1
|
Li X, Yang S, Zhang J, Xiao L, Feng X, Huang H, Xing Y. Intestinal microbial community well explain larval growth than feed types. Appl Microbiol Biotechnol 2024; 108:32. [PMID: 38175237 DOI: 10.1007/s00253-023-12857-x] [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: 05/29/2023] [Revised: 09/25/2023] [Accepted: 10/24/2023] [Indexed: 01/05/2024]
Abstract
Black soldier fly larvae (BSFL) are considered a sustainable ingredient in livestock feed. However, addressing issues related to feed substrate and intestinal microbiota is essential to ensure optimal larval development. The aim of this study was to assess and elucidate the contribution of substrate nutrients and intestinal microbes to protein and fat synthesis in BSFL. The results showed that larvae that were fed high-quality feed (chicken feed) had high fat biomass, while larvae that were fed medium-quality feed (wheat bran) had high protein biomass. These results indicate that the original nutritional content of the feed cannot fully explain larval growth and nutrient utilization. However, the phenomenon could be explained by the functional metabolism of intestinal microbes. Chicken feed enhanced the fatty acid metabolism of middle intestine microorganisms in larvae within 0-7 days. This process facilitated larval fat synthesis. In contrast, wheat bran stimulated the amino acid metabolism in posterior intestine microorganisms in larvae within 4-7 days, leading to better protein synthesis. The findings of this study highlight the importance of the microbial functional potential in the intestine in regulating protein and lipid synthesis in BSFL, which is also influenced by the type of feed. In conclusion, our study suggests that both feed type and intestinal microbes play a crucial role in efficiently converting organic waste into high-quality insect protein and fat. Additionally, a mixed culture of chicken feed and wheat bran was found to be effective in promoting larval biomass while reducing feed costs. KEY POINTS: • Intestinal microbes explain BSFL growth better than feed substrates. • Chicken feed promotes fatty acid synthesis in the middle intestine • Wheat bran promotes amino acid synthesis in the posterior intestine.
Collapse
Affiliation(s)
- Xiaomei Li
- School of Life Science, Guangzhou University, Guangzhou, 510006, China
| | - Shan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Jiaxue Zhang
- Haid Research Institute, Guangdong Haid Group Co. Ltd., 5 Eighth Street, Fu Ping Road, Guangzhou, 511400, China
| | - Lan Xiao
- Haid Research Institute, Guangdong Haid Group Co. Ltd., 5 Eighth Street, Fu Ping Road, Guangzhou, 511400, China
| | - Xiangchi Feng
- School of Life Science, Guangzhou University, Guangzhou, 510006, China
| | - Haobin Huang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Yang Xing
- Haid Research Institute, Guangdong Haid Group Co. Ltd., 5 Eighth Street, Fu Ping Road, Guangzhou, 511400, China.
| |
Collapse
|
2
|
Cui S, Zhou L, Fang Q, Xiao H, Jin D, Liu Y. Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175334. [PMID: 39117232 DOI: 10.1016/j.scitotenv.2024.175334] [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: 06/01/2024] [Revised: 07/29/2024] [Accepted: 08/04/2024] [Indexed: 08/10/2024]
Abstract
Phyllosphere microbes play a crucial role in plant health and productivity. However, the influence of abiotic and biotic factors on these communities is poorly understood. Here, we used amplicon sequencing to investigate the microbiome variations across eight grape cultivars and three distinct leaf ages. The diversity and richness of phyllosphere microbiomes were significantly affected by cultivars and leaf age. Young leaves of most grape cultivars had a higher diversity. Beta-diversity analyses revealed notable differences in microbial communities across leaf ages, with bacterial communities varying substantially between cultivars. The main bacterial genera included Staphylococcus, Exiguobacterium, Acinetobacter, Enterococcus, and Erwinia; the principal fungal genera were Cladosporium, Moesziomyces, Alternaria, Didymella, and Coprinellus across all samples. LEfSe analysis revealed significant differences in bacterial and fungal biomarkers at different leaf ages, with no biomarkers identified among different cultivars. Fungal biomarkers were more abundant than bacterial at three leaf ages, and older leaves had more fungal biomarkers. Notably, beneficial microbial taxa with biocontrol potential were present on the phyllosphere at 45 d, whereas certain fungal groups associated with increased disease risk were first detected at 100 d. The bacterial network was more complex than the fungal network, and young leaves had a more complex network in most cultivars. Our study elucidated the dynamics of early grape phyllosphere microbes, providing valuable insights for early detection and prediction of grape diseases and a foundation for leveraging the grape leaf microbiome for agricultural purposes.
Collapse
Affiliation(s)
- Shaowei Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Lianzhu Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiandong Fang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haijun Xiao
- School of Grassland Science, Beijing Forestry University, Beijing 100083, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Yongqiang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
3
|
Tian Y, Liu Y, Yue L, Zhao X, Zhou Q, Uwaremwe C, Wang Y, Chen G, Sha Y, Zhang Y, Wang R. Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions. Microbiol Res 2024; 287:127855. [PMID: 39079269 DOI: 10.1016/j.micres.2024.127855] [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: 05/31/2024] [Revised: 07/15/2024] [Accepted: 07/22/2024] [Indexed: 08/22/2024]
Abstract
Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.
Collapse
Affiliation(s)
- Yuan Tian
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Liu
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liang Yue
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xia Zhao
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qin Zhou
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Constantine Uwaremwe
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Gaofeng Chen
- Gansu Shangnong Biotechnology Co. Ltd, Baiyin 730900, China
| | - Yuexia Sha
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yubao Zhang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; Gansu Gaolan Field Scientific Observation and Research Station for Agricultural Ecosystem, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ruoyu Wang
- Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Chinese Academy of Sciences, Lanzhou 730000, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
4
|
Zhou K, Yin D, Liu C, Sun R. Investigating the role of poly-γ-glutamic acid in Pennisetum giganteum phytoextraction of mercury-contaminated soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173707. [PMID: 38866170 DOI: 10.1016/j.scitotenv.2024.173707] [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: 01/27/2024] [Revised: 05/16/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024]
Abstract
Farmland mercury (Hg) pollution poses a significant threat to human health, but there is a lack of highly efficient phytoextraction for its remediation at present. This study investigates the impact of poly-γ-glutamic acid (γ-PGA) on the phytoextraction capabilities of Pennisetum giganteum (P. giganteum) in Hg-contaminated soil. Our research indicates that amending γ-PGA to soil markedly enhances the assimilation of soil Hg by P. giganteum and transformation of Hg within itself, with observed increases in Hg concentrations in roots, stems, and leaves by 1.1, 4.3, and 18.9 times, respectively, compared to the control. This enhancement is attributed to that γ-PGA can facilitate the hydrophilic and bioavailable of soil Hg. Besides, γ-PGA can stimulate the abundance of Hg-resistance bacteria Proteobacteria in the rhizosphere of P. giganteum, thus increasing the mobility and uptake of soil Hg by P. giganteum roots. Moreover, the hydrophilic nature of Hg-γ-PGA complexes supports their transport via the apoplastic pathway, across the epidermis, and through the Casparian strip, eventually leading to immobilization in the mesophyll tissues. This study provides novel insights into the mechanisms of Hg phytoextraction, demonstrating that γ-PGA significantly enhances the effectiveness of P. giganteum in Hg uptake and translocation. The findings suggest a promising approach for the remediation of Hg-contaminated soil, offering a sustainable and efficient strategy for environmental management and health risk mitigation.
Collapse
Affiliation(s)
- Kun Zhou
- Guizhou Normal University, Guiyang 550001, PR China
| | - Deliang Yin
- Key Laboratory of Karst Georesources and Environment (Guizhou University), Ministry of Education, Guiyang 550025, PR China
| | - Chen Liu
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China
| | - Rongguo Sun
- Guizhou Key Laboratory for Mountainous Environmental Information and Ecological Protection, Guizhou Normal University, Guiyang 550001, PR China.
| |
Collapse
|
5
|
Addison SL, Rúa MA, Smaill SJ, Singh BK, Wakelin SA. Partner or perish: tree microbiomes and climate change. TRENDS IN PLANT SCIENCE 2024; 29:1029-1040. [PMID: 38641475 DOI: 10.1016/j.tplants.2024.03.008] [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: 10/25/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/21/2024]
Abstract
Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.
Collapse
Affiliation(s)
- S L Addison
- Scion, Rotorua 3010, New Zealand; Western Sydney University, Richmond, New South Wales 2753, Australia.
| | - M A Rúa
- Wright State University, Dayton, OH 45435-0001, USA
| | | | - B K Singh
- Western Sydney University, Richmond, New South Wales 2753, Australia
| | | |
Collapse
|
6
|
Shao Q, Ran Q, Li X, Dong C, Zhang Y, Han Y. Differential responses of the phyllosphere abundant and rare microbes of Eucommia ulmoides to phytohormones. Microbiol Res 2024; 286:127798. [PMID: 38964073 DOI: 10.1016/j.micres.2024.127798] [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: 04/04/2024] [Revised: 05/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
Abstract
Phyllosphere microbiota play a crucial role in plant productivity and adaptation, and the abundant and rare microbial taxa often possess distinct characteristics and ecological functions. However, it is unclear whether the different subcommunities of phyllosphere microbiota respond variably to the factors that influence their formation, which limits the understanding of community assembly. The effects of two phytohormones, namely, indole-3-acetic acid (IAA) and N6-(delta 2-isopentenyl)-adenine (IP), on the phyllosphere microbial subcommunities of Eucommia ulmoides were investigated using potted experiments. The results demonstrated that the phytohormones induced significant variations in the composition, diversity, and function of the abundant microbial subcommunity in the phyllosphere of E. ulmoides, however, their effects on the rare subcommunity were negligible, and their effects on the moderate subcommunity were between those of the abundant and rare taxa. The phytohormones also induced significant alterations in the phenotypic and physiological properties of E. ulmoides, which indirectly affected the phyllosphere microbial community. Leaf thickness and average leaf area were the main phenotypic variables that affected the composition of the phyllosphere microbial community. The total alkaloid content and activity of superoxide dismutase (SOD) were the main physiological variables that affected the composition of the phyllosphere microbial community. The phenotypic and physiological indices of E. ulmoides explained the variations in the phyllosphere microbial subcommunities in descending order: abundant > moderate > rare taxa. These variables explained a significant proportion of the variations in the abundant taxa, and an insignificant proportion of the variations in the rare taxa. This study improves our understanding of the assembly of the phyllosphere microbiota, which provides important theoretical knowledge for future sustainable agriculture and forestry management based on the precise regulation of phyllosphere microbiota.
