
| | | | - Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montreal, QC, Canada
| | - Wenqi Luo
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
| | - Yonghua Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, China
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Li X, Tseng HT, Hemmings G, Omolehin O, Taylor C, Taylor A, Kong P, Daughtrey M, Gouker F, Hong C. Characterization of Boxwood Shoot Bacterial Communities and Potential Impact from Fungicide Treatments. Microbiol Spectr 2023; 11:e0416322. [PMID: 36853063 PMCID: PMC10100737 DOI: 10.1128/spectrum.04163-22] [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: 10/12/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Phyllosphere bacterial communities play important roles in plant fitness and growth. The objective of this study was to characterize the epiphytic and endophytic bacterial communities of boxwood shoots and determine how they may respond to commonly used fungicides. In early summer and early fall, shoot samples were collected immediately before and 1, 7, and 14 days after three fungicides containing chlorothalonil and/or propiconazole were applied to the canopy. Total genomic DNA from shoot surface washings and surface-sterilized shoot tissues was used as the template for 16S rRNA metabarcoding, and the amplicons were sequenced on a Nanopore MinION sequencer to characterize the epiphytic and endophytic communities. The bacterial communities were phylogenetically more diverse on the boxwood shoot surface than in the internal tissue, although the two communities shared 12.7% of the total 1,649 identified genera. The most abundant epiphytes were Methylobacterium and Pantoea, while Stenotrophomonas and Brevundimonas were the dominant endophytes. Fungicide treatments had strong impacts on epiphytic bacterial community structure and composition. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) and analysis of variance (ANOVA)-like differential expression (ALDEx2) together identified 312 and 1,362 epiphytes changed in abundance due to fungicide treatments in early summer and early fall, respectively, and over 50% of these epiphytes were negatively impacted by fungicide. The two chlorothalonil-based contact fungicides demonstrated more marked effects than the propiconazole-based systemic fungicide. These results are foundational for exploring and utilizing the full potential of the microbiome and fungicide applications and developing a systems approach to boxwood health and production. IMPORTANCE Agrochemicals are important tools for safeguarding plants from invasive pathogens, insects, mites, and weeds. How they may affect the plant microbiome, a critical component of crop health and production, was poorly understood. Here, we used boxwood, an iconic low-maintenance landscape plant, to characterize shoot epiphytic and endophytic bacterial communities and their responses to contact and systemic fungicides. This study expanded our understanding of the above-ground microbiome in ornamental plants and is foundational for utilizing the full benefits of the microbiome in concert with different fungicide chemistries to improve boxwood health. This study also sets an example for a more thorough evaluation of these and other agrochemicals for their effects on boxwood microbiomes during production and offers an expanded systems approach that could be used with other crops for enhanced integrated pest management.
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Affiliation(s)
- Xiaoping Li
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Hsien Tzer Tseng
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Raleigh, North Carolina, USA
| | - Ginger Hemmings
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Dobson, North Carolina, USA
| | - Olanike Omolehin
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Chad Taylor
- North Carolina Department of Agriculture and Consumer Services, Plant Industry Division, Boone, North Carolina, USA
| | - Amanda Taylor
- North Carolina University Cooperative Extension, Morganton, North Carolina, USA
| | - Ping Kong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
| | - Margery Daughtrey
- Long Island Horticultural Research and Extension Center, Cornell University, Riverhead, New York, USA
| | - Fred Gouker
- USDA-ARS, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, Maryland, USA
| | - Chuanxue Hong
- Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Virginia Beach, Virginia, USA
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Šigutová H, Šigut M, Pyszko P, Kostovčík M, Kolařík M, Drozd P. Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet. Microbiol Spectr 2023; 11:e0316022. [PMID: 36629441 PMCID: PMC9927363 DOI: 10.1128/spectrum.03160-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.
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Affiliation(s)
- Hana Šigutová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Šigut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Pyszko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Kostovčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavel Drozd
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Yin X, Zhao J, Wang S, Dong Z, Li J, Shao T. The effects of epiphytic microbiota and chemical composition of Italian ryegrass harvested at different growth stages on silage fermentation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1385-1393. [PMID: 36151894 DOI: 10.1002/jsfa.12232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 09/06/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The influence of epiphytic microbiota and chemical composition on fermentation quality and microbial community of Italian ryegrass silage was evaluated. Italian ryegrass harvested at the filling stage (FS) and the dough stage (DS) was sterilized by gamma-ray irradiation and inoculated as follows: (I) FS epiphytic microbiota + irradiated FS (FF); (II) FS epiphytic microbiota + irradiated DS (FD); (III) DS epiphytic microbiota + irradiated DS (DD); (IV) DS epiphytic microbiota + irradiated FS (DF). RESULTS After 60 days of ensiling, silage made from irradiated FS had a lower pH and ammonia nitrogen (NH3 -N) content and a higher lactic acid (LA) content than that made from irradiated DS. Similarly, silage inoculated with the epiphytic microbiota of DS had a lower pH and NH3 -N content and a higher LA content than that inoculated with the epiphytic microbiota of FS. However, LA-type fermentation (lactic acid:acetic acid > 2:1) was presented at DF and DD. The principal coordinates analysis showed that the distance between FF and DF and FD and DD was closer than other treatments, suggesting that the microbial community of silages made from irradiated FS (or DS) was more similar. CONCLUSION The epiphytic microbiota played a more important role in the fermentation type, whereas the chemical composition had a great influence on the contents of fermentation end-products. However, chemical composition had a stronger effect on the microbial community of silage than the epiphytic microbiota. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Xuejing Yin
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Jie Zhao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Siran Wang
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Zhihao Dong
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Junfeng Li
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
| | - Tao Shao
- Institute of Ensiling and Processing of Grass, College of Agro-Grassland Science, Nanjing Agricultural University, Nanjing, China
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Zhang Y, Li X, Lu L, Huang F, Liu H, Zhang Y, Yang L, Usman M, Li S. Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees. Microorganisms 2023; 11:microorganisms11020233. [PMID: 36838198 PMCID: PMC9966171 DOI: 10.3390/microorganisms11020233] [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: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.
