1
|
Yang Z, Liu T, Fan J, Chen Y, Wu S, Li J, Liu Z, Yang Z, Li L, Liu S, Yang H, Yin H, Meng D, Tang Q. Biocontrol agents modulate phyllosphere microbiota interactions against pathogen Pseudomonas syringae. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100431. [PMID: 38883559 PMCID: PMC11177076 DOI: 10.1016/j.ese.2024.100431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024]
Abstract
The pathogen Pseudomonas syringae, responsible for a variety of diseases, poses a considerable threat to global crop yields. Emerging biocontrol strategies employ antagonistic microorganisms, utilizing phyllosphere microecology and systemic resistance to combat this disease. However, the interactions between phyllosphere microbial dynamics and the activation of the plant defense system remain poorly understood. Here we show significant alterations in phyllosphere microbiota structure and plant gene expression following the application of biocontrol agents. We reveal enhanced collaboration and integration of Sphingomonas and Methylobacterium within the microbial co-occurrence network. Notably, Sphingomonas inhibits P. syringae by disrupting pathogen chemotaxis and virulence. Additionally, both Sphingomonas and Methylobacterium activate plant defenses by upregulating pathogenesis-related gene expression through abscisic acid, ethylene, jasmonate acid, and salicylic acid signaling pathways. Our results highlighted that biocontrol agents promote plant health, from reconstructing beneficial microbial consortia to enhancing plant immunity. The findings enrich our comprehension of the synergistic interplays between phyllosphere microbiota and plant immunity, offering potential enhancements in biocontrol efficacy for crop protection.
Collapse
Affiliation(s)
- Zhaoyue Yang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Tianbo Liu
- Hunan Tobacco Research Institute, Changsha, 410004, Hunan, China
| | - Jianqiang Fan
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Yiqiang Chen
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Shaolong Wu
- Hunan Tobacco Research Institute, Changsha, 410004, Hunan, China
| | - Jingjing Li
- Technology Center, Fujian Tobacco Industrial Co.,Ltd., Xiamen, 361000, Fujian, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Zhendong Yang
- School of Architecture and Civil Engineering, Chengdu University, Chengdu, 610106, Sichuan, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Suoni Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| | - Hongwu Yang
- Yongzhou Tobacco Corporation, Yongzhou, 425000, Hunan, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, Hunan, China
| | - Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, Hunan, China
| |
Collapse
|
2
|
Dos-Santos CM, Nascimento WBA, Cesar MJSC, Baldani JI, Schwab S. Diversity of bacteria of the genus Sphingomonas associated with sugarcane (Saccharum spp.) culm apoplast fluid and their agrotechnological potential. World J Microbiol Biotechnol 2024; 40:304. [PMID: 39155347 DOI: 10.1007/s11274-024-04111-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: 03/11/2024] [Accepted: 08/13/2024] [Indexed: 08/20/2024]
Abstract
In sugarcane, sequences related to the genus Sphingomonas have been widely detected by microbiome studies. In this work, the presence of bacteria of this genus was confirmed using culture-dependent and independent techniques. A collection of thirty isolates was obtained using semispecific cultivation conditions, and a specific PCR assay was applied to help confirm the isolates as belonging to the genus. A series of laboratory evaluations were carried out to identify potential properties among the isolates in the collection, which consequently allowed the identification of some most promising isolates for the development of new agricultural bioinputs. In a separate analysis, the culture-independent fluorescence in situ hybridization (FISH) methodology was applied to demonstrate the natural occurrence of Sphingomonas in different organs and tissues of sugarcane. The results showed the presence of bacteria of the genus in the spaces between cells (apoplast) of the culm parenchyma, in vessels in the region of the leaf vein, on the adaxial surface of the leaf blade, and on the root surface, sometimes close to the base of root hairs, which suggests extensive colonization on the host plant. In summary, the present study corroborates previous metagenomic amplicon sequencing results that indicated a high occurrence of Sphingomonas associated with sugarcane. This is the first study that uses approaches other than amplicon sequencing to confirm the occurrence of the genus in sugarcane and, at the same time, demonstrates potentially beneficial activities to be explored by sugarcane cultivation.