Collapse
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, Guizhou 550025, 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, Guizhou 550025, 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, Guizhou 550025, 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, Guizhou 550025, China
| | - Yanwei Zhang
- Key Laboratory of Development and Utilization of Biological Resources in Colleges and Universities of Guizhou Province, Guizhou Education University, Guiyang, Guizhou 550018, 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, Guizhou 550025, China.
| |
Collapse
|
7
|
Kumari R, Kapoor P, Mir BA, Singh M, Parrey ZA, Rakhra G, Parihar P, Khan MN, Rakhra G. Unlocking the versatility of nitric oxide in plants and insights into its molecular interplays under biotic and abiotic stress. Nitric Oxide 2024; 150:1-17. [PMID: 38972538 DOI: 10.1016/j.niox.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/19/2024] [Accepted: 07/04/2024] [Indexed: 07/09/2024]
Abstract
In plants, nitric oxide (NO) has become a versatile signaling molecule essential for mediating a wide range of physiological processes under various biotic and abiotic stress conditions. The fundamental function of NO under various stress scenarios has led to a paradigm shift in which NO is now seen as both a free radical liberated from the toxic product of oxidative metabolism and an agent that aids in plant sustenance. Numerous studies on NO biology have shown that NO is an important signal for germination, leaf senescence, photosynthesis, plant growth, pollen growth, and other processes. It is implicated in defense responses against pathogensas well as adaptation of plants in response to environmental cues like salinity, drought, and temperature extremes which demonstrates its multifaceted role. NO can carry out its biological action in a variety of ways, including interaction with protein kinases, modifying gene expression, and releasing secondary messengers. In addition to these signaling events, NO may also be in charge of the chromatin modifications, nitration, and S-nitrosylation-induced posttranslational modifications (PTM) of target proteins. Deciphering the molecular mechanism behind its essential function is essential to unravel the regulatory networks controlling the responses of plants to various environmental stimuli. Taking into consideration the versatile role of NO, an effort has been made to interpret its mode of action based on the post-translational modifications and to cover shreds of evidence for increased growth parameters along with an altered gene expression.
Collapse
Affiliation(s)
- Ritu Kumari
- Department of Botany, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Preedhi Kapoor
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, India
| | - Bilal Ahmad Mir
- Department of Botany, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Maninder Singh
- Department of Biotechnology and Biosciences, Lovely Professional University, Phagwara, 144411, India
| | - Zubair Ahmad Parrey
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Gurseen Rakhra
- Department of Nutrition & Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research and Studies, Faridabad, Haryana, 121004, India
| | - Parul Parihar
- Department of Biosciences and Biotechnology, Banasthali Vidyapith, Rajasthan, 304022, India
| | - M Nasir Khan
- Renewable Energy and Environmental Technology Center, University of Tabuk, Tabuk, 47913, Saudi Arabia
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, India.
| |
Collapse
|
8
|
Fu X, Ma Y, Yang T, He S, Wang D, Jin L, Zhan L, Guo Z, Fan K, Li J, Chu H. Bacterial community composition of wheat aboveground compartments correlates with yield during the reproductive phase. Appl Environ Microbiol 2024:e0107824. [PMID: 39212378 DOI: 10.1128/aem.01078-24] [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: 05/31/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Plant-associated microbial communities play important roles in agricultural productivity, and their composition has been shown to vary across plant compartments and developmental stages. However, the response of microbial communities within different plant compartments and at different developmental stages to diverse long-term fertilization treatments, as well as their linkages with crop yields, remains underexplored. This study analyzed wheat-associated bacterial communities within various soil and plant compartments under three fertilization treatments throughout the vegetative and reproductive phases. The variance in bacterial community was primarily attributed to compartments, followed by fertilization treatments and developmental stages. The composition of belowground bacterial communities (bulk soil, rhizosphere soil, and root) exhibited stronger responses to fertilization treatments than aboveground compartments (stem and leaf). The composition of belowground bacterial communities responded to fertilization treatments at all developmental stages, and it was significantly correlated with crop yields during the vegetative phase, whereas the aboveground community composition only showed a response to fertilization during the reproductive phase, at which point it was significantly correlated with crop yields. Moreover, during this reproductive phase, the co-occurrence network of aboveground bacterial communities exhibited enhanced complexity, and it contained an increased number of keystone species associated with crop yields, such as Sphingomonas spp., Massilia spp., and Frigoribacterium spp. Structural equation modeling indicated that augmenting total phosphorus levels in aboveground compartments could enhance crop yields by increasing the relative abundance of these keystone species during the reproductive phase. These findings highlight the pivotal role of aboveground bacterial communities in wheat production during the reproductive phase. IMPORTANCE The developmental stage significantly influences crop-associated bacterial communities, but the relative importance of bacterial communities in different compartments to crop yields across various stages is still not well understood. This study reveals that belowground bacterial communities during the vegetative phase are significantly correlated with crop yields. Notably, during the reproductive phase, the composition of aboveground bacterial communities was significantly correlated with crop yields. During this phase, the complexity and enriched keystone species within the aboveground co-occurrence network underscore their role in boosting crop production. These results provide a foundation for developing microbiome-based products that are phase-specific and promote sustainable agricultural practices.
Collapse
Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuobing He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Lin Jin
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Jiasui Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
9
|
Dixon MH, Nellore D, Zaacks SC, Barak JD. Time of arrival during plant disease progression and humidity additively influence Salmonella enterica colonization of lettuce. Appl Environ Microbiol 2024:e0131124. [PMID: 39207142 DOI: 10.1128/aem.01311-24] [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: 07/02/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
The interplay between plant hosts, phytopathogenic bacteria, and enteric human pathogens in the phyllosphere has consequences for human health. Salmonella enterica has been known to take advantage of phytobacterial infection to increase its success on plants, but there is little knowledge of additional factors that may influence the relationship between enteric pathogens and plant disease. In this study, we investigated the role of humidity and the extent of plant disease progression on S. enterica colonization of plants. We found that high humidity was necessary for the replication of S. enterica on diseased lettuce, but not required for S. enterica ingress into the UV-protected apoplast. Additionally, the Xanthomonas hortorum pv. vitians (hereafter, X. vitians)-infected lettuce host was found to be a relatively hostile environment for S. enterica when it arrived prior to the development of watersoaking or following necrosis onset, supporting the existence of an ideal window during X. vitians infection progress that maximizes S. enterica survival. In vitro growth studies in sucrose media suggest that X. vitians may allow S. enterica to benefit from cross-feeding during plant infection. Overall, this study emphasizes the role of phytobacterial disease as a driver of S. enterica success in the phyllosphere, demonstrates how the time of arrival during disease progress can influence S. enterica's fate in the apoplast, and highlights the potential for humidity to transform an infected apoplast into a growth-promoting environment for bacterial colonizers. IMPORTANCE Bacterial leaf spot of lettuce caused by Xanthomonas hortorum pv. vitians is a common threat to leafy green production. The global impact caused by phytopathogens, including X. vitians, is likely to increase with climate change. We found that even under a scenario where increased humidity did not enhance plant disease, high humidity had a substantial effect on facilitating Salmonella enterica growth on Xanthomonas-infected plants. High humidity climates may directly contribute to the survival of human enteric pathogens in crop fields or indirectly affect bacterial survival via changes to the phyllosphere brought on by phytopathogen disease.
Collapse
Affiliation(s)
- Megan H Dixon
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin, Madison, Wisconsin, USA
| | - Dharshita Nellore
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, USA
| | - Sonia C Zaacks
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, USA
| | - Jeri D Barak
- Department of Plant Pathology, University of Wisconsin, Madison, Wisconsin, USA
| |
Collapse
|
10
|
Grossi CEM, Tani A, Mori IC, Matsuura T, Ulloa RM. Plant growth-promoting abilities of Methylobacterium sp. 2A involve auxin-mediated regulation of the root architecture. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39189962 DOI: 10.1111/pce.15116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 08/12/2024] [Indexed: 08/28/2024]
Abstract
Methylobacterium sp. 2A, a plant growth-promoting rhizobacteria (PGPR) able to produce indole-3-acetic acid (IAA), significantly promoted the growth of Arabidopsis thaliana plants in vitro. We aimed to understand the determinants of Methylobacterium sp. 2A-A. thaliana interaction, the factors underlying plant growth-promotion and the host range. Methylobacterium sp. 2A displayed chemotaxis to methanol and formaldehyde and was able to utilise 1-aminocyclopropane carboxylate as a nitrogen source. Confocal microscopy confirmed that fluorescent protein-labelled Methylobacterium sp. 2A colonises the apoplast of A. thaliana primary root cells and its inoculation increased jasmonic and salicylic acid in A. thaliana, while IAA levels remained constant. However, inoculation increased DR5 promoter activity in root tips of A. thaliana and tomato plants. Inoculation of this PGPR partially restored the agravitropic response in yucQ mutants and lateral root density was enhanced in iaa19, arf7, and arf19 mutant seedlings. Furthermore, Methylobacterium sp. 2A volatile organic compounds (VOCs) had a dose-dependent effect on the growth of A. thaliana. This PGPR is also able to interact with monocots eliciting positive responses upon inoculation. Methylobacterium sp. 2A plant growth-promoting effects can be achieved through the regulation of plant hormone levels and the emission of VOCs that act either locally or at a distance.
Collapse
Affiliation(s)
- Cecilia E M Grossi
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Izumi C Mori
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Takakazu Matsuura
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Rita M Ulloa
- Laboratorio de Transducción de Señales en Plantas, Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Departamento de Química Biológica, Universidad de Buenos Aires (UBA), Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
11
|
Yan X, White JC, He E, Peijnenburg WJGM, Zhang P, Qiu H. Temporal Dynamics of Copper-Based Nanopesticide Transfer and Subsequent Modulation of the Interplay Between Host and Microbiota Across Trophic Levels. ACS NANO 2024. [PMID: 39171664 DOI: 10.1021/acsnano.4c06047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
During agricultural production, significant quantities of copper-based nanopesticides (CBNPs) may be released into terrestrial ecosystems through foliar spraying, thereby posing a potential risk of biological transmission via food chains. Consequently, we investigated the trophic transfer of two commonly available commercial CBNPs, Reap2000 (RP) and HolyCu (HC), in a plant-caterpillar terrestrial food chain and evaluated impacts on host microbiota. Upon foliar exposure (with 4 rounds of spraying, totaling 6.0 mg CBNPs per plant), leaf Cu accumulation levels were 726 ± 180 and 571 ± 121 mg kg-1 for RP and HC, respectively. HC exhibited less penetration through the cuticle compared to RP (RP: 55.5%; HC: 32.8%), possibly due to size exclusion limitations. While caterpillars accumulated higher amounts of RP, HC exhibited a slightly higher trophic transfer factor (TTF; RP: 0.69 ± 0.20; HC: 0.74 ± 0.17, p > 0.05) and was more likely to be transferred through the food chain. The application of RP promoted the dispersal of phyllosphere microbes and perturbed the original host intestinal microbiota, whereas the HC group was largely host-modulated (control: 65%; RP: 94%; HC: 34%). Integrating multiomics analyses and modeling approaches, we elucidated two pathways by which plants exert bottom-up control over caterpillar health. Beyond the direct transmission of phyllosphere microbes, the leaf microbiome recruited upon exposure to CBNPs further influenced the ingestion behavior and intestinal microbiota of caterpillars via altered leaf metabolites. Elevated Proteobacteria abundance benefited caterpillar growth with RP, while the reduction of Proteobacteria with HC increased the risk of lipid metabolism issues and gut disease. The recruited Bacteroidota in the RP phyllosphere proliferated more extensively into the caterpillar gut to enhance stress resistance. Overall, the gut microbes reshaped in RP caterpillars exerted a strong regulatory effect on host health. These findings expand our understanding of the dynamic transmission of host-microbiota interactions with foliar CBNPs exposure, and provide critical insight necessary to ensure the safety and sustainability of nanoenabled agricultural strategies.
