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Sunil S, Walsky T, Henry M, Kemmerling L, Pajor M, Guo X, Murphy SI, Ivanek R, Wiedmann M. A longitudinal study on the bacterial quality of baby spinach cultivated in Arizona and California. Appl Environ Microbiol 2024:e0055324. [PMID: 38995040 DOI: 10.1128/aem.00553-24] [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: 03/22/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
In the U.S., baby spinach is mostly produced in Arizona (AZ) and California (CA). Characterizing the impact of growing region on the bacterial quality of baby spinach can inform quality management practices in industry. Between December 2021 and December 2022, baby spinach was sampled after harvest and packaging for microbiological testing, including shelf-life testing of packaged samples that were stored at 4°C. Samples were tested to (i) determine bacterial concentration, and (ii) obtain and identify bacterial isolates. Packaged samples from the Salinas, CA, area (n = 13), compared to those from the Yuma, AZ, area (n = 9), had a significantly higher bacterial concentration, on average, by 0.78 log10 CFU/g (P < 0.01, based on aerobic, mesophilic plate count data) or 0.67 log10 CFU/g (P < 0.01, based on psychrotolerant plate count data); the bacterial concentrations of harvest samples from the Yuma and Salinas areas were not significantly different. Our data also support that an increase in preharvest temperature is significantly associated with an increase in the bacterial concentration on harvested and packaged spinach. A Fisher's exact test and linear discriminant analysis (effect size), respectively, demonstrated that (i) the genera of 2,186 bacterial isolates were associated (P < 0.01) with growing region and (ii) Pseudomonas spp. and Exiguobacterium spp. were enriched in spinach from the Yuma and Salinas areas, respectively. Our findings provide preliminary evidence that growing region and preharvest temperature may impact the bacterial quality of spinach and thus could inform more targeted strategies to manage produce quality. IMPORTANCE In the U.S., most spinach is produced in Arizona (AZ) and California (CA) seasonally; typically, spinach is cultivated in the Yuma, AZ, area during the winter and in the Salinas, CA, area during the summer. As the bacterial quality of baby spinach can influence consumer acceptance of the product, it is important to assess whether the bacterial quality of baby spinach can vary between spinach-growing regions. The findings of this study provide insights that could be used to support region-specific quality management strategies for baby spinach. Our results also highlight the value of further evaluating the impact of growing region and preharvest temperature on the bacterial quality of different produce commodities.
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Affiliation(s)
- Sriya Sunil
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Tamara Walsky
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Mikayla Henry
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Leonie Kemmerling
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Magdalena Pajor
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Xiaodong Guo
- Department of Food Science, Cornell University, Ithaca, New York, USA
| | - Sarah I Murphy
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Renata Ivanek
- Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, USA
| | - Martin Wiedmann
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Qu X, Pan Y, Wang P, Ran L, Qin G, Li Q, Kang P. Response of Phyllosphere and Rhizosphere Microbial Communities to Salt Stress of Tamarix chinensis. PLANTS (BASEL, SWITZERLAND) 2024; 13:1091. [PMID: 38674498 PMCID: PMC11054833 DOI: 10.3390/plants13081091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
As carriers of direct contact between plants and the atmospheric environment, the microbiomes of phyllosphere microorganisms are increasingly recognized as an important area of study. Salt secretion triggered by salt-secreting halophytes elicits changes in the community structure and functions of phyllosphere microorganisms, and often provides positive feedback to the individual plant/community environment. In this study, the contents of Na+ and K+ in the rhizosphere, plant and phyllosphere of Tamarix chinensis were increased under 200 mmol/L NaCl stress. The increase in electrical conductivity, Na+ and K+ in the phyllosphere not only decreased the diversity of bacterial and fungal communities, but also decreased the relative abundance of Actinobacteriota and Basidiomycota. Influenced by electrical conductivity and Na+, the bacteria-fungus co-occurrence network under salt stress has higher complexity. Changes in the structure of the phyllosphere microbial community further resulted in a significant increase in the relative abundance of the bacterial energy source and fungal pathotrophic groups. The relative abundance of Actinobacteriota and Acidobacteriota in rhizosphere showed a decreasing trend under salt stress, while the complexity of the rhizosphere co-occurrence network was higher than that of the control. In addition, the relative abundances of functional groups of rhizosphere bacteria in the carbon cycle and phosphorus cycle increased significantly under stress, and were significantly correlated with electrical conductivity and Na+. This study investigated the effects of salinity on the structure and physicochemical properties of phyllosphere and rhizosphere microbial communities of halophytes, and highlights the role of phyllosphere microbes as ecological indicators in plant responses to stressful environments.