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Affiliation(s)
- Yifang Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaomin Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Correspondence: (L.L.); (S.L.)
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Yu Zhang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Luhua Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Muhammad Usman
- PEIE Research Chair for the Development of Industrial Estates and Free Zones, Center for Environmental Studies and Research, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence: (L.L.); (S.L.)
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Jahan R, McDonald IR. Diversity of Methylobacterium species associated with New Zealand native plants. FEMS Microbiol Lett 2023; 370:fnad124. [PMID: 37985695 PMCID: PMC10699869 DOI: 10.1093/femsle/fnad124] [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: 05/24/2023] [Revised: 09/26/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Methylobacterium species are abundant colonizers of the phyllosphere due to the availability of methanol, a waste product of pectin metabolism during plant cell division. The phyllosphere is an extreme environment, with a landscape that is heterogeneous and continuously changing as the plant grows and is exposed to high levels of ultraviolet irradiation. Geographically, New Zealand (NZ) has been isolated for over a million years, has a biologically diverse flora, and is considered a biodiversity hotspot, with most native plants being endemic. We therefore hypothesize that the phyllosphere of NZ native plants harbor diverse groups of Methylobacterium species. Leaf imprinting using methanol-supplemented agar medium was used to isolate bacteria, and diversity was determined using ARDRA and 16S rRNA gene sequencing. Methylobacterium species were successfully isolated from the phyllosphere of 18 of the 20 native NZ plant species in this study, and six different species were identified: M. marchantiae, M. mesophilicum, M. adhaesivum, M. komagatae, M. extorquens, and M. phyllosphaerae. Other α, β, and γ-Proteobacteria, Actinomycetes, Bacteroidetes, and Firmicutes were also isolated, highlighting the presence of other potentially novel methanol utilizers within this ecosystem. This study identified that Methylobacterium are abundant members of the NZ phyllosphere, with species diversity and composition dependent on plant species.
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Affiliation(s)
- Rowshan Jahan
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
| | - Ian R McDonald
- Te Aka Mātuatua—School of Science, Te Whare Wānanga o Waikato—University of Waikato, Private Bag 3105, Hamilton 3240, Aotearoa, New Zealand
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Tang G, Xu L, Wang X, Zhang J. Effects of Leaf Morphological and Chemical Properties on the Population Sizes of Epiphytes. MICROBIAL ECOLOGY 2023; 85:157-167. [PMID: 35037090 DOI: 10.1007/s00248-022-01963-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
To explore the main factors affecting the distribution of microbes on leaf surfaces, the relationship between population sizes of epiphytes and the morphological structure and main physical and chemical properties of leaves from stylo (Stylosanthes guianensis), alfalfa (Medicago sativa), maize (Zea mays), and cocksfoot (Dactylis glomerata) were investigated. The research results showed that the contents of soluble sugar and total phenolics on the leaf surfaces were positively correlated with those in the leaf tissues (P < 0.001). The leaves with high wax content had better moisture retention capacity. The content of soluble sugar on the leaf surfaces was positively correlated with population sizes of lactic acid bacteria (LAB), aerobic bacteria, yeasts, and molds (P < 0.001). Likewise, a positive correlation was found between the content of inorganic phosphorus on the leaf surfaces and population sizes of LAB and aerobic bacteria. The total amount of wax on leaf surfaces was negatively related to population sizes of microbes, especially aerobic bacteria (P < 0.01) and molds (P < 0.001). On the contrary, the presence of trichomes provides a shelter for epiphytes and was positively correlated with population sizes of epiphytes at different degrees of significance. In conclusion, population sizes of epiphytes on the leaf surfaces were not only affected by chemical properties, but also by morphological traits of leaves.
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Affiliation(s)
- Guojian Tang
- South Pratacultural Center, South China Agricultural University, Guangzhou, 510642, China
| | - Liuxing Xu
- South Pratacultural Center, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaoya Wang
- South Pratacultural Center, South China Agricultural University, Guangzhou, 510642, China
| | - Jianguo Zhang
- South Pratacultural Center, South China Agricultural University, Guangzhou, 510642, China.
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30
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Guzzon R, Bertoldi D, Roman T, Zanzotti R, Franciosi E. Spatial and Seasonal Structure of Bacterial Communities Within Alpine Vineyards: Trentino as a Case Study. MICROBIAL ECOLOGY 2023; 85:108-120. [PMID: 35028709 PMCID: PMC9849295 DOI: 10.1007/s00248-021-01948-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Bacteria have a fundamental role in determining the fitness of grapevine, the composition of grapes and the features of wines but at present, little information is available. In this work, the bacteria colonizing the different portions of grapevine (bark, leaves and grapes) were explored in the vineyards of the Alpine region of Trentino, considering the impact of different environmental and agronomical variables. The vineyards included in the work were selected based on their different geographical positions (altitude) and grapevine training systems in order to explore the whole variability of the grapevine ecosystem. Moreover, the surface amount of copper was measured on grapes and leaves during the vegetative growth. Bacterial analysis, performed using plate counts and Illumina MiSeq, revealed an increase in the concentration of grape bacteria proportional to the progress of the ripening stage. Conversely, the peak of bacterial concentration onto leaf and bark samples occurred in August, probably due to the more favourable environmental conditions. In bark samples, the bacterial microbiota reached the 7 log CFU/cm2, while 6 log UFC/g were measured in grape samples. A remarkable biodiversity was observed, with 13 phyla, 35 classes, 55 orders, 78 families and 95 genera of bacteria present. The presence of some taxa (Alphaproteobacteria, Desulfovibrionaceae, Clostriadiales, Oscillospira, Lachnospiraceae and Bacteroidales) was ubiquitous in all vineyards, but differences in terms of relative abundance were observed according to the vegetative stage, altitude of the vineyard and training system. Bacteria having oenological implication (Lactobacillus, Pediococcus and Oenococcus) were detected in grape samples collected in August, in low abundance. The data revealed a complex bacterial ecosystem inside the vineyard that, while maintaining common traits, evolves according to environmental and agronomical inputs. This study contributes to define the role of bacteria in the complex balance established in each vineyard between human actions and agricultural environment, known as terroir.