Collapse
Affiliation(s)
- Xuchen Yan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven06511, Connecticut, United States
| | - Erkai He
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Willie J G M Peijnenburg
- Center for the Safety of Substances and Products, National Institute of Public Health and the Environment, Bilthoven 3720BA, The Netherlands
- Institute of Environmental Sciences, Leiden University, Leiden 2300RA, The Netherlands
| | - Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, Birmingham, U.K
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
12
|
Compant S, Cassan F, Kostić T, Johnson L, Brader G, Trognitz F, Sessitsch A. Harnessing the plant microbiome for sustainable crop production. Nat Rev Microbiol 2024:10.1038/s41579-024-01079-1. [PMID: 39147829 DOI: 10.1038/s41579-024-01079-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
Global research on the plant microbiome has enhanced our understanding of the complex interactions between plants and microorganisms. The structure and functions of plant-associated microorganisms, as well as the genetic, biochemical, physical and metabolic factors that influence the beneficial traits of plant microbiota have also been intensively studied. Harnessing the plant microbiome has led to the development of various microbial applications to improve crop productivity in the face of a range of challenges, for example, climate change, abiotic and biotic stresses, and declining soil properties. Microorganisms, particularly nitrogen-fixing rhizobia as well as mycorrhizae and biocontrol agents, have been applied for decades to improve plant nutrition and health. Still, there are limitations regarding efficacy and consistency under field conditions. Also, the wealth of expanding knowledge on microbiome diversity, functions and interactions represents a huge source of information to exploit for new types of application. In this Review, we explore plant microbiome functions, mechanisms, assembly and types of interaction, and discuss current applications and their pitfalls. Furthermore, we elaborate on how the latest findings in plant microbiome research may lead to the development of new or more advanced applications. Finally, we discuss research gaps to fully leverage microbiome functions for sustainable plant production.
Collapse
Affiliation(s)
| | | | - Tanja Kostić
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | - Günter Brader
- AIT Austrian Institute of Technology, Vienna, Austria
| | | | | |
Collapse
|
13
|
Melnikov OI, Rozova ON, Reshetnikov AS, Khmelenina VN, Mustakhimov II. Mannitol as a Growth Substrate for Facultative Methylotroph Methylobrevis pamukkalensis PK2. Curr Microbiol 2024; 81:300. [PMID: 39110243 DOI: 10.1007/s00284-024-03795-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/02/2024] [Indexed: 08/15/2024]
Abstract
Biochemistry of carbon assimilation in aerobic methylotrophs growing on reduced C1 compounds has been intensively studied due to the vital role of these microorganisms in nature. The biochemical pathways of carbon assimilation in methylotrophs growing on multi-carbon substrates are insufficiently explored. Here we elucidated the metabolic route of mannitol assimilation in the alphaproteobacterial facultative methylotroph Methylobrevis pamukkalensis PK2. Two key enzymes of mannitol metabolism, mannitol-2-dehydrogenase (MTD) and fructokinase (FruK), were obtained as His-tagged proteins by cloning and expression of mtd and fruK genes in Escherichia coli and characterized. Genomic analysis revealed that further transformation of fructose-6-phosphate proceeds via the Entner-Doudoroff pathway. During growth on mannitol + methanol mixture, the strain PK2 consumed both substrates simultaneously demonstrating independence of C1 and C6 metabolic pathways. Genome screening showed that genes for mannitol utilization enzymes are present in other alphaproteobacterial methylotrophs predominantly capable of living in association with plants. The capability to utilize a variety of carbohydrates (sorbitol, glucose, fructose, arabinose and xylose) suggests a broad adaptability of the strain PK2 to live in environments where availability of carbon substrate dynamically changes.
Collapse
Affiliation(s)
- Oleg I Melnikov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Olga N Rozova
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation.
| | - Alexander S Reshetnikov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Valentina N Khmelenina
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| | - Ildar I Mustakhimov
- Laboratory of Methylotrophy, Federal Research Center Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Prospect Nauki 5, 142290, Pushchino, Russian Federation
| |
Collapse
|
14
|
Thomas G, Kay WT, Fones HN. Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere. BMC Biol 2024; 22:168. [PMID: 39113027 PMCID: PMC11304629 DOI: 10.1186/s12915-024-01967-1] [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: 03/06/2024] [Accepted: 08/01/2024] [Indexed: 08/11/2024] Open
Abstract
Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.
Collapse
Affiliation(s)
| | - William T Kay
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | | |
Collapse
|
15
|
Poupin MJ, González B. Embracing complexity in plant-microbiome systems. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e70000. [PMID: 39189551 PMCID: PMC11348195 DOI: 10.1111/1758-2229.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 07/27/2024] [Indexed: 08/28/2024]
Abstract
Despite recent advances in understanding the role of microorganisms in plant holobiont metabolism, physiology, and fitness, several relevant questions are yet to be answered, with implications for ecology, evolution, and sustainable agriculture. This article explores some of these questions and discusses emerging research areas in plant microbiomes. Firstly, it emphasizes the need to move beyond taxonomic characterization towards understanding microbial functions within plant ecosystems. Secondly, controlling methodological biases and enhancing OMICS technologies' standardization is imperative for a deeper comprehension of plant-microbiota interactions. Furthermore, while plant microbiota research has primarily centred on bacteria and fungi, other microbial players such as archaea, viruses, and microeukaryotes have been largely overlooked. Emerging evidence highlights their presence and potential roles, underscoring the need for thorough assessments. Future research should aim to elucidate the ecological microbial interactions, their impact on plant performance, and how the plant context shapes microbial community dynamics. Finally, a discussion is provided on how the multiple layers of abiotic and biotic factors influencing the spatiotemporal dynamics of plant-microbiome systems require in-depth attention. Examples illustrate how synthetic communities and computational methods such as machine learning and artificial intelligence provide alternatives to tackle these challenges and analyse the plant holobiont as a complex system.
Collapse
Affiliation(s)
- María Josefina Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| | - Bernardo González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y CienciasUniversidad Adolfo IbáñezSantiagoChile
- Center of Applied Ecology and Sustainability (CAPES)SantiagoChile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN‐SAP)SantiagoChile
| |
Collapse
|
16
|
Gao H, Guo Z, He X, Yang J, Jiang L, Yang A, Xiao X, Xu R. Stress mitigation mechanism of rice leaf microbiota amid atmospheric deposition of heavy metals. CHEMOSPHERE 2024; 362:142680. [PMID: 38908447 DOI: 10.1016/j.chemosphere.2024.142680] [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: 03/21/2024] [Revised: 06/01/2024] [Accepted: 06/20/2024] [Indexed: 06/24/2024]
Abstract
Leaf microbiota have been extensively applied in the biological control of plant diseases, but their crucial roles in mitigating atmospheric heavy metal (HM) deposition and promoting plant growth remain poorly understood. This study demonstrates that elevated atmospheric HM deposition on rice leaves significantly shapes distinct epiphytic and endophytic microbiota across all growth stages. HM stress consistently leads to the dominance of epiphytic Pantoea and endophytic Microbacterium in rice leaves, particularly during the booting and filling stages. Leaf-bound HMs stimulate the differentiation of specialized microbial communities in both endophytic and epiphytic compartments, thereby regulating leaf microbial interactions. Metagenomic binning retrieved high-quality genomes of keystone leaf microorganisms, indicating their potential for essential metabolic functions. Notably, Pantoea and Microbacterium show significant HM resistance, plant growth-promoting capabilities, and diverse element cycling functions. They possess genes associated with metal(loid) resistance, such as ars and czc, suggesting their ability to detoxify arsenic(As) and cadmium(Cd). They also support carbon, nitrogen, and sulfur cycling, with genes linked to carbon fixation, nitrogen fixation, and sulfur reduction. Additionally, these bacteria may enhance plant stress resistance and growth by producing antioxidants, phytohormones, and other beneficial compounds, potentially improving HM stress tolerance and nutrient availability in rice plants. This study shows that atmospheric HMs affect rice leaf microbial communities, prompting plants to seek microbial help to combat stress. The unique composition and metabolic potential of rice leaf microbiota offer a novel perspective for mitigating adverse stress induced by atmospheric HM deposition. This contributes to the utilization of leaf microbiota to alleviate the negative impact of heavy metal deposition on rice development and food security.
Collapse
Affiliation(s)
- Hanbing Gao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Zhaohui Guo
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Xiao He
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Jinbo Yang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Li Jiang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Aiping Yang
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Xiyuan Xiao
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China
| | - Rui Xu
- Institute of Environmental Engineering, School of Metallurgy and Environment, Central South University, Changsha, 410083, PR China.
| |
Collapse
|
17
|
Nookongbut P, Thiravetyan P, Salsabila S, Widiana A, Krobthong S, Yingchutrakul Y, Treesubsuntorn C. Application of Acinetobacter indicus to promote cigarette smoke particulate matter phytoremediation: removal efficiency and plant-microbe interactions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:52352-52370. [PMID: 39145908 DOI: 10.1007/s11356-024-34658-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/03/2024] [Indexed: 08/16/2024]
Abstract
Particulate matter (PM) is one of the most hazardous atmospheric pollutants. Several plant species show high potential to reduce air pollutants and are widely used as green belts to provide clean outdoor spaces for human well-being. However, high PM concentrations cause physiological changes and stress in plants. In this study, 11 species of Thai native perennial plants were exposed to PM generated from tobacco smoke. Wrightia religiosa (Teijsm. & Binn.) Benth. ex Kurz, Bauhinia purpurea DC. ex Walp. and Tectona grandis L.f. reduced PM effectively (which is in the typical range of 43.95 to 52.97%) compared to other plant species. In addition, the responses of perennial plants under PM stress at the proteomic level were also evaluated. Proteomic analysis of these three plant species showed that plants respond negatively to high PM concentrations, such as reducing several photosynthetic-related proteins and increasing plant stress response proteins. To improve PM phytoremediation efficiency and reduce plant stress from PM, perennial plant-microbe interactions were investigated. W. religiosa was inoculated with Acinetobacter indicus PS1, and high biosurfactant-producing strains clearly showed a higher PM removal efficiency than non-inoculated plants (9.48, 9.5 and 12.6% for PM1.0, PM2.5 and PM10, respectively). Inoculating W. religiosa with A. indicus PS1 maintained chlorophyll a and b concentrations. Moreover, the malondialdehyde (MDA) concentration of W. religiosa inoculated with A. indicus PS1 was lower than that of non-inoculated W. religiosa. The leaf wax content (µg/cm2) and biosurfactant (µg/cm2) of W. religiosa inoculated with A. indicus PS1 were also higher than those of non-inoculated W. religiosa. This study clearly showed that inoculating plants with A. indicus PS1 can help plants remediate PM and improve their PM stress response.