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Affiliation(s)
- Xuan Qu
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Yaqing Pan
- Shapotou Desert Research and Experiment Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Peiqin Wang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Lele Ran
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Guifei Qin
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Qunfang Li
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
| | - Peng Kang
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China; (X.Q.); (P.W.); (L.R.); (G.Q.); (Q.L.)
- Innovation Team for Genetic Improvement of Economic Forests, North Minzu University, Yinchuan 750021, China
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Duan Y, Siegenthaler A, Skidmore AK, Chariton AA, Laros I, Rousseau M, De Groot GA. Forest top canopy bacterial communities are influenced by elevation and host tree traits. ENVIRONMENTAL MICROBIOME 2024; 19:21. [PMID: 38581032 PMCID: PMC10998314 DOI: 10.1186/s40793-024-00565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). RESULTS We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. CONCLUSIONS While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.
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Affiliation(s)
- Yiwei Duan
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands.
| | - Andjin Siegenthaler
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Andrew K Skidmore
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Anthony A Chariton
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ivo Laros
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
| | - Mélody Rousseau
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - G Arjen De Groot
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
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Ren P, Sun A, Jiao X, Chen QL, Li F, He JZ, Hu HW. National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss. ENVIRONMENT INTERNATIONAL 2024; 185:108511. [PMID: 38382404 DOI: 10.1016/j.envint.2024.108511] [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: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.
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Affiliation(s)
- Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiaoyan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Zhao C, Liu X, Tan H, Yin S, Su L, Du B, Khalid M, Sinkkonen A, Hui N. Neighborhood garden's age shapes phyllosphere microbiota associated with respiratory diseases in cold seasons. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 18:100315. [PMID: 37886031 PMCID: PMC10598728 DOI: 10.1016/j.ese.2023.100315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 10/28/2023]
Abstract
Neighborhood gardens serve as sensitive sites for human microbial encounters, with phyllosphere microbes directly impacting our respiratory health. Yet, our understanding remains limited on how factors like season, garden age, and land use shape the risk of respiratory diseases (RDs) tied to these garden microbes. Here we examined the microbial communities within the phyllosphere of 72 neighborhood gardens across Shanghai, spanning different seasons (warm and cold), garden ages (old and young), and locales (urban and rural). We found a reduced microbial diversity during the cold season, except for Gammaproteobacteria which exhibited an inverse trend. While land use influenced the microbial composition, urban and rural gardens had strikingly similar microbial profiles. Alarmingly, young gardens in the cold season hosted a substantial proportion of RDs-associated species, pointing towards increased respiratory inflammation risks. In essence, while newer gardens during colder periods show a decline in microbial diversity, they have an increased presence of RDs-associated microbes, potentially escalating respiratory disease prevalence. This underscores the pivotal role the garden age plays in enhancing both urban microbial diversity and respiratory health.
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Affiliation(s)
- Chang Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Xinxin Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd., 200240, Shanghai, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Haoxin Tan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
| | - Shan Yin
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Lantian Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Baoming Du
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
| | - Muhammad Khalid
- Department of Biology, College of Science and Technology, Wenzhou-Kean University, Wenzhou, China
| | - Aki Sinkkonen
- Department of Garden Technologies, Horticulture Technologies, Natural Resources Institute Finland, Helsinki, Finland
| | - Nan Hui
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Rd., 200240, Shanghai, China
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Lahti, Finland
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Shao Q, Ran Q, Li X, Dong C, Huang J, Han Y. Deciphering the effect of phytohormones on the phyllosphere microbiota of Eucommia ulmoides. Microbiol Res 2024; 278:127513. [PMID: 37837828 DOI: 10.1016/j.micres.2023.127513] [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: 06/26/2023] [Revised: 07/30/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
Phytohormones are key signals mediating plant-microbe molecular communication. However, their roles in driving phyllosphere microbiota assembly remain unclear. Here, high throughput target assays for 12 phytohormones and microbial amplicon sequencing techniques were used to reveal the effects of hormone components on phyllosphere microbiota of Eucommia ulmoides. Most of the phytohormone components in old leaves were lower than in tender leaves, such as indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acid (JA), but the phyllosphere microbial community diversity in the older leaves was significantly higher than in the tender leaves, with more complex and aggregated microbial cooccurrence network. The E. ulmoides phyllosphere microbiota at tender and older leaf stage were dominated by the same dominant taxa at the phylum level, with Ascomycota and Basidiomycota as the main fungal taxa and Actinobacteriota, Bacteroidota, Firmicutes and Proteobacteria as the main bacterial taxa. FUNGuild and FAPROTAX functional predictions revealed that the high abundance functional groups of the E. ulmoides phyllosphere microbes were similar at tender and old leaf stages, with fungal functions mainly involving in plant pathogen, undefined saprotroph and endophyte, and bacterial functions mainly involving in chemoheterotrophy, fermentation and aerobic_chemoheterotrophy. Additionally, mantel test and variance partitioning analysis showed that IAA and N6-(delta 2-isopentenyl)-adenine (IP) were key phytohormones impacting the E. ulmoides phyllosphere microbiota, and their effects were largely interdependent. Our results improve the understanding of composition, diversity, function and influencing factors of phyllosphere microbiota, which might provide cue for sustainable agriculture and forestry management via precise regulation of the phyllosphere microbiota.