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Affiliation(s)
- Raffaele Guzzon
- , Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Daniela Bertoldi
- , Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Tomas Roman
- , Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Roberto Zanzotti
- , Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, TN, Italy
| | - Elena Franciosi
- , Fondazione Edmund Mach, Via Mach 1, 38010, San Michele all'Adige, TN, Italy
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Postiglione A, Prigioniero A, Zuzolo D, Tartaglia M, Scarano P, Maisto M, Ranauda MA, Sciarrillo R, Thijs S, Vangronsveld J, Guarino C. Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex. PLANTS (BASEL, SWITZERLAND) 2022; 11:3528. [PMID: 36559640 PMCID: PMC9782775 DOI: 10.3390/plants11243528] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring.
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Affiliation(s)
- Alessia Postiglione
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Antonello Prigioniero
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Daniela Zuzolo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Maria Tartaglia
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Pierpaolo Scarano
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Maria Maisto
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Maria Antonietta Ranauda
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Rosaria Sciarrillo
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
| | - Sofie Thijs
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan, Building D, 3590 Diepenbeek, Belgium
| | - Jaco Vangronsveld
- Environmental Biology, Centre for Environmental Sciences, Hasselt University, Agoralaan, Building D, 3590 Diepenbeek, Belgium
- Department of Plant Physiology and Biophysics, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Carmine Guarino
- Department of Science and Technology, University of Sannio, via de Sanctis snc, 82100 Benevento, Italy
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May-Mutul CG, López-Garrido MA, O’Connor-Sánchez A, Peña-Ramírez YJ, Labrín-Sotomayor NY, Estrada-Medina H, Ferrer MM. Hidden Tenants: Microbiota of the Rhizosphere and Phyllosphere of Cordia dodecandra Trees in Mayan Forests and Homegardens. PLANTS (BASEL, SWITZERLAND) 2022; 11:3098. [PMID: 36432829 PMCID: PMC9699097 DOI: 10.3390/plants11223098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
During domestication, the selection of cultivated plants often reduces microbiota diversity compared with their wild ancestors. Microbiota in compartments such as the phyllosphere or rhizosphere can promote fruit tree health, growth, and development. Cordia dodecandra is a deciduous tree used by Maya people for its fruit and wood, growing, to date, in remnant forest fragments and homegardens (traditional agroforestry systems) in Yucatán. In this work, we evaluated the microbiota's alpha and beta diversity per compartment (phyllosphere and rhizosphere) and per population (forest and homegarden) in the Northeast and Southwest Yucatán regions. Eight composite DNA samples (per compartment/population/region combination) were amplified for 16S-RNA (bacteria) and ITS1-2 (fungi) and sequenced by Illumina MiSeq. Bioinformatic analyses were performed with QIIME and phyloseq. For bacteria and fungi, from 107,947 and 128,786 assembled sequences, 618 and 1092 operating taxonomic units (OTUs) were assigned, respectively. The alpha diversity of bacteria and fungi was highly variable among samples and was similar among compartments and populations. A significant species turnover among populations and regions was observed in the rhizosphere. The core microbiota from the phyllosphere was similar among populations and regions. Forests and homegarden populations are reservoirs of the C. dodecandra phyllosphere core microbiome and significant rhizosphere biodiversity.