Collapse
Affiliation(s)
- Phitthaya Nookongbut
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Paitip Thiravetyan
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Salma Salsabila
- Department of Biology, Faculty of Science and Technology, State Islamic University Sunan Gunung Djati Bandung, Bandung City, West Java, 40614, Indonesia
| | - Ana Widiana
- Department of Biology, Faculty of Science and Technology, State Islamic University Sunan Gunung Djati Bandung, Bandung City, West Java, 40614, Indonesia
| | - Sucheewin Krobthong
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, 10900, Thailand
| | - Yodying Yingchutrakul
- Proteomics Research Team, National Omics Center, NSTDA, Khlong Luang, Pathum Thani, 12120, Thailand
| | - Chairat Treesubsuntorn
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand.
| |
Collapse
|
18
|
Geat N, Singh D, Singh D, Saha P, Jatoth R, Babu PL. Assessing the efficacy of phyllospheric growth-promoting and antagonistic bacteria for management of black rot disease of cauliflower incited by Xanthomonas campestris pv. campestris. Folia Microbiol (Praha) 2024; 69:789-804. [PMID: 38060139 DOI: 10.1007/s12223-023-01106-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
The study aimed to assess the potential of phyllospheric bacterial strains isolated from cauliflower plants as biocontrol agents against black rot disease caused by Xanthomonas campestris pv. campestris, through both in vitro and in vivo evaluations. A total of 46 bacterial strains were isolated from healthy and infected cauliflower leaves of both resistant and susceptible plants, and evaluated them for various traits, including plant growth-promoting activities and in vitro antagonistic activity against Xanthomonas campestris pv. campestris. Further, a pot experiment was conducted with the susceptible cauliflower genotype (Pusa Sharad) and 10 selected phyllospheric bacterial isolates to assess their biocontrol efficacy against the disease. The results showed that 82.60% of phyllospheric bacterial isolates were positive for phosphate solubilization, 63.04% for ammonia production, 58.69% for HCN production, 36.95% for siderophore production, and 78.26% had the capacity to produce IAA. Out of the 46 isolates, 23 exhibited in vitro antagonistic activity against X. campestris pv. campestris and 10 isolates were selected for a pot experiment under glasshouse conditions based on their good plant growth-promoting activities and antagonistic assay. The results revealed that bacterial isolate CFLB-27 exhibited the highest biocontrol efficiency (65.41%), followed by CFLB-24 (58.30%), CFLB-31 (47.11%), and CFLB-26 (46.03%). These four isolates were identified as Pseudomonas fluorescens CFLB-27, Bacillus velezensis CFLB-24, Bacillus amyloliquefaciens CFLB-31, and Stenotrophomonas rhizophila CFLB-26. This study provides valuable insights into the potential of phyllospheric bacteria as an effective tool for disease management in sustainable agriculture.
Collapse
Affiliation(s)
- Neelam Geat
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
- Agricultural Research Station, Mandor, Agriculture University, Jodhpur, Rajasthan, 342304, India.
| | - Dinesh Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Devendra Singh
- Division of Plant Improvement and Pest Management, ICAR-Central Arid Zone Research Institute, Jodhpur, 342003, India
| | - Partha Saha
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajender Jatoth
- Agriculture College, Sircilla, Professor Jayashanker Telangana State Agricultural University Hyderabad, Telangana, 500030, India
| | - Pedapudi Lokesh Babu
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| |
Collapse
|
19
|
Hying ZT, Miller TJ, Loh CY, Bazurto JV. Glycine betaine metabolism is enabled in Methylorubrum extorquens PA1 by alterations to dimethylglycine dehydrogenase. Appl Environ Microbiol 2024; 90:e0209023. [PMID: 38534142 PMCID: PMC11267896 DOI: 10.1128/aem.02090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/22/2024] [Indexed: 03/28/2024] Open
Abstract
Low nutrient availability is a key characteristic of the phyllosphere (the aerial surface of plants). Phyllospheric bacteria utilize a wide array of carbon sources generated by plant hosts. Glycine betaine (GB) is a plant-derived compound that can be metabolized by certain members of the phyllosphere microbiota. Metabolism of glycine betaine generates formaldehyde, an intermediate of methylotrophic metabolism, leading us to investigate how the ubiquitous plant colonizing bacterium Methylorubrum extorquens PA1 might metabolize GB encountered in its native environment. M. extorquens PA1 cannot utilize GB as a sole carbon source. Through suppressor mutation analysis, we show that M. extorquens PA1 encodes a conserved GB utilization pathway that can be activated by single point mutations conferring GB utilization as a carbon source. We identified the gene cluster encoding the GB catabolic enzymes and found that gene expression was induced in the presence of GB. We show that utilization of GB is conserved among representative Methylobacterium species and generates the one-carbon metabolism intermediate formaldehyde, which M. extorquens utilizes as a source of energy. Our results support a model where suppressor mutations in Mext_3745 or ftsH (Mext_4840) prevent the degradation of the dimethylglycine dehydrogenase subunit DgcB by the membrane integral protease FtsH, conferring the ability to utilize GB by either (i) restoring stable membrane topology of DgcB or (ii) decreasing FtsH protease activity, respectively. Both mutations alleviate the bottleneck at the second step of GB degradation catalyzed by DgcAB.IMPORTANCEOvercoming low nutrient availability is a challenge many bacteria encounter in the environment. Facultative methylotrophs are able to utilize one-carbon and multi-carbon compounds as carbon and energy sources. The utilization of plant-derived glycine betaine (GB) represents a possible source of multi-carbon and one-carbon substrates. The metabolism of glycine betaine produces formaldehyde and glycine, which may be used simultaneously by facultative methylotrophs. However, the genes required for the utilization of GB in the ubiquitous plant-associated bacterium Methylorubrum extorquens have yet to be identified or described. Our work identifies and validates the genes required for glycine betaine metabolism in M. extorquens and shows that it directly intersects with methylotrophic metabolism through the production of formaldehyde.
Collapse
Affiliation(s)
- Zachary T. Hying
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Tyler J. Miller
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Chin Yi Loh
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| | - Jannell V. Bazurto
- Department of Plant and Microbial Biology, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
- Biotechnology Institute, University of Minnesota Twin Cities, St. Paul, Minnesota, USA
| |
Collapse
|
20
|
Bruger EL, Hying ZT, Singla D, Márquez Reyes NL, Pandey SK, Patel JS, Bazurto JV. Enhanced catabolism of glycine betaine and derivatives provides improved osmotic stress protection in Methylorubrum extorquens PA1. Appl Environ Microbiol 2024; 90:e0031024. [PMID: 38934615 PMCID: PMC11323934 DOI: 10.1128/aem.00310-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024] Open
Abstract
Integration of metabolites into the overall metabolic network of a cell requires careful coordination dependent upon the ultimate usage of the metabolite. Different stoichiometric needs, and thus pathway fluxes, must exist for compounds destined for diverse uses, such as carbon sources, nitrogen sources, or stress-protective agents. Herein, we expand upon our previous work that highlighted the nature of glycine betaine (GB) metabolism in Methylobacteria to examine the utilization of GB-derivative compounds dimethylglycine (DMG) and sarcosine into Methylorubrum extorquens in different metabolic capacities, including as sole nitrogen and/or carbon sources. We isolated gain-of-function mutations that allowed M. extorquens PA1 to utilize dimethylglycine as a carbon source and dimethylglycine and sarcosine as nitrogen source. Characterization of mutants demonstrated selection for variants of the AraC-like regulator Mext_3735 that confer constitutive expression of the GB metabolic gene cluster, allowing direct utilization of the downstream GB derivatives. Finally, among the distinct isolates examined, we found that catabolism of the osmoprotectant used for selection (GB or dimethylglycine) enhanced osmotic stress resistance provided in the presence of that particular osmolyte. Thus, access to the carbon and nitrogen and osmoprotective effects of GB and DMG are made readily accessible through adaptive mutations. In M. extorquens PA1, the limitations to exploiting this group of compounds appear to exist predominantly at the levels of gene regulation and functional activity, rather than being constrained by transport or toxicity.IMPORTANCEOsmotic stress is a common challenge for bacteria colonizing the phyllosphere, where glycine betaine (GB) can be found as a prevalent osmoprotectant. Though Methylorubrum extorquens PA1 cannot use GB or its demethylation products, dimethylglycine (DMG) and sarcosine, as a sole carbon source, utilization is highly selectable via single nucleotide changes for both GB and DMG growth. The innate inability to use these compounds is due to limited flux through steps in the pathway and regulatory constraints. Herein, the characterization of the transcriptional regulator, Mext_3735 (GbdR), expands our understanding of the various roles in which GB derivatives can be used in M. extorquens PA1. Interestingly, increased catabolism of GB and derivatives does not interfere with, but rather improves, the ability of cells to thrive under increased salt stress conditions, suggesting that metabolic flux improves stress tolerance rather than providing a distinct tension between uses.
Collapse
Affiliation(s)
- Eric L. Bruger
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Zachary T. Hying
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Deepanshu Singla
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Nicole L. Márquez Reyes
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| | - Shubham Kumar Pandey
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jagdish Suresh Patel
- Department of Chemical
and Biological Engineering, University of
Idaho, Moscow,
Idaho, USA
| | - Jannell V. Bazurto
- Department of Plant
and Microbial Biology, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
- Biotechnology
Institute, University of Minnesota-Twin
Cities, St. Paul,
Minnesota, USA
| |
Collapse
|
21
|
Zhang H, Li S, Zhou S, Guo W, Chen P, Li Y, Wu W. Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness. Genes (Basel) 2024; 15:955. [PMID: 39062734 PMCID: PMC11275861 DOI: 10.3390/genes15070955] [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: 06/15/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Wei Wu
- Scarce and Quality Economic Forest Engineering Technology Research Center, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (H.Z.); (S.L.); (S.Z.); (W.G.); (P.C.); (Y.L.)
| |
Collapse
|
22
|
Zhang C, Zhou DF, Wang MY, Song YZ, Zhang C, Zhang MM, Sun J, Yao L, Mo XH, Ma ZX, Yuan XJ, Shao Y, Wang HR, Dong SH, Bao K, Lu SH, Sadilek M, Kalyuzhnaya MG, Xing XH, Yang S. Phosphoribosylpyrophosphate synthetase as a metabolic valve advances Methylobacterium/Methylorubrum phyllosphere colonization and plant growth. Nat Commun 2024; 15:5969. [PMID: 39013920 PMCID: PMC11252147 DOI: 10.1038/s41467-024-50342-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/06/2024] [Indexed: 07/18/2024] Open
Abstract
The proficiency of phyllosphere microbiomes in efficiently utilizing plant-provided nutrients is pivotal for their successful colonization of plants. The methylotrophic capabilities of Methylobacterium/Methylorubrum play a crucial role in this process. However, the precise mechanisms facilitating efficient colonization remain elusive. In the present study, we investigate the significance of methanol assimilation in shaping the success of mutualistic relationships between methylotrophs and plants. A set of strains originating from Methylorubrum extorquens AM1 are subjected to evolutionary pressures to thrive under low methanol conditions. A mutation in the phosphoribosylpyrophosphate synthetase gene is identified, which converts it into a metabolic valve. This valve redirects limited C1-carbon resources towards the synthesis of biomass by up-regulating a non-essential phosphoketolase pathway. These newly acquired bacterial traits demonstrate superior colonization capabilities, even at low abundance, leading to increased growth of inoculated plants. This function is prevalent in Methylobacterium/Methylorubrum strains. In summary, our findings offer insights that could guide the selection of Methylobacterium/Methylorubrum strains for advantageous agricultural applications.