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Affiliation(s)
- Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Qingsong Ran
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Xu Li
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350108, Fujian, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China.
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Carper DL, Lawrence TJ, Quiroz D, Kueppers LM, Frank AC. Needle bacterial community structure across the species range of limber pine. ISME COMMUNICATIONS 2024; 4:ycae062. [PMID: 38800125 PMCID: PMC11128189 DOI: 10.1093/ismeco/ycae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/12/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.
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Affiliation(s)
- Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
- Quantitative and Systems Biology Program, University of California, Merced, Merced, CA 95343, United States
| | - Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Dianne Quiroz
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Lara M Kueppers
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - A Carolin Frank
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Life and Environmental Sciences Department, School of Natural Sciences, University of California, Merced, 5200 Lake Rd, Merced, CA 95343, United States
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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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Song W, Li Y. Tidal flat microbial communities between the Huaihe estuary and Yangtze River estuary. ENVIRONMENTAL RESEARCH 2023; 238:117141. [PMID: 37717808 DOI: 10.1016/j.envres.2023.117141] [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: 05/22/2023] [Revised: 09/02/2023] [Accepted: 09/13/2023] [Indexed: 09/19/2023]
Abstract
Tidal flats have important ecological functions and offer great economic value. Using field sampling, numerical simulation, and high-throughput sequencing, the ecological state of typical tidal flats along the eastern coast of China was investigated. The findings demonstrated that the area may be separated into subregions with notable differences in the features of microbial communities due to the variations in water quality and total pollutant discharge of seagoing rivers. With a ratio of 62%, the development of the microbial community revealed that homogenous selection predominated. In general, the formation of microbial communities follows deterministic processes, especially those of environmental selection. The wetland microbial communities are impacted by pollutants discharged into the sea from the Huaihe River and the Yangtze River. The Yangtze River's nitrogen pollutants affected the wetland zone, and denitrification dominated. The study established ecological patterns between the river and the sea and we offer suggestions for managing watersheds and safeguarding the ecology of coastal tidal flats.
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Affiliation(s)
- Weiwei Song
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing, 210098, China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; National Engineering Research Center of Water Resources Efficient Utilization and Engineering Safety, Hohai University, Nanjing, 210098, China.
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Pulcini L, Bona E, Vaudano ET, Tsolakis C, Garcia-Moruno E, Costantini A, Gamalero E. The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera. Microorganisms 2023; 11:1873. [PMID: 37630432 PMCID: PMC10457965 DOI: 10.3390/microorganisms11081873] [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: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Reducing the use of fungicides, insecticides, and herbicides in order to limit environmental pollution and health risks for agricultural operators and consumers is one of the goals of European regulations. In fact, the European Commission developed a package of measures (the European Green Deal) to promote the sustainable use of natural resources and strengthen the resilience of European agri-food systems. As a consequence, new plant protection products, such as biostimulants, have been proposed as alternatives to agrochemicals. Their application in agroecosystems could potentially open new scenarios regarding the microbiota. In particular, the vineyard microbiota and the microbiota on the grape surface can be affected by biostimulants and lead to different wine features. The aim of this work was to assess the occurrence of a possible variation in the mycobiota due to the biostimulant application. Therefore, our attention has been focused on the yeast community of grape bunches from vines subjected to the phytostimulant BION®50WG treatment. This work was carried out in the CREA-VE experimental vineyard of Vitis vinifera cv. Barbera in Asti (Piedmont, Italy). The composition of fungal communities on grapes from three experimental conditions such as IPM (integrated pest management), IPM+BION®50WG, and IPM+water foliar nebulization was compared by a metabarcoding approach. Our results revealed the magnitude of alpha and beta diversity, and the microbial biodiversity index and specific fungal signatures were highlighted by comparing the abundance of yeast and filamentous fungi in IPM and BION®50WG treatments. No significant differences in the mycobiota of grapevines subjected to the three treatments were detected.