Collapse
Affiliation(s)
- Carlos M Dos-Santos
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Pró-Reitoria de Pesquisa e Pós-Graduação, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
- Instituto SENAI de Inovação em Química Verde, Rio de Janeiro, Rio de Janeiro State, 20271-030, Brazil
| | - W Bruno A Nascimento
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Instituto de Agronomia, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
| | - M Joana S C Cesar
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal Rural do Rio de Janeiro, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23897-000, Brazil
| | - José Ivo Baldani
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Rodovia BR 465, Km 7, Seropédica, Rio de Janeiro State, 23891-000, Brazil.
| |
Collapse
|
3
|
Zhi Q, Tan G, Wu S, Ma Q, Fan J, Chen Y, Li J, Hu Z, Xiao Y, Li L, Liu Z, Yang Z, Yang Z, Meng D, Yin H, Tang Q, Liu T. What role do biocontrol agents with Mg 2+ play in the fate of antibiotic resistome and pathogenic bacteria in the phyllosphere? mSystems 2024; 9:e0112623. [PMID: 38506511 PMCID: PMC11019836 DOI: 10.1128/msystems.01126-23] [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: 11/20/2023] [Accepted: 01/10/2024] [Indexed: 03/21/2024] Open
Abstract
The contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg2+ (T1), BA with Mn2+ (T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg2+ was lower than that in the CK group. The abundance of cphA3 (carbapenem resistance), PME-1 (carbapenem resistance), tcr3 (tetracycline antibiotic resistance), and AAC (3)-VIIIa (aminoglycoside antibiotic resistance) in BA-Mg2+ was significantly higher than that in BA-Mn2+ (P < 0.05). The abundance of cphA3, PME_1, and tcr3 was significantly negatively related to the abundance of the phyllosphere pathogen Pseudomonas syringae (P < 0.05). We also found that the upstream and downstream regions of cphA3 were relatively conserved, in which rpl, rpm, and rps gene families were identified in most sequences (92%). The Ka/Ks of cphA3 was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg2+ on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process. IMPORTANCE Our study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg2+ had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen Pseudomonas syringae was negatively related to three specific ARGs, cphA3, PME-1, and tcr3. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.
Collapse
Affiliation(s)
- Qiqi Zhi
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Ge Tan
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Shaolong Wu
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Qianqian Ma
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Jianqiang Fan
- Technology Center, China Tobacco Fujian Industrial Co., Ltd, Xiamen, Fujian, China
| | - Yiqiang Chen
- Technology Center, China Tobacco Fujian Industrial Co., Ltd, Xiamen, Fujian, China
| | - Jingjing Li
- Technology Center, China Tobacco Fujian Industrial Co., Ltd, Xiamen, Fujian, China
| | - Zhengrong Hu
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Zhaoyue Yang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Zhendong Yang
- School of Architecture and Civil Engineering, Chengdu University, Chengdu, Sichuan, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy, Ministry of Education, Changsha, China
| | - Qianjun Tang
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Tianbo Liu
- Tobacco Research Institute of Hunan Province, Changsha, China
| |
Collapse
|
4
|
Mehlferber EC, Debray R, Conover AE, Sherman JK, Kaulbach G, Reed R, McCue KF, Ferrel JE, Khanna R, Koskella B. Phyllosphere microbial associations improve plant reproductive success. FRONTIERS IN PLANT SCIENCE 2023; 14:1273330. [PMID: 38143578 PMCID: PMC10739325 DOI: 10.3389/fpls.2023.1273330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023]
Abstract
The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.