Collapse
Affiliation(s)
- Cong Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Di-Fei Zhou
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Meng-Ying Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Ya-Zhen Song
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Chong Zhang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
| | - Ming-Ming Zhang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Jing Sun
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong, PR China
| | - Xu-Hua Mo
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Zeng-Xin Ma
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Xiao-Jie Yuan
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Yi Shao
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Hao-Ran Wang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Si-Han Dong
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Kai Bao
- School of Life Sciences, Hubei University, Wuhan, Hubei, PR China
| | - Shu-Huan Lu
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, Hubei, PR China
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | | | - Xin-Hui Xing
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, PR China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen, PR China
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen, PR China
| | - Song Yang
- School of Life Sciences, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, PR China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, PR China.
| |
Collapse
|
23
|
Boisseaux M, Troispoux V, Bordes A, Cazal J, Cazal SO, Coste S, Stahl C, Schimann H. Are plant traits drivers of endophytic communities in seasonally flooded tropical forests? AMERICAN JOURNAL OF BOTANY 2024:e16366. [PMID: 39010811 DOI: 10.1002/ajb2.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 07/17/2024]
Abstract
PREMISE In the Amazon basin, seasonally flooded (SF) forests offer varying water constraints, providing an excellent way to investigate the role of habitat selection on microbial communities within plants. However, variations in the microbial community among host plants cannot solely be attributed to environmental factors, and how plant traits contribute to microbial assemblages remains an open question. METHODS We described leaf- and root-associated microbial communities using ITS2 and 16 S high-throughput sequencing and investigated the stochastic-deterministic balance shaping these community assemblies using two null models. Plant ecophysiological functioning was evaluated by focusing on 10 leaf and root traits in 72 seedlings, belonging to seven tropical SF tree species in French Guiana. We then analyzed how root and leaf traits drove the assembly of endophytic communities. RESULTS While both stochastic and deterministic processes governed the endophyte assembly in the leaves and roots, stochasticity prevailed. Discrepancies were found between fungi and bacteria, highlighting that these microorganisms have distinct ecological strategies within plants. Traits, especially leaf traits, host species and spatial predictors better explained diversity than composition, but they were modest predictors overall. CONCLUSIONS This study widens our knowledge about tree species in SF forests, a habitat sensitive to climate change, through the combined analyses of their associated microbial communities with functional traits. We emphasize the need to investigate other plant traits to better disentangle the drivers of the relationship between seedlings and their associated microbiomes, ultimately enhancing their adaptive capacities to climate change.
Collapse
Affiliation(s)
- Marion Boisseaux
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Valérie Troispoux
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Alice Bordes
- Université Grenoble Alpes, INRAE, URLESSEM, Saint-Martin-d'Hères, France, Grenoble, France
| | - Jocelyn Cazal
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Saint-Omer Cazal
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Sabrina Coste
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Clément Stahl
- UMR EcoFoG, Agroparistech, Cirad, CNRS, INRAE, Université des Antilles, Université de la Guyane. Campus Agronomique, Kourou, 97310, France
| | - Heidy Schimann
- INRAE, Université de Bordeaux, BIOGECO, Cestas, 33610, France
| |
Collapse
|
24
|
Phan D, Bhattacharjee AS, Hanan D, Park S, Herrera D, Ashworth D, Schmidt M, Men Y, Ferreira JFS, Ibekwe AM. Dissemination of antimicrobial resistance in agricultural ecosystems following irrigation with treated municipal wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 934:173288. [PMID: 38768725 DOI: 10.1016/j.scitotenv.2024.173288] [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: 04/16/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
The spread of antimicrobial resistance (AMR) in agricultural systems via irrigation water is a serious public health issue as it can be transmitted to humans through the food chain. Therefore, understanding the dissemination routes of antibiotic resistance genes (ARGs) in agricultural systems is crucial for the assessment of health risks associated with eating fresh vegetables such as spinach and radish irrigated with treated municipal wastewater (TMW). In this study, we investigated the bacterial community structure and resistome in the soil-plant-earthworm continuum after irrigation of spinach and radish with TMW containing the antibiotics trimethoprim (TMP), sulfamethoxazole (SMZ), and sulfapyridine (SPD) using 16S rRNA gene sequencing and high throughput quantitative PCR (HT-qPCR). The study was conducted in two phases: Phase I involved eight weeks of spinach and radish production using TMW for irrigation, whereas Phase II entailed three weeks of earthworm exposure to contaminated plant material obtained in Phase I. The 16S data indicated that the rhizosphere bacterial community composition and structure were more resilient to antibiotic residuals in the irrigated water, with radish showing less susceptibility than spinach than those of bulk soils. The HT-qPCR analysis revealed that a total of 271 ARGs (out of 285) and 9 mobile genetic elements (MGEs) (out of 10) were detected in all samples. Higher diversity and abundance of ARGs were observed for samples irrigated with higher concentrations of antibiotics in both spinach and radish treatments. However, compared to spinach, radish ARG dynamics in the soil biome were more stable due to the change of antibiotic introduction to the soil. At the class level, multi-drug resistance (MDR) class was altered significantly by the presence of antibiotics in irrigation water. Compared to earthworm fecal samples, their corresponding soil environments showed a higher number of detected ARGs, suggesting that earthworms could play a role in reducing ARG dissemination in the soil environments. These findings will not only provide insight into the dissemination of ARGs in agricultural environments due to antibiotic residuals in irrigated water but could help understand the potential human health risks associated with ARGs.
Collapse
Affiliation(s)
- Duc Phan
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Ananda S Bhattacharjee
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA; Department of Environmental Sciences, University of California, Riverside, CA 92507, USA
| | - Desmond Hanan
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Stanley Park
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Daisy Herrera
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92507, USA
| | - Daniel Ashworth
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Michael Schmidt
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Yujie Men
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92507, USA
| | - Jorge F S Ferreira
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA
| | - Abasiofiok M Ibekwe
- US Salinity Laboratory, USDA-ARS, 450 W. Big Springs Rd., Riverside, CA 92507, USA.
| |
Collapse
|
25
|
Wang H, Feng Y, Zhang Q, Zou M, Li T, Ai L, Wang H. Urban greenspace types and climate factors jointly drive the microbial community structure and co-occurrence network. Sci Rep 2024; 14:16042. [PMID: 38992141 PMCID: PMC11239843 DOI: 10.1038/s41598-024-66588-8] [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: 04/10/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024] Open
Abstract
The benefits of urban green space are socially widely recognized as a direct link between plant-microbe interactions and the maintenance of biodiversity, community stability, and ecosystem functioning. Nevertheless, there is a lack of knowledge about the factors influencing microbial communities in urban green spaces, especially those related to phyllosphere epiphytes and stem epiphytes. In this study, we analyzed the microbial community assembly in leaf and stem bark samples collected from Square, Road, Campus, and Park. Illumina sequecing of 16S amplicons was performed to characterize microbial diversity and composition. The α-diversity was significantly higher in the bark epiphytic community, compared to the phyllosphere. Moreover, urban greenspaces'type altered the way communities gathered. The main soil and air properties factors of the urban greenhouse (e.g. soil temperature, atmospheric moisture, air temperature) were shaping the characteristics of bacterial communities on the leaf surface and bark epiphytic. In addition, in the co-occurrence network analysis, keystone taxa were not mostly observed in abundant species, which may be necessary to maintain ecosystem functions. Finally, our findings provide a deeper understanding of the ecological dynamics and microbial interactions within plant phyllosphere and stem epiphytes microbiomes.
Collapse
Affiliation(s)
- Huan Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400718, China
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Yilong Feng
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Qiaoyong Zhang
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Min Zou
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Ting Li
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China
| | - Lijiao Ai
- Chongqing Landscape and Gardening Research Institute, Chongqing, 401329, China.
- Chongqing Key Laboratory of Germplasm Innovation and Utilization of Native Plants, Chongqing, 401329, China.
| | - Haiyang Wang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400718, China.
| |
Collapse
|
26
|
Chen H, Song Y, Wang Y, Wang H, Ding Z, Fan K. Zno nanoparticles: improving photosynthesis, shoot development, and phyllosphere microbiome composition in tea plants. J Nanobiotechnology 2024; 22:389. [PMID: 38956645 PMCID: PMC11221027 DOI: 10.1186/s12951-024-02667-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Nanotechnology holds revolutionary potential in the field of agriculture, with zinc oxide nanoparticles (ZnO NPs) demonstrating advantages in promoting crop growth. Enhanced photosynthetic efficiency is closely linked to improved vigor and superior quality in tea plants, complemented by the beneficial role of phyllosphere microorganisms in maintaining plant health. However, the effects of ZnO NPs on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms have not been fully investigated. RESULTS This study investigated the photosynthetic physiological parameters of tea plants under the influence of ZnO NPs, the content of key photosynthetic enzymes such as RubisCO, chlorophyll content, chlorophyll fluorescence parameters, transcriptomic and extensive targeted metabolomic profiles of leaves and new shoots, mineral element composition in these tissues, and the epiphytic and endophytic microbial communities within the phyllosphere. The results indicated that ZnO NPs could enhance the photosynthesis of tea plants, upregulate the expression of some genes related to photosynthesis, increase the accumulation of photosynthetic products, promote the development of new shoots, and alter the content of various mineral elements in the leaves and new shoots of tea plants. Furthermore, the application of ZnO NPs was observed to favorably influence the microbial community structure within the phyllosphere of tea plants. This shift in microbial community dynamics suggests a potential for ZnO NPs to contribute to plant health and productivity by modulating the phyllosphere microbiome. CONCLUSION This study demonstrates that ZnO NPs have a positive impact on the photosynthesis of tea plants, the sprouting of new shoots, and the community of phyllosphere microorganisms, which can improve the growth condition of tea plants. These findings provide new scientific evidence for the application of ZnO NPs in sustainable agricultural development and contribute to advancing research in nanobiotechnology aimed at enhancing crop yield and quality.
Collapse
Affiliation(s)
- Hao Chen
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yujie Song
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Huan Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| | - Kai Fan
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
| |
Collapse
|
27
|
Fessia A, Sartori M, Orlando J, Barros G, Nesci A. Draft genome sequences of two biocontrol agents isolated from the maize phyllosphere : Bacillus subtilis strain EM-A7 and Bacillus velezensis strain EM-A8. Heliyon 2024; 10:e32607. [PMID: 39021968 PMCID: PMC11252862 DOI: 10.1016/j.heliyon.2024.e32607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/06/2024] [Accepted: 06/06/2024] [Indexed: 07/20/2024] Open
Abstract
In the present study, the genomes of B. subtilis EM-A7 and B. velezensis EM-A8 were sequenced and annotated. The Illumina sequencing platform (NovaSeq PE150) was used to sequence the genomic DNA. There were 6 277 054 raw reads for EM-A7, with a Q20 of 97.52 % and 43.78 % GC, and 8 030 262 raw reads for EM-A8, with a Q20 of 97.53 % and 46.21 % GC. Annotation was carried out by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The strains were classified taxonomically on the basis of an average nucleotide identity analysis (ANI), as well as through a dDDh analysis on the Genome-to-Genome Distance Calculator (GGDC v3.0). The pipeline predicted 4062 protein-coding sequences (CDSs) and 73 RNA genes (62 tRNA and 6 rRNA) for EM-A7, and 3797 protein-coding sequences (CDSs) and 80 RNA genes for EM-A8. These findings enhance our understanding of the two strains' potential as biocontrol agents to manage disease in maize.