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Affiliation(s)
- Carla G. May-Mutul
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miguel A. López-Garrido
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Aileen O’Connor-Sánchez
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida 97205, Mexico
| | - Yuri J. Peña-Ramírez
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Natalia Y. Labrín-Sotomayor
- Departamento de Ciencias de la Sustentabilidad, El Colegio de la Frontera Sur Unidad Campeche, Lerma 24500, Mexico
| | - Héctor Estrada-Medina
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
| | - Miriam M. Ferrer
- Departamento de Manejo y Conservación de Recursos Naturales Tropicales, Universidad Autónoma de Yucatán, Mérida 97313, Mexico
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Liu J, Ding C, Zhang W, Wei Y, Zhou Y, Zhu W. Litter mixing promoted decomposition rate through increasing diversities of phyllosphere microbial communities. Front Microbiol 2022; 13:1009091. [PMID: 36425041 PMCID: PMC9678933 DOI: 10.3389/fmicb.2022.1009091] [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: 08/01/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Decomposition of forest litter is an essential process for returning nutrients to the soil, which is crucial for preserving soil fertility and fostering the regular biological cycle and nutrient balance of the forest ecosystem. About 70% of the land-based forest litter is made up primarily of leaf litter. However, research on the complex effects and key determinants of leaf litter decomposition is still lacking. In this study, we examined the characteristics of nutrient release and microbial diversity structure during the decomposition of three types of litter in arid and semi-arid regions using 16S rRNA and ITS sequencing technology as well as nutrient content determination. It was revealed that the nutrient content and rate of decomposition of mixed litters were significantly different from those of single species. Following litter mixing, the richness and diversity of the microbial community on leaves significantly increased. It was determined that there was a significant correlation between bacterial diversity and content (Total N, Total P, N/P, and C/P). This study provided a theoretical framework for investigating the decomposition mechanism of mixed litters by revealing the microbial mechanism of mixed decomposition of litters from the microbial community and nutrient levels.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Changjun Ding,
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yawei Wei
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Yongbin Zhou
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), Shenyang Agricultural University, Tieling, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Lin Q, Wang Y, Li M, Xu Z, Li L. Ecological niche selection shapes the assembly and diversity of microbial communities in Casuarina equisetifolia L. FRONTIERS IN PLANT SCIENCE 2022; 13:988485. [PMID: 36340378 PMCID: PMC9632346 DOI: 10.3389/fpls.2022.988485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
The plant microbiome profoundly affects many aspects of host performance; however, the ecological processes by which plant hosts govern microbiome assembly, function, and dispersal remain largely unknown. Here, we investigated the bacterial and fungal communities in multiple compartment niches (bulk soil, rhizosphere soil, root endosphere, phylloplane, and leaf endosphere) of Casuarina equisetifolia L. at three developmental stages in Hainan Province, China. We found that microbiome assemblages along the soil-plant continuum were shaped by the compartment niches. Bacterial diversity and richness decreased from the soils to roots to leaves, with the highest network complexity found in the roots and the lowest found in the phylloplane. However, fungal diversity gradually increased from the soils to roots to phyllosphere, whereas fungal richness decreased from the soils to roots but increased from the roots to phyllosphere; the greatest network complexity was found in bulk soils and the lowest was found in the roots. Different biomarker taxa occurred in the different ecological niches. Bacterial and fungal communities exhibited distinct ecological functions; the former played important roles in maintaining plant growth and providing nutrients, whereas the latter predominantly decomposed organic matter. The bacterial community of C. equisetifolia mostly originated from bulk soil, whereas the fungal community was mainly derived from rhizosphere soil and air. Leaf endophytes were positively correlated with organic carbon, and root and soil microorganisms were positively correlated with total nitrogen, total phosphorus, and total potassium. Our findings provide empirical evidence for plant-microbiome interactions and contribute to future research on non-crop management and the manipulation of non-crop microbiomes.
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Sun P, Wu J, Lin X, Wang Y, Zhu J, Chen C, Wang Y, Jia H, Shen J. Effect of ozonated water, mancozeb, and thiophanate-methyl on the phyllosphere microbial diversity of strawberry. FRONTIERS IN PLANT SCIENCE 2022; 13:967797. [PMID: 36186019 PMCID: PMC9521403 DOI: 10.3389/fpls.2022.967797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Phyllosphere microorganisms are closely linked to plant health. This study investigated the effect of ozonated water, mancozeb, and thiophanate-methyl on phyllosphere microorganisms in strawberry plants of the "Hongyan" variety. Sequencing analysis of the phyllosphere bacterial and fungal communities was performed using 16S rRNA gene fragment and ITS1 region high-throughput sequencing after spraying ozonated water, mancozeb, thiophanate-methyl, and clear water. Proteobacteria, Actinobacteria, and Firmicutes were the dominant bacterial phyla in strawberry. The relative abundance of Proteobacteria (82.71%) was higher in the ozonated water treatment group than in the other treatment groups, while the relative abundance of Actinobacteria (9.38%) was lower than in the other treatment groups. The strawberry phyllosphere fungal communities were mainly found in the phyla Basidiomycota and Ascomycota. The relative abundance of Basidiomycota was highest in the ozonated water treatment group (81.13%), followed by the mancozeb treatment group (76.01%), while the CK group only had an abundance of 43.38%. The relative abundance of Ascomycota was lowest in the ozonated water treatment group (17.98%), 23.12% in the mancozeb treatment group, 43.39% in the thiophanate-methyl treatment group, and 55.47% in the CK group. Pseudomonas, Halomonas, and Nesterenkonia were the dominant bacterial genera on strawberry surfaces, while Moesziomyces, Aspergillus, and Dirkmeia were the dominant fungal genera. Ozonated water was able to significantly increase the richness of bacteria and fungi and decrease fungal diversity. However, bacterial diversity was not significantly altered. Ozonated water effectively reduced the relative abundance of harmful fungi, such as Aspergillus, and Penicillium, and enriched beneficial bacteria, such as Pseudomonas and Actinomycetospora, more effectively than mancozeb and thiophanate-methyl. The results of the study show that ozonated water has potential as a biocide and may be able to replace traditional agents in the future to reduce environmental pollution.