Collapse
Affiliation(s)
- Elijah C. Mehlferber
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Reena Debray
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Asa E. Conover
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Julia K. Sherman
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Griffin Kaulbach
- Department of Environmental Studies, Haverford College, PA, United States
| | - Robert Reed
- i-Cultiver, Inc., Manteca, CA, United States
| | - Kent F. McCue
- Crop Improvement and Genetics Research Unit, Agricultural Research Service, Western Regional Research Center, United States Department of Agriculture, Albany, CA, United States
| | - Jon E. Ferrel
- i-Cultiver, Inc., Manteca, CA, United States
- Azomite Mineral Products, Inc., Nephi, UT, United States
| | - Rajnish Khanna
- i-Cultiver, Inc., Manteca, CA, United States
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Britt Koskella
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
| |
Collapse
|
5
|
Si H, Cui B, Liu F, Zhao M. Microbial community and chemical composition of cigar tobacco ( Nicotiana tabacum L.) leaves altered by tobacco wildfire disease. PLANT DIRECT 2023; 7:e551. [PMID: 38099080 PMCID: PMC10719477 DOI: 10.1002/pld3.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Tobacco wildfire disease caused by Pseudomonas syringae pv. tabaci is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar tobacco leaves has not been clarified in detail. In this study, the differences in microbiota and chemical factors between wildfire disease-infected leaves and healthy leaves were characterized using high-throughput Illumina sequencing and a continuous-flow analytical system, respectively. The results demonstrated significant alterations in the structure of the phyllosphere microbial community in response to wildfire disease, and the infection of P. syringae pv. tabaci led to a decrease in bacterial richness and diversity. Furthermore, the content of nicotine, protein, total nitrogen, and Cl- in diseased leaves significantly increased by 47.86%, 17.46%, 20.08%, and 72.77% in comparison to healthy leaves, while the levels of total sugar and reducing sugar decreased by 59.59% and 70.0%, respectively. Notably, the wildfire disease had little effect on the content of starch and K+. Redundancy analysis revealed that Pseudomonas, Staphylococcus, Cladosporium, and Wallemia displayed positive correlations with nicotine, protein, total nitrogen, Cl- and K+ contents, while Pantoea, Erwinia, Sphingomonas, Terrisporobacter, Aspergillus, Alternaria, Sampaiozyma, and Didymella displayed positive correlations with total sugar and reducing sugar contents. Brevibacterium, Brachybacterium, and Janibacter were found to be enriched in diseased leaves, suggesting their potential role in disease suppression. Co-occurrence network analysis indicated that positive correlations were prevalent in microbial networks, and the bacterial network of healthy tobacco leaves exhibited greater complexity compared to diseased tobacco leaves. This study revealed the impact of wildfire disease on the microbial community and chemical compositions of tobacco leaves and provides new insights for the biological control of tobacco wildfire disease.
Collapse
Affiliation(s)
- Hongyang Si
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Bing Cui
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Fang Liu
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Mingqin Zhao
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| |
Collapse
|
6
|
De Mandal S, Jeon J. Phyllosphere Microbiome in Plant Health and Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:3481. [PMID: 37836221 PMCID: PMC10575124 DOI: 10.3390/plants12193481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.
Collapse
Affiliation(s)
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| |
Collapse
|
7
|
Liu Y, Ge W, Dong C, Shao Q, Zhang Z, Zou X, Hu H, Han Y. The Analysis of Microbial Community Characteristics Revealed that the Pathogens of Leaf Spot of Rosa roxburghii Originated from the Phyllosphere. Indian J Microbiol 2023; 63:324-336. [PMID: 37781006 PMCID: PMC10533460 DOI: 10.1007/s12088-023-01093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 08/13/2023] [Indexed: 10/03/2023] Open
Abstract
Members of the plant mycobiota are all associated to varying degrees with the development of plant diseases. Although many reports on the plant mycobiota are well documented, the relationships between mycobiota of Rosa roxburghii and plant diseases are poorly understood. Mutual interactions and extent of the roles of microbial communities associated with R. roxburghii and the source of pathogens are still unclear, and more research is needed on the health benefits of this ecologically important population. Using high-throughput sequencing, we analyzed the mycobiota composition and ecological guilds of the rhizosphere, root, and phyllosphere of healthy and diseased R. roxburghii from the Tianfu R. roxburghii Industrial Park in Panzhou city, Guizhou province. Analysis of community