Collapse
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, Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina. - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Melina Sartori
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina. - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Germán Barros
- Laboratorio de Ecología Microbiana, Departamento de Microbiología e Inmunología, Facultad de Ciencias Exactas, Físico-Químicas y Naturales. Universidad Nacional de Río Cuarto, Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina. - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 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, Ruta Nacional 36, Km 601, X5804ZAB Río Cuarto, Córdoba, Argentina. - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| |
Collapse
|
28
|
Carmichael MJ, Martinez M, Bräuer SL, Ardón M. Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic. Curr Microbiol 2024; 81:229. [PMID: 38896154 PMCID: PMC11186919 DOI: 10.1007/s00284-024-03767-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.
Collapse
Affiliation(s)
- Mary Jane Carmichael
- Departments of Biology and Environmental Studies, Hollins University, Roanoke, VA, 24020, USA.
| | - Melinda Martinez
- U.S. Geological Survey, Eastern Ecological Science Center, Laurel, MD, 20708, USA
| | - Suzanna L Bräuer
- Department of Biology, Appalachian State University, Boone, NC, 28608, USA
| | - Marcelo Ardón
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| |
Collapse
|
29
|
Ossola R, Rossell RK, Riches M, Osburn C, Farmer D. Development of a sampling protocol for collecting leaf surface material for multiphase chemistry studies. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:1008-1021. [PMID: 38770594 PMCID: PMC11188671 DOI: 10.1039/d4em00065j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/14/2024] [Indexed: 05/22/2024]
Abstract
Plant leaves and water drops residing on them interact with atmospheric oxidants, impacting the deposition and emission of trace gases and mediating leaf damage from air pollution. Characterizing the chemical composition and reactivity of the water-soluble material on leaf surfaces is thus essential for improving our understanding of atmosphere-biosphere interactions. However, the limited knowledge of sources and nature of these chemicals challenges sampling decisions. This work investigates how sampling variables and environmental factors impact the quantity and composition of water-soluble material sampled from wet leaves and proposes a flexible protocol for its collection. The ratio of solvent volume-to-leaf area, the solvent-to-leaf contact time, and environmental parameters - including the occurrence of rain, plant location and its metabolism - drive solute concentration in leaf soaks. Despite minor variations, UV-vis absorption spectra of leaf soaks are comparable to authentic raindrops collected from the same tree and share features with microbial dissolved organic matter - including overall low aromaticity, low chromophore content, and low average molecular weight. In addition to guiding the development of a sampling protocol, our data corroborate recent hypotheses on the amount, origin, nature, and reactivity of water-soluble organics on wet leaves, providing new directions of research into this highly interdisciplinary topic.
Collapse
Affiliation(s)
- Rachele Ossola
- Department of Chemistry, Colorado State University, 80523, Fort Collins, Colorado, USA.
| | - Rose K Rossell
- Department of Chemistry, Colorado State University, 80523, Fort Collins, Colorado, USA.
| | - Mj Riches
- Department of Chemistry, Colorado State University, 80523, Fort Collins, Colorado, USA.
| | - Cameron Osburn
- Department of Chemistry, Colorado State University, 80523, Fort Collins, Colorado, USA.
| | - Delphine Farmer
- Department of Chemistry, Colorado State University, 80523, Fort Collins, Colorado, USA.
| |
Collapse
|
30
|
Xu L, Liu Y, Feng S, Liu C, Zhong X, Ren Y, Liu Y, Huang Y, Yang M. The relationship between atmospheric particulate matter, leaf surface microstructure, and the phyllosphere microbial diversity of Ulmus L. BMC PLANT BIOLOGY 2024; 24:566. [PMID: 38880875 PMCID: PMC11181616 DOI: 10.1186/s12870-024-05232-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/31/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Plants can retain atmospheric particulate matter (PM) through their unique foliar microstructures, which has a profound impact on the phyllosphere microbial communities. Yet, the underlying mechanisms linking atmospheric particulate matter (PM) retention by foliar microstructures to variations in the phyllosphere microbial communities remain a mystery. In this study, we conducted a field experiment with ten Ulmus lines. A series of analytical techniques, including scanning electron microscopy, atomic force microscopy, and high-throughput amplicon sequencing, were applied to examine the relationship between foliar surface microstructures, PM retention, and phyllosphere microbial diversity of Ulmus L. RESULTS We characterized the leaf microstructures across the ten Ulmus lines. Chun exhibited a highly undulated abaxial surface and dense stomatal distribution. Langya and Xingshan possessed dense abaxial trichomes, while Lieye, Zuiweng, and Daguo had sparsely distributed, short abaxial trichomes. Duomai, Qingyun, and Lang were characterized by sparse stomata and flat abaxial surfaces, whereas Jinye had sparsely distributed but extensive stomata. The mean leaf retention values for total suspended particulate (TSP), PM2.5, PM2.5-10, PM10-100, and PM> 100 were 135.76, 6.60, 20.10, 90.98, and 13.08 µg·cm- 2, respectively. Trichomes substantially contributed to PM2.5 retention, while larger undulations enhanced PM2.5-10 retention, as evidenced by positive correlations between PM2.5 and abaxial trichome density and between PM2.5-10 and the adaxial raw microroughness values. Phyllosphere microbial diversity patterns varied among lines, with bacteria dominated by Sediminibacterium and fungi by Mycosphaerella, Alternaria, and Cladosporium. Redundancy analysis confirmed that dense leaf trichomes facilitated the capture of PM2.5-associated fungi, while bacteria were less impacted by PM and struggled to adhere to leaf microstructures. Long and dense trichomes provided ideal microhabitats for retaining PM-borne microbes, as evidenced by positive feedback loops between PM2.5, trichome characteristics, and the relative abundances of microorganisms like Trichoderma and Aspergillus. CONCLUSIONS Based on our findings, a three-factor network profile was constructed, which provides a foundation for further exploration into how different plants retain PM through foliar microstructures, thereby impacting phyllosphere microbial communities.
Collapse
Grants
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 216Z6301G Science and Technology Development Fund of Central Guidance on Local, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
- 21326301D Key Research and Development Program of Hebei Province, China
Collapse
Affiliation(s)
- Liren Xu
- Hebei Agricultural University, Baoding, 071000, Hebei, China
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yichao Liu
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
| | - Shuxiang Feng
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China
| | - Chong Liu
- Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Xinyu Zhong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yachao Ren
- Hebei Agricultural University, Baoding, 071000, Hebei, China
| | - Yujun Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Yinran Huang
- Hebei Agricultural University, Baoding, 071000, Hebei, China.
- Hebei Academy of Forestry and Grassland Science, Shijiazhuang, 050061, Hebei, China.
| | - Minsheng Yang
- Hebei Agricultural University, Baoding, 071000, Hebei, China.
| |
Collapse
|
31
|
Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [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: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
Collapse
Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
| |
Collapse
|
32
|
Yu T, Liu Z, Hu B, Zhu L. Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172636. [PMID: 38653418 DOI: 10.1016/j.scitotenv.2024.172636] [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: 02/28/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 04/25/2024]
Abstract
Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.
Collapse
Affiliation(s)
- Tao Yu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Zishu Liu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Baolan Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Lizhong Zhu
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Hangzhou, Zhejiang 310058, China.
| |
Collapse
|
33
|
Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
Collapse
Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Jibril SM, Yan W, Wang Y, Zhu X, Yunying Z, Wu J, Wang L, Zhang L, Li C. Highly diverse microbial community of regenerated seedlings reveals the high capacity of the bulb in lily, Lilium brownii. Front Microbiol 2024; 15:1387870. [PMID: 38903799 PMCID: PMC11188333 DOI: 10.3389/fmicb.2024.1387870] [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: 02/18/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Lily bulbs, which have both nutrient storage and reproductive functions, are a representative group of plants for studying the maintenance and transfer of plant-associated microbiomes. In this study, a comparison of the microbial composition of bulbs and their regenerated seedlings cultured under aseptic conditions, as well as subcultured seedlings that succeeded five times, was examined by amplicon sequencing. A total of 62 bacterial taxa and 56 fungal taxa were found to be transferred to the 5th generation in seedlings, which are the core microbiome of lily. After the regeneration of seedlings from bulbs, there was a significant increase in the number of detectable microbial species, and after 1, 3, and 5 successive generations, there was a decrease in the number of detectable species. Interestingly, some "new" microorganisms appeared in each generation of samples; for instance, 167 and 168 bacterial operational taxonomic units (OTUs) in the 3rd and 5th generations of seedlings that were not detected in either bulbs or seedlings of the previous two generations. These results suggest that bulbs can maintain a high diversity of microorganisms, including some with ultra-low abundance, and have a high transfer capacity to tuck shoots through continuous subculture. The diversity and maintenance of the microbiome can provide the necessary microbial reservoir support for regenerating seedlings. This habit of maintaining low abundance and high diversity may be biologically and ecologically critical for maintaining microbiome stability and function due to the sequestration nature of the plant.
Collapse
Affiliation(s)
- Sauban Musa Jibril
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Wu Yan
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Xishen Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Zhou Yunying
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Jie Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Ling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Limin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Yunnan-CABI Joint Laboratory for Integrated Prevention and Control of Transboundary Pests, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
36
|
Boutin S, Lussier E, Laforest-Lapointe I. Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards. Can J Microbiol 2024; 70:238-251. [PMID: 38452350 DOI: 10.1139/cjm-2023-0215] [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] [Indexed: 03/09/2024]
Abstract
The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.
Collapse
Affiliation(s)
- Sophie Boutin
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Ema Lussier
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Isabelle Laforest-Lapointe
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| |
Collapse
|
37
|
Sierra AM, Meléndez O, Bethancourt R, Bethancourt A, Rodríguez-Castro L, López CA, Sedio BE, Saltonstall K, Villarreal A JC. Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms. J Chem Ecol 2024:10.1007/s10886-024-01511-z. [PMID: 38809282 DOI: 10.1007/s10886-024-01511-z] [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: 12/04/2023] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.
Collapse
Affiliation(s)
- Adriel M Sierra
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
| | - Omayra Meléndez
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Rita Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Ariadna Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Lilisbeth Rodríguez-Castro
- Departamento de Microbiología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Christian A López
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
- Smithsonian Tropical Research Institute, Ancón, Panamá.
- Canada Research Chair in Genomics of Tropical Symbioses, Department of Biology, Université Laval, Québec, G1V 0A6, Canadá.
| |
Collapse
|
38
|
Gong F, He C, Li X, Wang K, Li M, Zhou X, Xu M, He X. Impacts of fertilization methods on Salvia miltiorrhiza quality and characteristics of the epiphytic microbial community. FRONTIERS IN PLANT SCIENCE 2024; 15:1395628. [PMID: 38817929 PMCID: PMC11138495 DOI: 10.3389/fpls.2024.1395628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
Plant epiphytic microorganisms have established a unique symbiotic relationship with plants, which has a significant impact on their growth, immune defense, and environmental adaptation. However, the impact of fertilization methods on the epiphytic microbial community and their correlation with the yield and quality of medicinal plant was still unclear. In current study, we conducted a field fertilization experiment and analyzed the composition of epiphytic bacterial and fungal communities employing high throughput sequencing data in different organs (roots, stems, and leaves) of Salvia miltiorrhiza, as well as their correlation with plant growth. The results showed that fertilization significantly affected the active ingredients and hormone content, soil physicochemical properties, and the composition of epiphytic microbial communities. After fertilization, the plant surface was enriched with a core microbial community mainly composed of bacteria from Firmicutes, Proteobacteria, and Actinobacteria, as well as fungi from Zygomycota and Ascomycota. Additionally, plant growth hormones were the principal factors leading to alterations in the epiphytic microbial community of S. miltiorrhiza. Thus, the most effective method of fertilization involved the application of base fertilizer in combination with foliar fertilizer. This study provides a new perspective for studying the correlation between microbial community function and the quality of S. miltiorrhiza, and also provides a theoretical basis for the cultivation and sustainable development of high-quality medicinal plants.