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Affiliation(s)
- Ping Sun
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Jiaqi Wu
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Xianrui Lin
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Yi Wang
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Jianxi Zhu
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Chenfei Chen
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Yanqiao Wang
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
| | - Huijuan Jia
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jiansheng Shen
- Jinhua Academy of Agricultural Sciences, Zhejiang Institute of Agricultural Machinery, Jinhua, China
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Yang J, Masoudi A, Li H, Gu Y, Wang C, Wang M, Yu Z, Liu J. Microbial community structure and niche differentiation under different health statuses of Pinus bungeana in the Xiong'an New Area in China. Front Microbiol 2022; 13:913349. [PMID: 36118200 PMCID: PMC9481298 DOI: 10.3389/fmicb.2022.913349] [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: 04/05/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Pinus bungeana is a native but endangered plant species in China, with high ornamental value and adaptability to drought and cold. The relationship between the soil community structure and endophytic microbes in the tissues of P. bungeana under different health statuses is poorly understood. In this study, the endophytic bacterial and fungal communities of P. bungeana under different health statuses were compared and analyzed in the Xiong'an New Area. Using high-throughput deep sequencing [16S and internal transcribed spacer (ITS) rRNA] techniques, the effect of the health status of P. bungeana on the microbial communities in bulk soil, rhizospheric soil, roots, stems, and leaves was determined in this study. We observed that the diversity of the bacterial and fungal communities of the aboveground parts (stems and leaves) of healthy P. bungeana plants was much higher than that of the unhealthy plants. However, the diversity of bacterial and fungal communities in the belowground parts (bulk soil, rhizospheric soil, and roots) showed almost no difference in microbial community richness, indicating that the possible cause of illness was transmitted in a “top-down” manner. Furthermore, there were significant differences in the microbial diversity and community structure in different ecological niches of P. bungeana (P < 0.01). Proteobacteria and Actinobacteria were the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the predominant fungal phyla. Redundancy analysis (RDA) revealed that soil organic matter (SOM), total phosphorous (TP), total potassium (TK), total nitrogen (TN), water content (WC), power of hydrogen (pH), total carbon (TC), and the ratio of carbon to nitrogen (C/N) were significantly correlated with the composition of the microbial communities. Altogether, these results provide a scientific basis for further studies on the mechanism underlying the “aboveground–underground” microbial interactions in plantation forests, which can aid in promoting the healthy and sustainable development of the Millennium Xiulin forest in the Xiong'an New Area.
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Affiliation(s)
- Jia Yang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Abolfazl Masoudi
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Hao Li
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Yifan Gu
- School of Geographic Sciences, Hebei Normal University, Shijiazhuang, China
| | - Can Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Min Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Zhijun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Zhijun Yu
| | - Jingze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Jingze Liu
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Johnston-Monje D, Gutiérrez JP, Becerra Lopez-Lavalle LA. Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants. Life (Basel) 2022; 12:life12091372. [PMID: 36143410 PMCID: PMC9506401 DOI: 10.3390/life12091372] [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: 07/28/2022] [Revised: 08/22/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022] Open
Abstract
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.
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Affiliation(s)
- David Johnston-Monje
- Max Planck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali 76001, Colombia
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Correspondence: ; Tel.: +57-315-545-6227
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Sanjenbam P, Shivaprasad PV, Agashe D. Impact of Phyllosphere Methylobacterium on Host Rice Landraces. Microbiol Spectr 2022; 10:e0081022. [PMID: 35856668 PMCID: PMC9431194 DOI: 10.1128/spectrum.00810-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/24/2022] [Indexed: 11/20/2022] Open
Abstract
The genus Methylobacterium includes widespread plant-associated bacteria that are abundant in the plant phyllosphere (leaf surfaces), consume plant-secreted methanol, and can produce plant growth-promoting metabolites. However, despite the potential to increase agricultural productivity, their impact on host fitness in the natural environment is relatively poorly understood. Here, we conducted field experiments with three traditionally cultivated rice landraces from northeastern India. We inoculated seedlings with native versus nonnative phyllosphere Methylobacterium strains and found significant impacts on plant growth and grain yield. However, these effects were variable. Whereas some Methylobacterium isolates were beneficial for their host, others had no impact or were no more beneficial than the bacterial growth medium on its own. Host plant benefits were not consistently associated with Methylobacterium colonization and did not have altered phyllosphere microbiome composition, changes in the early expression of plant stress response pathways, or bacterial auxin production. We provide the first demonstration of the benefits of phyllosphere Methylobacterium for rice yield under field conditions and highlight the need for further analysis to understand the mechanisms underlying these benefits. Given that the host landrace-Methylobacterium relationship was not generalizable, future agricultural applications will require careful testing to identify coevolved host-bacterium pairs that may enhance the productivity of high-value rice varieties. IMPORTANCE Plants are associated with diverse microbes in nature. Do the microbes increase host plant health, and can they be used for agricultural applications? This is an important question that must be answered in the field rather than in the laboratory or greenhouse. We tested the effects of native, leaf-inhabiting bacteria (genus Methylobacterium) on traditionally cultivated rice varieties in a crop field. We found that inoculation with some bacteria increased rice grain production substantially while a nonnative bacterium reduced plant health. Overall, the effect of bacterial inoculation varied across pairs of rice varieties and their native bacteria. Thus, knowledge of evolved associations between specific bacteria hosted by specific rice varieties is necessary to develop ways to increase the yield of traditional rice landraces and preserve these important sources of cultural and genetic diversity.
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Affiliation(s)
- Pratibha Sanjenbam
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - P. V. Shivaprasad
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Deepa Agashe
- National Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
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Microbial endophytes: application towards sustainable agriculture and food security. Appl Microbiol Biotechnol 2022; 106:5359-5384. [PMID: 35902410 DOI: 10.1007/s00253-022-12078-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023]
Abstract
Microbial endophytes are ubiquitous and exist in each recognised plant species reported till date. Within the host plant, the entire community of microbes lives non-invasively within the active internal tissues without causing any harm to the plant. Endophytes interact with their host plant via metabolic communication enables them to generate signal molecules. In addition, the host plant's genetic recombination with endophytes helps them to imitate the host's physicochemical functions and develop identical active molecules. Therefore, when cultured separately, they begin producing the host plant phytochemicals. The fungal species Penicillium chrysogenum has portrayed the glory days of antibiotics with the invention of the antibiotic penicillin. Therefore, fungi have substantially supported social health by developing many bioactive molecules utilised as antioxidant, antibacterial, antiviral, immunomodulatory and anticancerous agents. But plant-related microbes have emanated as fountainheads of biologically functional compounds with higher levels of medicinal perspective in recent years. Researchers have been motivated by the endless need for potent drugs to investigate alternate ways to find new endophytes and bioactive molecules, which tend to be a probable aim for drug discovery. The current research trends with these promising endophytic organisms are reviewed in this review paper. KEY POINTS: • Identified 54 important bioactive compounds as agricultural relevance • Role of genome mining of endophytes and "Multi-Omics" tools in sustainable agriculture • A thorough description and graphical presentation of agricultural significance of plant endophytes.