composition showed that the relative abundance of pathogens of leaf spot, including Alternaria, Pestalotiopsis and Neofusicoccum in the phyllosphere of diseased plant (LD), were 1.15%, 0.15% and 0.06%, and the relative abundance of Alternaria and Pestalotiopsis were 0.96% and 0.58% in healthy plant (LH). The alpha diversity indices indicated that fungal diversity was higher in healthy plants compared to diseased plants in each compartment. The alpha diversity index of fungi in the phyllosphere (LH) of healthy R. roxburghii, including Shannon, Chao-1, and Faith-pd indices, was 1.02, 81.50 and 10.42 higher than that of the diseased (LD), respectively. The fungi in the rhizosphere of healthy was 1.03, 59.00 and 5.56 higher than the diseased, respectively. The Shannon index of fungi in the root of healthy was 0.29 higher than that of diseased. Principal Coordinate analysis and ANOSIM results showed that there were significant differences in mycobiota composition between healthy and diseased phyllospheres (P < 0.05), as well as rhizosphere fungal community, while there was no significant difference between healthy and diseased roots (P > 0.05). Linear discriminant analysis effect size revealed that, at different taxonomic levels, there were significantly different taxa between the healthy and diseased plants in each compartment. The ecological guilds differed between healthy and diseased plants according to the FUNGuild analysis. For example, of healthy compared to diseased plants, the percentages of "lichenized-undefined saprotroph" were increased by 2.34%, 0.44%, and 1.54% in the phyllosphere, root, and rhizosphere, respectively. In addition, the plant pathogens existed in each compartment of R. roxburghii, but the percentages of "plant pathogen" were increased by 1.16% in the phyllosphere of diseased compared to healthy plants. Together, the ecological guild and co-occurrence network indicated that the potential pathogens of leaf spot were mainly found in the phyllosphere. This study explained one of pathogen origin of leaf spots of R. roxburghii by the microbial community ecology, which will provide the new insights for identification of plant pathogens.
Collapse
Affiliation(s)
- Yuxing Liu
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Wei Ge
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Zhiyuan Zhang
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Xiao Zou
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Haiyan Hu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang, 550081 Guizhou China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology, College of Life Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| |
Collapse
|
8
|
Li ZR, Luo SQ, Peng YJ, Jin CZ, Liu DC. Effect of long-term application of bioorganic fertilizer on the soil property and bacteria in rice paddy. AMB Express 2023; 13:60. [PMID: 37310515 DOI: 10.1186/s13568-023-01559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/14/2023] [Indexed: 06/14/2023] Open
Abstract
The application of novel bioorganic fertilizer (BIO) has been established as a weed biocontrol strategy, and reduce herbicides pollution and negatively effects on agricultural ecosystems. However, its long-term influences on soil bacterial communities are unknown. Here, 16 S rRNA sequencing to identify the changes that occur in soil bacterial community and enzyme under BIO treatments after five years in a field experiment. BIO application effectively controlled weeds, however no obvious differences between treatments were observed under BIO-50, BIO-100, BIO-200 and BIO-400 treatment. Anaeromyxobacter and Clostridium_ sensu_ stricto_1 were the two dominant genera among BIO-treated soil samples. The BIO-800 treatment had a slight influence on the species diversity index, which was more remarkable after five years. The seven significantly-different genera between BIO-800 treatment and untreated soils included C._sensu_stricto_1, Syntrophorhabdus, Candidatus_Koribacter, Rhodanobacter, Bryobacter, Haliangium, Anaeromyxobacter. In addition, BIO application had different effects on soil enzymatic activities and chemical properties. The extractable P and pH saliency correlated with Haliangium and C._Koribacter, and C._sensu_stricto_1 observably correlated with exchangeable K, hydrolytic N and organic matter. Taken together, our data suggest that BIO application effectively controlled weeds and a slight influence on soil bacterial communities and enzymes. These findings expand our knowledge of the application of BIO as widely used as a sustainable weed control in rice paddy.
Collapse
Affiliation(s)
- Zu-Ren Li
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China.
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| | - Si-Quan Luo
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Ya-Jun Peng
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Chen-Zhong Jin
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Du-Cai Liu
- Key laboratory of Pesticide Assessment, Ministry of Agriculture and Rural Affairs, Beijing, P.R. China.