Collapse
Affiliation(s)
- Feng Gong
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kehan Wang
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Min Li
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xiangyun Zhou
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Minghui Xu
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding, China
- Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, China
| |
Collapse
|
39
|
Roch FF, Dzieciol M, Quijada NM, Alteio LV, Mester PJ, Selberherr E. Microbial community structure of plant-based meat alternatives. NPJ Sci Food 2024; 8:27. [PMID: 38740858 DOI: 10.1038/s41538-024-00269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/22/2024] [Indexed: 05/16/2024] Open
Abstract
A reduction in animal-based diets has driven market demand for alternative meat products, currently raising a new generation of plant-based meat alternatives (PBMAs). It remains unclear whether these substitutes are a short-lived trend or become established in the long term. Over the last few years, the trend of increasing sales and diversifying product range has continued, but publication activities in this field are currently limited mainly to market research and food technology topics. As their popularity increases, questions emerge about the safety and nutritional risks of these novel products. Even though all the examined products must be heated before consumption, consumers lack experience with this type of product and thus further research into product safety, is desirable. To consider these issues, we examined 32 PBMAs from Austrian supermarkets. Based on 16S rRNA gene amplicon sequencing, the majority of the products were dominated by lactic acid bacteria (either Leuconostoc or Latilactobacillus), and generally had low alpha diversity. Pseudomonadota (like Pseudomonas and Shewanella) dominated the other part of the products. In addition to LABs, a high diversity of different Bacillus, but also some Enterobacteriaceae and potentially pathogenic species were isolated with the culturing approach. We assume that especially the dominance of heterofermentative LABs has high relevance for the product stability and quality with the potential to increase shelf life of the products. The number of isolated Enterobacteriaceae and potential pathogens were low, but they still demonstrated that these products are suitable for their presence.
Collapse
Affiliation(s)
- Franz-Ferdinand Roch
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Monika Dzieciol
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Narciso M Quijada
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, 37185, Villamayor (Salamanca), Spain
| | - Lauren V Alteio
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, 3430, Tulln, Austria
| | - Patrick-Julian Mester
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria
| | - Evelyne Selberherr
- Centre for Food Science and Veterinary Public Health, Clincal Department for Farm Animals and Food System Science, University of Veterinary Medicine, 1210, Vienna, Austria.
| |
Collapse
|
40
|
Shi Y, He Y, Zheng Y, Liu X, Wang S, Xiong T, Wen T, Duan H, Liao X, Cui Q, Nian F. Characteristics of the phyllosphere microbial community and its relationship with major aroma precursors during the tobacco maturation process. FRONTIERS IN PLANT SCIENCE 2024; 15:1346154. [PMID: 38799095 PMCID: PMC11116568 DOI: 10.3389/fpls.2024.1346154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
Numerous bacteria, fungi and other microorganisms in the tobacco phyllosphere interstellar area participate in the physiological metabolism of plants by interacting with the host. However, there is currently little research on the characteristics of tobacco phyllosphere microbial communities, and the correlation between tobacco phyllosphere microbial communities and phyllosphere factor indicators is still unknown. Therefore, high-throughput sequencing technology based on the 16S rRNA/ITS1 gene was used to explore the diversity and composition characteristics of tobacco phyllosphere bacterial and fungal communities from different maturation processes, and to identify marker genera that distinguish phyllosphere microbial communities. In this study, the correlations between tobacco phyllosphere bacterial and fungal communities and the precursors of major aroma compounds were explored. The results showed that as the tobacco plants matured, the density of glandular trichomes on the tobacco leaves gradually decreased. The surface physicochemical properties of tobacco leaves also undergo significant changes. In addition, the overall bacterial alpha diversity in the tobacco phyllosphere area increased with maturation, while the overall fungal alpha diversity decreased. The beta diversity of bacteria and fungi in the tobacco phyllosphere area also showed significant differences. Specifically, with later top pruning time, the relative abundances of Acidisoma, Ralstonia, Bradyrhizobium, Alternaria and Talaromyces gradually increased, while the relative abundances of Pseudomonas, Filobassidium, and Tausonia gradually decreased. In the bacterial community, Acidisoma, Ralstonia, Bradyrhizobium, and Alternaria were significantly positively correlated with tobacco aroma precursors, with significant negative correlations with tobacco phyllosphere trichome morphology, while Pseudomonas showed the opposite pattern; In the fungal community, Filobasidium and Tausonia were significantly negatively correlated with tobacco aroma precursors, and significantly positively correlated with tobacco phyllosphere trichome morphology, while Alternaria showed the opposite pattern. In conclusion, the microbiota (bacteria and fungi) and aroma precursors of the tobacco phyllosphere change significantly as tobacco matures. The presence of Acidisoma, Ralstonia, Bradyrhizobium and Alternaria in the phyllosphere microbiota of tobacco may be related to the aroma precursors of tobacco.
Collapse
Affiliation(s)
- Yixuan Shi
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuansheng He
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Yuanxian Zheng
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Xixi Liu
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Shuzhong Wang
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Tian’e Xiong
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Tao Wen
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Hong Duan
- Technology and Research Center, Lincang Branch Company of Yunnan Tobacco Company, Lincang Yunnan, China
| | - Xiaolin Liao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Quanren Cui
- Tobacco Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Fuzhao Nian
- College of Tobacco Science, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
41
|
Ossola R, Farmer D. The Chemical Landscape of Leaf Surfaces and Its Interaction with the Atmosphere. Chem Rev 2024; 124:5764-5794. [PMID: 38652704 PMCID: PMC11082906 DOI: 10.1021/acs.chemrev.3c00763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 04/03/2024] [Accepted: 04/11/2024] [Indexed: 04/25/2024]
Abstract
Atmospheric chemists have historically treated leaves as inert surfaces that merely emit volatile hydrocarbons. However, a growing body of evidence suggests that leaves are ubiquitous substrates for multiphase reactions-implying the presence of chemicals on their surfaces. This Review provides an overview of the chemistry and reactivity of the leaf surface's "chemical landscape", the dynamic ensemble of compounds covering plant leaves. We classified chemicals as endogenous (originating from the plant and its biome) or exogenous (delivered from the environment), highlighting the biological, geographical, and meteorological factors driving their contributions. Based on available data, we predicted ≫2 μg cm-2 of organics on a typical leaf, leading to a global estimate of ≫3 Tg for multiphase reactions. Our work also highlighted three major knowledge gaps: (i) the overlooked role of ambient water in enabling the leaching of endogenous substances and mediating aqueous chemistry; (ii) the importance of phyllosphere biofilms in shaping leaf surface chemistry and reactivity; (iii) the paucity of studies on the multiphase reactivity of atmospheric oxidants with leaf-adsorbed chemicals. Although biased toward available data, we hope this Review will spark a renewed interest in the leaf surface's chemical landscape and encourage multidisciplinary collaborations to move the field forward.
Collapse
Affiliation(s)
- Rachele Ossola
- Department of Chemistry, Colorado
State University, 80523 Fort Collins, Colorado (United States)
| | - Delphine Farmer
- Department of Chemistry, Colorado
State University, 80523 Fort Collins, Colorado (United States)
| |
Collapse
|
42
|
Li J, Jin MK, Huang L, Liu ZF, Wang T, Chang RY, Op de Beeck M, Lambers H, Hui D, Xiao KQ, Chen QL, Sardans J, Peñuelas J, Yang XR, Zhu YG. Assembly and succession of the phyllosphere microbiome and nutrient-cycling genes during plant community development in a glacier foreland. ENVIRONMENT INTERNATIONAL 2024; 187:108688. [PMID: 38685158 DOI: 10.1016/j.envint.2024.108688] [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: 02/26/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
The phyllosphere, particularly the leaf surface of plants, harbors a diverse range of microbiomes that play a vital role in the functioning of terrestrial ecosystems. However, our understanding of microbial successions and their impact on functional genes during plant community development is limited. In this study, considering core and satellite microbial taxa, we characterized the phyllosphere microbiome and functional genes in various microhabitats (i.e., leaf litter, moss and plant leaves) across the succession of a plant community in a low-altitude glacier foreland. Our findings indicate that phyllosphere microbiomes and associated ecosystem stability increase during the succession of the plant community. The abundance of core taxa increased with plant community succession and was primarily governed by deterministic processes. In contrast, satellite taxa abundance decreased during plant community succession and was mainly governed by stochastic processes. The abundance of microbial functional genes (such as C, N, and P hydrolysis and fixation) in plant leaves generally increased during the plant community succession. However, in leaf litter and moss leaves, only a subset of functional genes (e.g., C fixation and degradation, and P mineralization) showed a tendency to increase with plant community succession. Ultimately, the community of both core and satellite taxa collaboratively influenced the characteristics of phyllosphere nutrient-cycling genes, leading to the diverse profiles and fluctuating abundance of various functional genes during plant community succession. These findings offer valuable insights into the phyllosphere microbiome and plant-microbe interactions during plant community development, advancing our understanding of the succession and functional significance of the phyllosphere microbial community.
Collapse
Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Lijie Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
| | - Zhan-Feng Liu
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tao Wang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Rui-Ying Chang
- Key Laboratory of Mountain Environment Evolvement and Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Michiel Op de Beeck
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Hans Lambers
- School of Biological Sciences, University of Western Australia, Perth, Western Australia, Australia; Department of Plant Nutrition, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plan-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, TN, USA
| | - Ke-Qing Xiao
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Jordi Sardans
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Josep Peñuelas
- CSIC, Global Ecology Unit, CREAF-CSIC-UAB, Bellaterra, 08193 Barcelona, Catalonia, Spain; CREAF, Cerdanyola del Vallès, 08193 Barcelona, Catalonia, Spain
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
43
|
Jangra A, Kumar K, Maikhuri S, Bhandari MS, Pandey S, Singh H, Barthwal S. Unveiling stress-adapted endophytic bacteria: Characterizing plant growth-promoting traits and assessing cross-inoculation effects on Populus deltoides under abiotic stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108610. [PMID: 38615447 DOI: 10.1016/j.plaphy.2024.108610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
In the face of the formidable environmental challenges precipitated by the ongoing climate change, Plant Growth-Promoting Bacteria (PGPB) are gaining widespread acknowledgement for their potential as biofertilizers, biocontrol agents, and microbial inoculants. However, a knowledge gap pertains to the ability of PGPB to improve stress tolerance in forestry species via cross-inoculation. To address this gap, the current investigation centres on PGPBs, namely, Acinetobacter johnsonii, Cronobacter muytjensii, and Priestia endophytica, selected from the phyllosphere of robust and healthy plants thriving in the face of stress-inducing conditions. These strains were selected based on their demonstrated adaptability to saline, arid, and nitrogen-deficient environments. The utilization of PGPB treatment resulted in an improvement of stomatal conductance (gs) and transpiration rate (E) in poplar plants exposed to both salt and drought stress. It also induced an increase in essential biochemical components such as proline (PRO), catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). These reactions were accompanied by a decrease in leaf malonaldehyde (MDA) content and electrolyte leakage (EL). Furthermore, the PGPB treatment demonstrated a notable enhancement in nutrient absorption, particularly nitrogen and carbon, achieved through the solubilization of nutrients. The estimation of canopy temperature via thermal imaging proved to be an efficient method for distinguishing stress reactions in poplar than conventional temperature recording techniques. In summation, the utilization of PGPB especially Cronobacter muytjensii in this study, yielded profound improvements in the stress tolerance of poplar plants, manifesting in reduced membrane lipid peroxidation, enhanced photosynthesis, and bolstered antioxidant capacity within the leaves.