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Dai YF, Wu XM, Wang HC, Li WH, Cai LT, Li JX, Wang F, Sehar S, Shamsi IH. Spatio-Temporal Variation in the Phyllospheric Microbial Biodiversity of Alternaria Alternata-Infected Tobacco Foliage. Front Microbiol 2022; 13:920109. [PMID: 35966692 PMCID: PMC9370072 DOI: 10.3389/fmicb.2022.920109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Phyllospheric microbial composition of tobacco (Nicotiana tabacum L.) is contingent upon certain factors, such as the growth stage of the plant, leaf position, and cultivar and its geographical location, which influence, either directly or indirectly, the growth, overall health, and production of the tobacco plant. To better understand the spatiotemporal variation of the community and the divergence of phyllospheric microflora, procured from healthy and diseased tobacco leaves infected by Alternaria alternata, the current study employed microbe culturing, high-throughput technique, and BIOLOG ECO. Microbe culturing resulted in the isolation of 153 culturable fungal isolates belonging to 33 genera and 99 bacterial isolates belonging to 15 genera. High-throughput sequencing revealed that the phyllosphere of tobacco was dominantly colonized by Ascomycota and Proteobacteria, whereas, the most abundant fungal and bacterial genera were Alternaria and Pseudomonas. The relative abundance of Alternaria increased in the upper and middle healthy groups from the first collection time to the third, whereas, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium from the same positions increased during gradual leaf aging. Non-metric multi-dimensional scaling (NMDs) showed clustering of fungal communities in healthy samples, while bacterial communities of all diseased and healthy groups were found scattered. FUNGuild analysis, from the first collection stage to the third one in both groups, indicated an increase in the relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Pathotroph-Symbiotroph. Inclusive of all samples, as per the PICRUSt analysis, the predominant pathway was metabolism function accounting for 50.03%. The average values of omnilog units (OUs) showed relatively higher utilization rates of carbon sources by the microbial flora of healthy leaves. According to the analysis of genus abundances, leaf growth and leaf position were the important drivers of change in structuring the microbial communities. The current findings revealed the complex ecological dynamics that occur in the phyllospheric microbial communities over the course of a spatiotemporal varying environment with the development of tobacco brown spots, highlighting the importance of community succession.
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Affiliation(s)
- Yuan-feng Dai
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Bijie Tobacco Company, Bijie, China
| | - Xiao-mao Wu
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Xiao-mao Wu
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Han-cheng Wang
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Ji-xin Li
- Guizhou Tobacco Company of CNTC, China National Tobacco Corporation, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Feng Wang
| | - Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Imran Haider Shamsi
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Wang Y, Wu J, Sun P, Chen C, Shen J. Community Structure of Phyllosphere Bacteria in Different Cultivars of Fingered Citron ( Citrus medica 'Fingered') and Their Correlations With Fragrance. FRONTIERS IN PLANT SCIENCE 2022; 13:936252. [PMID: 35909778 PMCID: PMC9335054 DOI: 10.3389/fpls.2022.936252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
In recent years, plant metabolomics and microbiome studies have suggested that the synthesis and secretion of plant secondary metabolites are affected by microbial-host symbiotic interactions. In this study, six varieties of fingered citron (Citrus medica 'Fingered') are sampled to study their phyllosphere bacterial communities and volatile organic compounds (VOCs). High-throughput sequencing is used to sequence the V5-V7 region of the 16S rRNA of the fingered citron phyllosphere bacteria, and the results showed that Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were the dominant bacterial phylum in the phyllosphere of fingered citron. There were significant differences in the phyllosphere bacteria community between XiuZhen and the remaining five varieties. The relative abundance of Actinomycetospora was highest in XiuZhen, and Halomonas, Methylobacterium, Nocardioides, and Pseudokineococcus were also dominant. Among the remaining varieties, Halomonas was the genus with the highest relative abundance, while the relative abundances of all the other genera were low. Headspace solid-phase microextraction (HS-SPME) and gas chromatography-mass spectrometry (GC-MS) were used to analyze and identify the aroma compounds of six different fingered citron, and a total of 76 aroma compounds were detected in six varieties. Pinene, geraniol, and linalool were found to be the primary VOCs that affect the aroma of fingered citron based on relative odor activity value. The correlation analysis showed 55 positive and 60 negative correlations between the phyllosphere bacterial flora and aroma compounds of fingered citron. The top 10 genera in the relative abundance were all significantly associated with aroma compounds. This study provides deep insight into the relation between bacteria and VOCs of fingered citron, and this may better explain the complexity of the analysis of bacterial and metabolic interactions.
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Vermote L, Verce M, Mozzi F, De Vuyst L, Weckx S. Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity. Front Microbiol 2022; 13:872281. [PMID: 35898900 PMCID: PMC9309516 DOI: 10.3389/fmicb.2022.872281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.