- Hunan Provincial Key Laboratory for Biology and Control of Weeds, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
| |
Collapse
|
9
|
Ma YN, Gu YL, Liu J, Zhang Y, Wang X, Xia Z, Wei HL. Deciphering the rhizosphere bacteriome associated with biological control of tobacco black shank disease. FRONTIERS IN PLANT SCIENCE 2023; 14:1152639. [PMID: 37077642 PMCID: PMC10108594 DOI: 10.3389/fpls.2023.1152639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Introduction The black shank disease seriously affects the health of tobacco plants. Conventional control methods have limitations in terms of effectiveness or economic aspects and cause public health concerns. Thus, biological control methods have come into the field, and microorganisms play a key role in suppressing tobacco black shank disease. Methods In this study, we examined the impact of soil microbial community on black shank disease basing on the structural difference of bacterial communities in rhizosphere soils. We used Illumina sequencing to compare the bacterial community diversity and structure in different rhizosphere soil samples in terms of healthy tobacco, tobacco showing typical black shank symptoms, and tobacco treated with the biocontrol agent, Bacillus velezensis S719. Results We found that Alphaproteobacteria in the biocontrol group, accounted for 27.2% of the ASVs, was the most abundant bacterial class among three groups. Heatmap and LEfSe analyses were done to determine the distinct bacterial genera in the three sample groups. For the healthy group, Pseudomonas was the most significant genus; for the diseased group, Stenotrophomonas exhibited the strongest enrichment trend, and Sphingomonas showed the highest linear discriminant analysis score, and was even more abundant than Bacillus; for the biocontrol group, Bacillus, and Gemmatimonas were the largely distributed genus. In addition, co-occurrence network analysis confirmed the abundance of taxa, and detected a recovery trend in the network topological parameters of the biocontrol group. Further functional prediction also provided a possible explanation for the bacterial community changes with related KEGG annotation terms. Discussion These findings will improve our knowledge of plant-microbe interactions and the application of biocontrol agents to improve plant fitness, and may contribute to the selection of biocontrol strains.
Collapse
Affiliation(s)
- Yi-Nan Ma
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi-Lin Gu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Liu
- Zunyi Tobacco Company of Guizhou Provincial Tobacco Corporation, Zunyi, China
| | - Yuqin Zhang
- China National Tobacco Corporation Shandong Branch, Jinan, China
| | - Xinwei Wang
- Key Laboratory of Tobacco Pest Monitoring & Integrated Management in Tobacco, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhenyuan Xia
- Yunnan Academy of Tobacco Agricultural Science, Kunming, China
- *Correspondence: Zhenyuan Xia, ; Hai-Lei Wei,
| | - Hai-Lei Wei
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Zhenyuan Xia, ; Hai-Lei Wei,
| |
Collapse
|
10
|
Gorrochategui-Ortega J, Muñoz-Colmenero M, Kovačić M, Filipi J, Puškadija Z, Kezić N, Parejo M, Büchler R, Estonba A, Zarraonaindia I. A short exposure to a semi-natural habitat alleviates the honey bee hive microbial imbalance caused by agricultural stress. Sci Rep 2022; 12:18832. [PMID: 36336704 PMCID: PMC9637708 DOI: 10.1038/s41598-022-23287-6] [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: 01/18/2022] [Accepted: 10/28/2022] [Indexed: 11/08/2022] Open
Abstract
Honeybee health and the species' gut microbiota are interconnected. Also noteworthy are the multiple niches present within hives, each with distinct microbiotas and all coexisting, which we termed "apibiome". External stressors (e.g. anthropization) can compromise microbial balance and bee resilience. We hypothesised that (1) the bacterial communities of hives located in areas with different degrees of anthropization differ in composition, and (2) due to interactions between the multiple microbiomes within the apibiome, changes in the community of a niche would impact the bacteria present in other hive sections. We characterised the bacterial consortia of different niches (bee gut, bee bread, hive entrance and internal hive air) of 43 hives from 3 different environments (agricultural, semi-natural and natural) through 16S rRNA amplicon sequencing. Agricultural samples presented lower community evenness, depletion of beneficial bacteria, and increased recruitment of stress related pathways (predicted via PICRUSt2). The taxonomic and functional composition of gut and hive entrance followed an environmental gradient. Arsenophonus emerged as a possible indicator of anthropization, gradually decreasing in abundance from agriculture to the natural environment in multiple niches. Importantly, after 16 days of exposure to a semi-natural landscape hives showed intermediate profiles, suggesting alleviation of microbial dysbiosis through reduction of anthropization.