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Affiliation(s)
- Laura Pulcini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, Italy;
| | - Enrico Tommaso Vaudano
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Christos Tsolakis
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Emilia Garcia-Moruno
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Antonella Costantini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
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11
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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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12
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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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13
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Bhatt K, Suyal DC, Kumar S, Singh K, Goswami P. New insights into engineered plant-microbe interactions for pesticide removal. CHEMOSPHERE 2022; 309:136635. [PMID: 36183882 DOI: 10.1016/j.chemosphere.2022.136635] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/21/2022] [Accepted: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Over the past decades, rapid industrialization along with the overutilization of organic pollutants/pesticides has altered the environmental circumstances. Moreover, various anthropogenic, xenobiotics and natural activities also affected plants, soil, and human health, in both direct and indirect ways. To counter this, several conventional methods are currently practiced, but are uneconomical, noxious, and is yet inefficient for large-scale application. Plant-microbe interactions are mediated naturally in an ecosystem and are practiced in several areas. Plant growth promoting rhizobacteria (PGPR) possess certain attributes affecting plant and soil consequently performing decontamination activity via a direct and indirect mechanism. PGPR also harbors indispensable genes stimulating the mineralization of several organic and inorganic compounds. This makes microbes potential candidates for contributing to sustainably remediating the harmful pesticide contaminants. There is a limited piece of information about the plant-microbe interaction pertaining predict and understand the overall interaction concerning a sustainable environment. Therefore, this review focuses on the plant-microbe interaction in the rhizosphere and inside the plant's tissues, along with the utilization augmenting the crop productivity, reduction in plant stress along with decontamination of pesticides/organic pollutants in soil for sustainable environmental management.
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Affiliation(s)
- Kalpana Bhatt
- Department of Food Science, Purdue University, West Lafayette, IN, 47907, USA.
| | - Deep Chandra Suyal
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour, Himachal Pradesh, India.
| | - Saurabh Kumar
- ICAR-Research Complex for Eastern Region, Patna, 800014, Bihar, India
| | - Kuldeep Singh
- Department of Microbiology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, 125004, India
| | - Priya Goswami
- Department of Biotechnology, Mangalayatan University, Uttar Pradesh, India
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14
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Fungi are more transient than bacteria in caterpillar gut microbiomes. Sci Rep 2022; 12:15552. [PMID: 36114345 PMCID: PMC9481635 DOI: 10.1038/s41598-022-19855-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/06/2022] [Indexed: 11/24/2022] Open
Abstract
Despite an increasing number of studies on caterpillar (Insecta: Lepidoptera) gut microbiota, bacteria have been emphasized more than fungi. Therefore, we lack data on whether fungal microbiota is resident or transient and shaped by factors similar to those of bacteria. We sampled nine polyphagous caterpillar species from several tree species at multiple sites to determine the factors shaping leaf and gut bacterial and fungal microbiota as well as the extent to which caterpillars acquire microbiota from their diet. We performed 16S and ITS2 DNA metabarcoding of the leaves and guts to determine the composition and richness of the respective microbiota. While spatial variables shaped the bacterial and fungal microbiota of the leaves, they only affected fungi in the guts, whereas the bacteria were shaped primarily by caterpillar species, with some species harboring more specific bacterial consortia. Leaf and gut microbiota significantly differed; in bacteria, this difference was more pronounced. The quantitative similarity between leaves and guts significantly differed among caterpillar species in bacteria but not fungi, suggesting that some species have more transient bacterial microbiota. Our results suggest the complexity of the factors shaping the gut microbiota, while highlighting interspecific differences in microbiota residency within the same insect functional group.
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15
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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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16
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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17
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Sahu KP, Kumar A, Sakthivel K, Reddy B, Kumar M, Patel A, Sheoran N, Gopalakrishnan S, Prakash G, Rathour R, Gautam RK. Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease. ENVIRONMENTAL MICROBIOME 2022; 17:28. [PMID: 35619157 PMCID: PMC9134649 DOI: 10.1186/s40793-022-00421-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/09/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future. RESULTS The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings. CONCLUSIONS PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.