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Affiliation(s)
- Louise Vermote
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernanda Mozzi
- Technology and Development Laboratory, Centro de Referencia para Lactobacilos (CERELA)-CONICET, San Miguel de Tucumán, Argentina
| | - Luc De Vuyst
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
- *Correspondence: Stefan Weckx,
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [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: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Félix CR, Nascimento BEDS, Valente P, Landell MF. Different plant compartments, different yeasts: the example of the bromeliad phyllosphere. Yeast 2022; 39:363-400. [PMID: 35715939 DOI: 10.1002/yea.3804] [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: 03/09/2022] [Revised: 05/14/2022] [Accepted: 06/14/2022] [Indexed: 11/09/2022] Open
Abstract
The plant phyllosphere is one of the largest sources of microorganisms, including yeasts. In bromeliads, the knowledge of yeasts is dispersed and still incipient. To understand the extent of our knowledge on the subject, this review proposes to compile and synthesize existing knowledge, elucidating possible patterns, biotechnological and taxonomic potentials, bringing to light new knowledge, and identifying information gaps. For such, we systematically review scientific production on yeasts in bromeliads using various databases. The results indicated that the plant compartments flowers, fruits, leaves, and water tank (phytotelma) have been studied when focusing on the yeast community in the bromeliad phyllosphere. More than 180 species of yeasts and yeast-like fungi were recorded from the phyllosphere, 70% were exclusively found in one of these four compartments and only 2% were shared among all. In addition, most of the community had a low frequency of occurrence, and approximately half of the species had a single record. Variables such as bromeliad subfamilies and functional types, as well as plant compartments, were statistically significant, though inconclusive and with low explanatory power. At least 50 yeast species with some biotechnological potentials have been isolated from bromeliads. More than 90% of these species were able to produce extracellular enzymes. In addition, other biotechnological applications have also been recorded. Moreover, new species have been described, though yeasts were only exploited in approximately 1% of the existing bromeliads species, which highlights that there is still much to be explored. Nevertheless, it appears that we are still far from recovering the completeness of the diversity of yeasts in this host. Furthermore, bromeliads proved to be a good ecological model for prospecting new yeasts and for studies on the interaction between plants and yeasts. In addition, the yeast community diverged among plant compartments, establishing bromeliads as a microbiologically complex and heterogeneous mosaic. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Ciro Ramon Félix
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas e da Saúde, Maceió, AL, Brazil.,Programa de Pós-graduação em Diversidade Biológica e Conservação nos Trópicos, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | | | - Patrícia Valente
- Universidade Federal do Rio Grande do Sul, Departamento de Microbiologia, Imunologia e Parasitologia, Porto Alegre, RS, Brazil
| | - Melissa Fontes Landell
- Universidade Federal de Alagoas, Instituto de Ciências Biológicas e da Saúde, Maceió, AL, Brazil
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Leaf-Associated Epiphytic Fungi of Gingko biloba, Pinus bungeana and Sabina chinensis Exhibit Delicate Seasonal Variations. J Fungi (Basel) 2022; 8:jof8060631. [PMID: 35736114 PMCID: PMC9225447 DOI: 10.3390/jof8060631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/06/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
Plant-leaf surface on Earth harbors complex microbial communities that influence plant productivity and health. To gain a detailed understanding of the assembly and key drivers of leaf microbial communities, especially for leaf-associated fungi, we investigated leaf-associated fungal communities in two seasons for three plant species at two sites by high-throughput sequencing. The results reveal a strong impact of growing season and plant species on fungal community composition, exhibiting clear temporal patterns in abundance and diversity. For the deciduous tree Gingko biloba, the number of enriched genera in May was much higher than that in October. The number of enriched genera in the two evergreen trees Pinus bungeana and Sabina chinensis was slightly higher in October than in May. Among the genus-level biomarkers, the abundances of Alternaria, Cladosporium and Filobasidium were significantly higher in October than in May in the three tree species. Additionally, network correlations between the leaf-associated fungi of G. biloba were more complex in May than those in October, containing extra negative associations, which was more obvious than the network correlation changes of leaf-associated fungi of the two evergreen plant species. Overall, the fungal diversity and community composition varied significantly between different growing seasons and host plant species.
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Li M, Hong L, Ye W, Wang Z, Shen H. Phyllosphere bacterial and fungal communities vary with host species identity, plant traits and seasonality in a subtropical forest. ENVIRONMENTAL MICROBIOME 2022; 17:29. [PMID: 35681245 PMCID: PMC9185928 DOI: 10.1186/s40793-022-00423-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/31/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Phyllosphere microbes play important roles in host plant performance and fitness. Recent studies have suggested that tropical and temperate forests harbor diverse phyllosphere bacterial and fungal communities and their assembly is driven by host species identity and plant traits. However, no study has yet examined how seasonality (e.g. dry vs. wet seasons) influences phyllosphere microbial community assembly in natural forests. In addition, in subtropical forests characterized as the transitional zonal vegetation type from tropical to temperate forests, how tree phyllosphere microbial communities are assembled remains unknown. In this study, we quantified bacterial and fungal community structure and diversity on the leaves of 45 tree species with varying phylogenetic identities and importance values within a 20-ha lower subtropical evergreen broad-leaved forest plot in dry and wet seasons. We explored if and how the microbial community assembly varies with host species identity, plant traits and seasonality. RESULTS Phyllosphere microbial communities in the subtropical forest are more abundant and diverse than those in tropical and temperate forests, and the tree species share a "core microbiome" in either bacteria or fungi. Variations in phyllosphere bacterial and fungal community assembly are explained more by host species identity than by seasonality. There is a strong clustering of the phyllosphere microbial assemblage amongst trees by seasonality, and the seasonality effects are more pronounced on bacterial than fungal community assembly. Host traits have different effects on community compositions and diversities of both bacteria and fungi, and among them calcium concentration and importance value are the most powerful explaining variables for bacteria and fungi, respectively. There are significant evolutionary associations between host species and phyllosphere microbiome. CONCLUSIONS Our results suggest that subtropical tree phyllosphere microbial communities vary with host species identity, plant traits and seasonality. Host species identity, compared to seasonality, has greater effects on phyllosphere microbial community assembly, and such effects differ between bacterial and fungal communities. These findings advance our understanding of the patterns and drivers of phyllosphere microbial community assembly in zonal forests at a global scale.