Collapse
Affiliation(s)
- Anamika Jangra
- Plant Physiology Discipline, Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| | - Kishan Kumar
- Plant Physiology Discipline, Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| | - Sandeep Maikhuri
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
| | - Shailesh Pandey
- Forest Pathology Discipline, Division of Forest Protection, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| | - Hukum Singh
- Plant Physiology Discipline, Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| | - Santan Barthwal
- Plant Physiology Discipline, Division of Genetics & Tree Improvement, Forest Research Institute, Dehradun, 248 006, Uttarakhand, India.
| |
Collapse
|
44
|
Batuman O, Britt-Ugartemendia K, Kunwar S, Yilmaz S, Fessler L, Redondo A, Chumachenko K, Chakravarty S, Wade T. The Use and Impact of Antibiotics in Plant Agriculture: A Review. PHYTOPATHOLOGY 2024; 114:885-909. [PMID: 38478738 DOI: 10.1094/phyto-10-23-0357-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Growers have depended on the specificity and efficacy of streptomycin and oxytetracycline as a part of their plant disease arsenal since the middle of the 20th century. With climate change intensifying plant bacterial epidemics, the established success of these antibiotics remains threatened. Our strong reliance on certain antibiotics for devastating diseases eventually gave way to resistance development. Although antibiotics in plant agriculture equal to less than 0.5% of overall antibiotic use in the United States, it is still imperative for humans to continue to monitor usage, environmental residues, and resistance in bacterial populations. This review provides an overview of the history and use, resistance and mitigation, regulation, environmental impact, and economics of antibiotics in plant agriculture. Bacterial issues, such as the ongoing Huanglongbing (citrus greening) epidemic in Florida citrus production, may need antibiotics for adequate control. Therefore, preserving the efficacy of our current antibiotics by utilizing more targeted application methods, such as trunk injection, should be a major focus. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Ozgur Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Kellee Britt-Ugartemendia
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Sanju Kunwar
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Salih Yilmaz
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Lauren Fessler
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Ana Redondo
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Kseniya Chumachenko
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL
| | - Shourish Chakravarty
- Department of Food and Resource Economics, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| | - Tara Wade
- Department of Food and Resource Economics, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL
| |
Collapse
|
45
|
Kunzler M, Schlechter RO, Schreiber L, Remus-Emsermann MNP. Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R. MICROBIAL ECOLOGY 2024; 87:62. [PMID: 38683223 PMCID: PMC11058625 DOI: 10.1007/s00248-024-02381-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.
Collapse
Affiliation(s)
- Michael Kunzler
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany
| | - Rudolf O Schlechter
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany
| | - Lukas Schreiber
- Institute for Cellular and Molecular Botany, Bonn University, Kirschallee 1-3, 53115, Bonn, Germany
| | - Mitja N P Remus-Emsermann
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany.
| |
Collapse
|
46
|
Yue C, Du C, Wang X, Tan Y, Liu X, Fan H. Powdery mildew-induced changes in phyllosphere microbial community dynamics of cucumber. FEMS Microbiol Ecol 2024; 100:fiae050. [PMID: 38599637 PMCID: PMC11062426 DOI: 10.1093/femsec/fiae050] [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: 07/09/2023] [Revised: 02/22/2024] [Accepted: 04/09/2024] [Indexed: 04/12/2024] Open
Abstract
As an important habitat for microorganisms, the phyllosphere has a great impact on plant growth and health, and changes in phyllosphere microorganisms are closely related to the occurrence of leaf diseases. However, there remains a limited understanding regarding alterations to the microbial community in the phyllosphere resulting from pathogen infections. Here, we analyzed and compared the differences in phyllosphere microorganisms of powdery mildew cucumber from three disease severity levels (0% < L1 < 30%, 30% ≤ L2 < 50%, L3 ≥ 50%, the number represents the lesion coverage rate of powdery mildew on leaves). There were significant differences in α diversity and community structure of phyllosphere communities under different disease levels. Disease severity altered the community structure of phyllosphere microorganisms, Rosenbergiella, Rickettsia, and Cladosporium accounted for the largest proportion in the L1 disease grade, while Bacillus, Pantoea, Kocuria, and Podosphaera had the highest relative abundance in the L3 disease grade. The co-occurrence network analysis of the phyllosphere microbial community indicated that the phyllosphere bacterial community was most affected by the severity of disease. Our results suggested that with the development of cucumber powdery mildew, the symbiotic relationship between species was broken, and the entire bacterial community tended to compete.
Collapse
Affiliation(s)
- Cong Yue
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| | - Changxia Du
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| | - Xiaodan Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| | - Yinqing Tan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| | - Xingchen Liu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| | - Huaifu Fan
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A and F University, Hangzhou, Zhejiang 311300, China
| |
Collapse
|
47
|
Han J, Dong Z, Ji W, Lv W, Luo M, Fu B. From predator to protector: Myxococcus fulvus WCH05 emerges as a potent biocontrol agent for fire blight. Front Microbiol 2024; 15:1378288. [PMID: 38650871 PMCID: PMC11033317 DOI: 10.3389/fmicb.2024.1378288] [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: 01/29/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Fire blight, caused by the Gram-negative bacterium Erwinia amylovora, poses a substantial threat to pome fruit production worldwide. Despite existing control strategies, a pressing need remains for sustainable and environmentally friendly fire blight management. Myxobacteria, renowned for their predatory behavior and potent enzymes, emerge as a groundbreaking biocontrol approach with significant potential. Here, we report the biocontrol potential of a novel Myxococcus fulvus WCH05, against E. amylovora. Using various in vitro and planta assays, we demonstrated the multifaceted biocontrol abilities of strain WCH05. In plate predation assays, strain WCH05 exhibited not only strong predation against E. amylovora but also broad-spectrum activities against other plant pathogenic bacteria. Pre-treatment with strain WCH05 significantly decreased pear blossom blight incidence in detached inflorescence assays, achieving a controlled efficacy of 76.02% that rivaled the antibiotic streptomycin (79.79%). In greenhouse trials, strain WCH05 effectively reduced the wilting rate and disease index in young pear seedlings, exhibiting both protective (73.68%) and curative (68.66%) control. Further investigation revealed that the biocontrol activity of strain WCH05 relies on both direct contact and extracellular enzyme secretion. While cell extracts lacked inhibitory activity, ammonium sulfate-precipitated secreted proteins displayed potent lytic activity against E. amylovora. Substrate spectrum analysis identified peptidases, lipases, and glycosidases among the secreted enzymes, suggesting their potential roles in pathogen degradation and biocontrol efficacy. This study presents the first evidence of Myxococcus fulvus WCH05 as a biocontrol agent against fire blight. Its potent predatory abilities and enzymatic arsenal highlight its potential for sustainable disease management in pome fruit production. Future research will focus on identifying and characterizing specific lytic enzymes and optimizing strain WCH05 application strategies for field efficacy.
Collapse
Affiliation(s)
- Jian Han
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Zhiming Dong
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Wenbo Ji
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Wen Lv
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Ming Luo
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Benzhong Fu
- Department of Plant Pathology, College of Agronomy, Xinjiang Agriculture University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of Xinjiang Uygur Autonomous Region, Urumqi, China
- Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Urumqi, China
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Rill A, Zhao L, Bode HB. Genetic toolbox for Photorhabdus and Xenorhabdus: pSEVA based heterologous expression systems and CRISPR/Cpf1 based genome editing for rapid natural product profiling. Microb Cell Fact 2024; 23:98. [PMID: 38561780 PMCID: PMC10983751 DOI: 10.1186/s12934-024-02363-8] [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: 12/17/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bacteria of the genus Photorhabdus and Xenorhabdus are motile, Gram-negative bacteria that live in symbiosis with entomopathogenic nematodes. Due to their complex life cycle, they produce a large number of specialized metabolites (natural products) encoded in biosynthetic gene clusters (BGC). Genetic tools for Photorhabdus and Xenorhabdus have been rare and applicable to only a few strains. In the past, several tools have been developed for the activation of BGCs and the deletion of individual genes. However, these often have limited efficiency or are time consuming. Among the limitations, it is essential to have versatile expression systems and genome editing tools that could facilitate the practical work. RESULTS In the present study, we developed several expression vectors and a CRISPR-Cpf1 genome editing vector for genetic manipulations in Photorhabdus and Xenorhabdus using SEVA plasmids. The SEVA collection is based on modular vectors that allow exchangeability of different elements (e.g. origin of replication and antibiotic selection markers with the ability to insert desired sequences for different end applications). Initially, we tested different SEVA vectors containing the broad host range origins and three different resistance genes for kanamycin, gentamycin and chloramphenicol, respectively. We demonstrated that these vectors are replicative not only in well-known representatives, e.g. Photorhabdus laumondii TTO1, but also in other rarely described strains like Xenorhabdus sp. TS4. For our CRISPR/Cpf1-based system, we used the pSEVA231 backbone to delete not only small genes but also large parts of BGCs. Furthermore, we were able to activate and refactor BGCs to obtain high production titers of high value compounds such as safracin B, a semisynthetic precursor for the anti-cancer drug ET-743. CONCLUSIONS The results of this study provide new inducible expression vectors and a CRISPR/CPf1 encoding vector all based on the SEVA (Standard European Vector Architecture) collection, which can improve genetic manipulation and genome editing processes in Photorhabdus and Xenorhabdus.
Collapse
Affiliation(s)
- Alexander Rill
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany
| | - Lei Zhao
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Helge B Bode
- Department of Natural Products in Organismic Interactions, Max-Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.
- Department of Chemistry, Chemical Biology, Phillips University Marburg, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043, Marburg, Germany.
- Senckenberg Gesellschaft für Naturforschung, 60325, Frankfurt, Germany.
| |
Collapse
|
50
|
Welsh BL, Eisenhofer R. The prevalence of controls in phyllosphere microbiome research: a methodological review. THE NEW PHYTOLOGIST 2024; 242:23-29. [PMID: 38339825 DOI: 10.1111/nph.19573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
DNA contamination can critically confound microbiome studies. Here, we take a systematic approach to review the current literature and investigate the prevalence of contamination controls in phyllosphere microbiome research over the past decade. By utilising systematic review principles for this review, we were able to conduct a thorough investigation, screening 450 articles from three databases for eligibility and extracting data in a controlled and methodical manner. Worryingly, we observed a surprisingly low usage of both positive and negative contamination controls in phyllosphere research. As a result, we propose a set of minimum standards to combat the effects of contamination in future phyllosphere research.
Collapse
Affiliation(s)
- Brady L Welsh
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
| | - Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, North Terrace Campus, Adelaide, SA, 5005, Australia
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, 1353, Denmark
| |
Collapse
|