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Affiliation(s)
- Kuleshwar Prasad Sahu
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - A Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - K Sakthivel
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mukesh Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Asharani Patel
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Ganesan Prakash
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, 176062, India
| | - R K Gautam
- Division of Field Crop Improvement and Protection, ICAR-Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, 744101, India
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18
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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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19
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Manirakiza B, Zhang S, Addo FG, Isabwe A, Nsabimana A. Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151821. [PMID: 34808175 DOI: 10.1016/j.scitotenv.2021.151821] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.
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Affiliation(s)
- Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Antoine Nsabimana
- University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
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20
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Bastías DA, Bustos LB, Jáuregui R, Barrera A, Acuña-Rodríguez IS, Molina-Montenegro MA, Gundel PE. Epichloë Fungal Endophytes Influence Seed-Associated Bacterial Communities. Front Microbiol 2022; 12:795354. [PMID: 35058911 PMCID: PMC8764391 DOI: 10.3389/fmicb.2021.795354] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022] Open
Abstract
Seeds commonly harbour diverse bacterial communities that can enhance the fitness of future plants. The bacterial microbiota associated with mother plant’s foliar tissues is one of the main sources of bacteria for seeds. Therefore, any ecological factor influencing the mother plant’s microbiota may also affect the diversity of the seed’s bacterial community. Grasses form associations with beneficial vertically transmitted fungal endophytes of genus Epichloë. The interaction of plants with Epichloë endophytes and insect herbivores can influence the plant foliar microbiota. However, it is unknown whether these interactions (alone or in concert) can affect the assembly of bacterial communities in the produced seed. We subjected Lolium multiflorum plants with and without its common endophyte Epichloë occultans (E+, E-, respectively) to an herbivory treatment with Rhopalosiphum padi aphids and assessed the diversity and composition of the bacterial communities in the produced seed. The presence of Epichloë endophytes influenced the seed bacterial microbiota by increasing the diversity and affecting the composition of the communities. The relative abundances of the bacterial taxa were more similarly distributed in communities associated with E+ than E- seeds with the latter being dominated by just a few bacterial groups. Contrary to our expectations, seed bacterial communities were not affected by the aphid herbivory experienced by mother plants. We speculate that the enhanced seed/seedling performance documented for Epichloë-host associations may be explained, at least in part, by the Epichloë-mediated increment in the seed-bacterial diversity, and that this phenomenon may be applicable to other plant-endophyte associations.
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Affiliation(s)
- Daniel A Bastías
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Ludmila Bubica Bustos
- IFEVA, CONICET, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruy Jáuregui
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Andrea Barrera
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ian S Acuña-Rodríguez
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Marco A Molina-Montenegro
- Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile.,Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile.,Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Pedro E Gundel
- IFEVA, CONICET, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.,Laboratorio de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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21
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Zhang L, Yan C, Qi R, Yang F. Quantifying the contribution rates of sulfonamide antibiotics removal mechanisms in constructed wetlands using multivariate statistical analysis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 292:118463. [PMID: 34742821 DOI: 10.1016/j.envpol.2021.118463] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
The removal of antibiotics in subsurface flow constructed wetlands is performed through various removal mechanisms, such as adsorption, hydrolysis, microbial degradation and plant uptake. However, the contribution rates of the removal mechanisms in constructed wetlands are still not well studied. This study conducted a series of experiments and used multivariate statistical analysis to determine contribution rates for substrate adsorption, hydrolysis, and microbial degradation. Multiple stepwise regression analysis indicated that specific surface area and salt content were the main factors influencing sulfonamide adsorption, while temperature and pH were the main factors influencing sulfonamide hydrolysis. Variance partitioning analysis showed that the influence of physical-chemical factors was greater than that of nutrients on the microbial community. Partial least squares path analysis showed that the path coefficients of microbial degradation, adsorption and hydrolysis for sulfonamides removal in vertical subsurface flow constructed wetlands were 0.6339, 0.3608 and 0.0351, respectively, while the corresponding path coefficient were 0.5658, 0.4707 and 0.1079 in horizontal subsurface flow constructed wetlands, respectively. This means that microbial degradation contributes the most to the removal of sulfonamides in subsurface flow constructed wetlands. Enhanced microbial degradation may be a powerful measure to improve the removal of sulfonamides. These results will be helpful for understanding the removal mechanism of antibiotics and will provide a definite direction for pertinently improving sulfonamide removal efficiency in constructed wetlands.