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Affiliation(s)
- Mengjiao Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lan Hong
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 China
| | - Wanhui Ye
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhangming Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
| | - Hao Shen
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden/Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049 China
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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Fessia A, Barra P, Barros G, Nesci A. Could Bacillus biofilms enhance the effectivity of biocontrol strategies in the phyllosphere? J Appl Microbiol 2022; 133:2148-2166. [PMID: 35476896 DOI: 10.1111/jam.15596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/30/2022]
Abstract
Maize (Zea mays L.), a major crop in Argentina and a staple food around the world, is affected by the emergence and re-emergence of foliar diseases. Agrochemicals are the main control strategy nowadays, but they can cause resistance in insects and microbial pathogens and have negative effects on the environment and human health. An emerging alternative is the use of living organisms, i.e. microbial biocontrol agents, to suppress plant pathogen populations. This is a risk-free approach when the organisms acting as biocontrol agents come from the same ecosystem as the foliar pathogens they are meant to antagonize. Some epiphytic microorganisms may form biofilm by becoming aggregated and attached to a surface, as is the case of spore-forming bacteria from the genus Bacillus. Their ability to sporulate and their tolerance to long storage periods make them a frequently used biocontrol agent. Moreover, the biofilm that they create protects them against different abiotic and biotic factors and helps them to acquire nutrients, which ensures their survival on the plants they protect. This review analyzes the interactions that the phyllosphere-inhabiting Bacillus genus establishes with its environment through biofilm, and how this lifestyle could serve to design effective biological control strategies.
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Affiliation(s)
- Aluminé Fessia
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Paula Barra
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Germán Barros
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
| | - Andrea Nesci
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales, Universidad Nacional de Río Cuarto, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina
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Xu N, Zhao Q, Zhang Z, Zhang Q, Wang Y, Qin G, Ke M, Qiu D, Peijnenburg WJGM, Lu T, Qian H. Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4860-4870. [PMID: 35435673 DOI: 10.1021/acs.jafc.2c01113] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, Xinjiang 830011, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Post Office Box 1, 3720 BA Bilthoven, Netherlands
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
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Xu P, Stirling E, Xie H, Li W, Lv X, Matsumoto H, Cheng H, Xu A, Lai W, Wang Y, Zheng Z, Wang M, Liu X, Ma B, Xu J. Continental scale deciphering of microbiome networks untangles the phyllosphere homeostasis in tea plant. J Adv Res 2022; 44:13-22. [PMID: 36725184 PMCID: PMC9936419 DOI: 10.1016/j.jare.2022.04.002] [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: 11/07/2021] [Revised: 03/21/2022] [Accepted: 04/05/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Assembly and co-occurrence of the host co-evolved microbiota are essential ecological and evolutionary processes, which is not only crucial for managing individual plant fitness but also ecological function. However, understanding of the microbiome assembly and co-occurrence in higher plants is not well understood. The tea plant was shown to contribute the forest fitness due to the microbiome assembled in the phyllosphere; the landscape of microbiome assembly in the tea plants and its potential implication on phyllosphere homestasis still remains untangled. OBJECTIVES This study aimed to deciphering of the microbiome networks of the tea plants at a continental scale. It would provide fundamental insights into the factors driving the microbiome assembly, with an extended focus on the resilience towards the potential pathogen in the phyllosphere. METHODS We collected 225 samples from 45 locations spanning approximately 2000-km tea growing regions across China. By integration of high-throughput sequencing data, physicochemical properties profiling and bioinformatics analyses, we investigated continental scale microbiome assembly and co-occurrence in the tea plants. Synthetic assemblages, interaction assay and RT-qPCR were further implemented to analyze the microbial interaction indexed in phyllosphere. RESULTS A trade-off between stochastic and deterministic processes in microbiomes community assembly was highlighted. Assembly processes were dominated by deterministic processes in bulk and rhizosphere soils, and followed by stochastic processes in roots and leaves with amino acids as critical drivers for environmental selection. Sphingobacteria and Proteobacteria ascended from soils to leaves to sustain a core leaf taxa. The core taxa formed a close association with a prevalent foliar pathogen in the co-occurrence network and significantly attenuated the expression of a set of essential virulence genes in pathogen. CONCLUSION Our study unveils the mechanism underpinning microbiome assembly in the tea plants, and a potential implication of the microbiome-mediated resilience framework on the phyllosphere homeostasis.
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Affiliation(s)
- Ping Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Erinne Stirling
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China,Acid Sulfate Soils Centre, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Hengtong Xie
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wenbing Li
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, PR China
| | - Xiaofei Lv
- Department of Environmental Engineering, China Jiliang University, Hangzhou 310018, China
| | - Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China
| | - Haiyan Cheng
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Anan Xu
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Wanyi Lai
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yuefei Wang
- Department of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Zuntao Zheng
- Institute for the Control of Agrochemicals, Ministry of Agriculture and Rural Affairs, Beijing 100125, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China.
| | - Xingmei Liu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
| | - Bin Ma
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China; Hangzhou Innovation Center, Zhejiang University, Hangzhou 311200, China.
| | - Jianming Xu
- College of Environmental and Natural Resource Sciences, Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou 310058, China
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