Collapse
Affiliation(s)
- June Gorrochategui-Ortega
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Marta Muñoz-Colmenero
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain ,grid.419099.c0000 0001 1945 7711Instituto de Investigaciones Marinas (CSIC)/Institute of Marine Research, Eduardo Cabello 6, 36208 Vigo, Pontevedra Spain
| | - Marin Kovačić
- grid.412680.90000 0001 1015 399XFaculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, V.Preloga 1, 31000 Osijek, Croatia
| | - Janja Filipi
- grid.424739.f0000 0001 2159 1688Department of Ecology, Agronomy and Aquaculture, University of Zadar, Trg Kneza Višeslava 9, 23000 Zadar, Croatia
| | - Zlatko Puškadija
- grid.412680.90000 0001 1015 399XFaculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, V.Preloga 1, 31000 Osijek, Croatia
| | - Nikola Kezić
- grid.4808.40000 0001 0657 4636Department of Fisheries, Apiculture and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Melanie Parejo
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Ralph Büchler
- grid.506460.10000 0004 4679 6788Landesbetrieb Landwirtschaft Hessen (LLH), Bieneninstitut, Erlenstraße 9, 35274 Kirchhain, Germany
| | - Andone Estonba
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain
| | - Iratxe Zarraonaindia
- grid.11480.3c0000000121671098Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940 Leioa, Spain ,grid.424810.b0000 0004 0467 2314IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| |
Collapse
|
11
|
Agbavor C, Mirza BS, Wait A. The Effects of Phyllosphere Bacteria on Plant Physiology and Growth of Soybean Infected with Pseudomonas syringae. PLANTS (BASEL, SWITZERLAND) 2022; 11:2634. [PMID: 36235499 PMCID: PMC9571934 DOI: 10.3390/plants11192634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/28/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Phyllosphere bacteria are an important determinant of plant growth and resistance to pathogens. However, the efficacy of phyllosphere bacteria in regulating infection of Pseudomonas syringae pv. glycinea (Psg) and its influence on soybean growth and physiology is unknown. In a greenhouse study, we assessed the influence of a phyllosphere bacterial consortium (BC) of 13 species isolated from field-grown soybean leaves on uninfected and deliberately Psg infected soybean plants. We measured Psg density on infected leaves with and without the application of the BC. The BC application resulted in a significant reduction in Psg cells. We also measured plant biomass, nodule mass and number, gas exchange, and leaf chlorophyll and nitrogen in four treatment groups: control plants, plants with a BC and no infection (BC), plants with BC and infected with Psg (BC + Psg), and plants infected with Psg alone. For all variables, plants infected with Psg alone showed significant reduction in measured variables compared to both BC treatments. Therefore, the bacterial consortium was effective in controlling the negative effects of Psg on growth and physiology. The BC treatment sometimes resulted in increases in measured variables such as plant biomass, nodule numbers, and leaf chlorophyll as compared to control and BC + Psg treatments. Overall, the positive influence of BC treatment on plant growth and physiology highlights its potential applications to increase crop yield and control bacterial pathogens.