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Affiliation(s)
- Ling Zhang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changzhou Yan
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Ran Qi
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Yang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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22
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Sahu KP, Patel A, Kumar M, Sheoran N, Mehta S, Reddy B, Eke P, Prabhakaran N, Kumar A. Integrated Metabarcoding and Culturomic-Based Microbiome Profiling of Rice Phyllosphere Reveal Diverse and Functional Bacterial Communities for Blast Disease Suppression. Front Microbiol 2021; 12:780458. [PMID: 34917058 PMCID: PMC8669949 DOI: 10.3389/fmicb.2021.780458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/20/2021] [Indexed: 11/13/2022] Open
Abstract
Phyllosphere-the harsh foliar plant part exposed to vagaries of environmental and climatic variables is a unique habitat for microbial communities. In the present work, we profiled the phyllosphere microbiome of the rice plants using 16S rRNA gene amplicon sequencing (hereafter termed metabarcoding) and the conventional microbiological methods (culturomics) to decipher the microbiome assemblage, composition, and their functions such as antibiosis and defense induction against rice blast disease. The blast susceptible rice genotype (PRR78) harbored far more diverse bacterial species (294 species) than the resistant genotype (Pusa1602) that showed 193 species. Our metabarcoding of bacterial communities in phyllomicrobiome revealed the predominance of the phylum, Proteobacteria, and its members Pantoea, Enterobacter, Pseudomonas, and Erwinia on the phyllosphere of both rice genotypes. The microbiological culturomic validation of metabarcoding-taxonomic annotation further confirmed the prevalence of 31 bacterial isolates representing 11 genera and 16 species with the maximum abundance of Pantoea. The phyllomicrobiome-associated bacterial members displayed antifungal activity on rice blast fungus, Magnaporthe oryzae, by volatile and non-volatile metabolites. Upon phyllobacterization of rice cultivar PB1, the bacterial species such as Enterobacter sacchari, Microbacterium testaceum, Pantoea ananatis, Pantoea dispersa, Pantoea vagans, Pseudomonas oryzihabitans, Rhizobium sp., and Sphingomonas sp. elicited a defense response and contributed to the suppression of blast disease. qRT-PCR-based gene expression analysis indicated over expression of defense-associated genes such as OsCEBiP, OsCERK1, and phytohormone-associated genes such as OsPAD4, OsEDS1, OsPR1.1, OsNPR1, OsPDF2.2, and OsFMO in phyllobacterized rice seedlings. The phyllosphere bacterial species showing blast suppressive activity on rice were found non-plant pathogenic in tobacco infiltration assay. Our comparative microbiome interrogation of the rice phyllosphere culminated in the isolation and identification of agriculturally significant bacterial communities for blast disease management in rice farming through phyllomicrobiome engineering in the future.
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Affiliation(s)
- Kuleshwar Prasad Sahu
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Asharani Patel
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mukesh Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sahil Mehta
- Crop Improvement Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Bhaskar Reddy
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pierre Eke
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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23
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Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities. Microorganisms 2021; 9:microorganisms9102088. [PMID: 34683409 PMCID: PMC8540654 DOI: 10.3390/microorganisms9102088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/27/2021] [Accepted: 10/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ambient air pollution exerts deleterious effects on our environment. Continuously exposed to the atmosphere, diverse communities of microorganisms thrive on leaf surfaces, the phylloplane. The composition of these communities is dynamic, responding to many environmental factors including ambient air pollution. In this field study, over a 2 year period, we sampled Hedera helix (ivy) leaves at six locations exposed to different ambient air pollution conditions. Daily, we monitored ambient black carbon (BC), PM2.5, PM10, nitrogen dioxide, and ozone concentrations and found that ambient air pollution led to a 2–7-fold BC increase on leaves, the phylloplane BC load. Our results further indicated that the phylloplane BC load correlates with the diversity of bacterial and fungal leaf communities, impacting diversity more than seasonal effects. The bacterial genera Novosphingobium, Hymenobacter, and Methylorubrum, and the fungal genus Ampelomyces were indicators for communities exposed to the highest phylloplane BC load. Parallel to this, we present one fungal and two bacterial phylloplane strains isolated from an air-polluted environment able to degrade benzene, toluene, and/or xylene, including a genomics-based description of the degradation pathways involved. The findings of this study suggest that ambient air pollution shapes microbial leaf communities, by affecting diversity and supporting members able to degrade airborne pollutants.
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