Collapse
Affiliation(s)
| | - Babur S. Mirza
- Correspondence: ; Tel.: +1-417-836-5062; Fax: +1-417-836-4204
| | | |
Collapse
|
12
|
Li Z, Chen Y, Ling A, Li H, Lin Z, Wang Y. Effects of Biocontrol Agents Application on Soil Bacterial Community and the Quality of Tobacco. Curr Microbiol 2022; 79:320. [PMID: 36121540 DOI: 10.1007/s00284-022-02937-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/13/2022] [Indexed: 11/30/2022]
Abstract
In this study, to evaluate the effect of different biocontrol agents (BCAs) on the soil bacterial community, we investigated the effects of Bacillus amyloliquefaciens, synthetic bacterial community (Aspergillus niger:Bacillus subtilis:Bacillus licheniformis:Streptomyces microflavus = 3:3:3:1, SynCom), and BCAs combined with lime-nitrogen on soil bacterial community by utilizing 16S rRNA sequencing technology. The sequencing shows that BCAs application can improve the value of Shannon and Sobs index of bacterial community during tobacco rosette and vigorous growing period. With the growth of tobacco, the effect of BCAs on the composition and difference of soil bacterial community structure becomes more and more obvious. In terms of average relative richness, the top six phyla of soil bacterial community are Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Gemmatimonadetes, and Bacteroidetes. Bacillus amyloliquefaciens application can increase the relative richness of Proteobacteria and Bacteroidetes. And the combination between BCAs and lime-nitrogen can increase the relative richness of Gemmatimonadetes and Bacteroidetes. The SynCom also can increase the relative richness of Bacteroidetes, whereas it decreases the relative richness of Acidobacteria. Proteobacteria, Acidobacteria, Gemmatimonadetes, and Bacteroidetes showing an extremely significant correlation with pH and exchangeable magnesium (EMg). BCAs application can improve the tobacco yield, effective leaves, and reducing sugar content that also has extremely significant positive correlation with pH and EMg. In conclusion, the results of our field experiments clearly show that BCAs application can significantly affect the soil pH and EMg by changing most of the dominant soil bacterial species. The richness of Bacteroidetes can serve as an indicator of the changes in soil pH and EMg caused by BCAs application.
Collapse
Affiliation(s)
- Zhongkui Li
- School of Chemical Engineering, Zhengzhou University, Zhengzhou, 450001, China
| | - Yulan Chen
- Liangshan Company of Sichuan Tobacco Company, Xichang, 615000, China
| | - Aifen Ling
- Liangshan Company of Sichuan Tobacco Company, Xichang, 615000, China
| | - Hongli Li
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China.
| | - Zhengquan Lin
- Liangshan Prefecture Tobacco Company Ningnan Branch, Dechang, 615400, China
| | - Yan Wang
- School of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China
| |
Collapse
|
13
|
Dai YF, Wu XM, Wang HC, Li WH, Cai LT, Li JX, Wang F, Sehar S, Shamsi IH. Spatio-Temporal Variation in the Phyllospheric Microbial Biodiversity of Alternaria Alternata-Infected Tobacco Foliage. Front Microbiol 2022; 13:920109. [PMID: 35966692 PMCID: PMC9370072 DOI: 10.3389/fmicb.2022.920109] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
Phyllospheric microbial composition of tobacco (Nicotiana tabacum L.) is contingent upon certain factors, such as the growth stage of the plant, leaf position, and cultivar and its geographical location, which influence, either directly or indirectly, the growth, overall health, and production of the tobacco plant. To better understand the spatiotemporal variation of the community and the divergence of phyllospheric microflora, procured from healthy and diseased tobacco leaves infected by Alternaria alternata, the current study employed microbe culturing, high-throughput technique, and BIOLOG ECO. Microbe culturing resulted in the isolation of 153 culturable fungal isolates belonging to 33 genera and 99 bacterial isolates belonging to 15 genera. High-throughput sequencing revealed that the phyllosphere of tobacco was dominantly colonized by Ascomycota and Proteobacteria, whereas, the most abundant fungal and bacterial genera were Alternaria and Pseudomonas. The relative abundance of Alternaria increased in the upper and middle healthy groups from the first collection time to the third, whereas, the relative abundance of Pseudomonas, Sphingomonas, and Methylobacterium from the same positions increased during gradual leaf aging. Non-metric multi-dimensional scaling (NMDs) showed clustering of fungal communities in healthy samples, while bacterial communities of all diseased and healthy groups were found scattered. FUNGuild analysis, from the first collection stage to the third one in both groups, indicated an increase in the relative abundance of Pathotroph-Saprotroph, Pathotroph-Saprotroph-Symbiotroph, and Pathotroph-Symbiotroph. Inclusive of all samples, as per the PICRUSt analysis, the predominant pathway was metabolism function accounting for 50.03%. The average values of omnilog units (OUs) showed relatively higher utilization rates of carbon sources by the microbial flora of healthy leaves. According to the analysis of genus abundances, leaf growth and leaf position were the important drivers of change in structuring the microbial communities. The current findings revealed the complex ecological dynamics that occur in the phyllospheric microbial communities over the course of a spatiotemporal varying environment with the development of tobacco brown spots, highlighting the importance of community succession.
Collapse
Affiliation(s)
- Yuan-feng Dai
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Bijie Tobacco Company, Bijie, China
| | - Xiao-mao Wu
- Department of Plant Protection, Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Xiao-mao Wu
| | - Han-cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Han-cheng Wang
| | - Wen-hong Li
- Guizhou Institute of Plant Protection, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Liu-ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Ji-xin Li
- Guizhou Tobacco Company of CNTC, China National Tobacco Corporation, Guiyang, China
| | - Feng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
- Feng Wang
| | - Shafaque Sehar
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Imran Haider Shamsi
- Zhejiang Key Laboratory of Crop Germplasm Resource, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Imran Haider Shamsi
| |
Collapse
|
14
|
Xiong J, Peng S, Liu Y, Yin H, Zhou L, Zhou Z, Tan G, Gu Y, Zhang H, Huang J, Meng D. Soil properties, rhizosphere bacterial community, and plant performance respond differently to fumigation and bioagent treatment in continuous cropping fields. Front Microbiol 2022; 13:923405. [PMID: 35935223 PMCID: PMC9354655 DOI: 10.3389/fmicb.2022.923405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/27/2022] [Indexed: 11/15/2022] Open
Abstract
Continuous cropping barriers lead to huge agriculture production losses, and fumigation and biological agents are developed to alleviate the barriers. However, there is a lack of literature on the differences between strong chemical fumigant treatment and moderate biological agent treatment. In this study, we investigated those differences and attempted to establish the links between soil properties, rhizosphere microbial community, and plant performance in both fumigation- and bioagent-treated fields. The results showed that the fumigation had a stronger effect on both soil functional microbes, i.e., ammonia oxidizers and soil-borne bacterial pathogens, and therefore, led to a significant change in soil properties, higher fertilizer efficiency, lower disease infections, and improved plant growth, compared with untreated control fields. Biological treatment caused less changes to soil properties, rhizosphere bacterial community, and plant physiology. Correlation and modeling analyses revealed that the bioagent effect was mainly direct, whereas fumigation resulted in indirect effects on alleviating cropping barriers. A possible explanation would be the reconstruction of the soil microbial community by the fumigation process, which would subsequently lead to changes in soil characteristics and plant performance, resulting in the effective alleviation of continuous cropping barriers.
Collapse
Affiliation(s)
- Jing Xiong
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Shuguang Peng
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Yongjun Liu
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Lei Zhou
- Beijing Research Institute of Chemical Engineering and Metallurgy, Beijing, China
| | - Zhicheng Zhou
- Tobacco Research Institute of Hunan Province, Changsha, China
| | - Ge Tan
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Hetian Zhang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Jingyi Huang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Delong Meng
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- *Correspondence: Delong Meng,
| |
Collapse
|
15
|
Banik S, Uchil A, Kalsang T, Chakrabarty S, Ali MA, Srisungsitthisunti P, Mahato KK, Surdo S, Mazumder N. The revolution of PDMS microfluidics in cellular biology. Crit Rev Biotechnol 2022; 43:465-483. [PMID: 35410564 DOI: 10.1080/07388551.2022.2034733] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microfluidics is revolutionizing the way research on cellular biology has been traditionally conducted. The ability to control the cell physicochemical environment by adjusting flow conditions, while performing cellular analysis at single-cell resolution and high-throughput, has made microfluidics the ideal choice to replace traditional in vitro models. However, such a revolution only truly started with the advent of polydimethylsiloxane (PDMS) as a microfluidic structural material and soft-lithography as a rapid manufacturing technology. Indeed, before the "PDMS age," microfluidic technologies were: costly, time-consuming and, more importantly, accessible only to specialized laboratories and users. The simplicity of molding PDMS in various shapes along with its inherent properties (transparency, biocompatibility, and gas permeability) has spread the applications of innovative microfluidic devices to diverse and important biological fields and clinical studies. This review highlights how PDMS-based microfluidic systems are innovating pre-clinical biological research on cells and organs. These devices were able to cultivate different cell lines, enhance the sensitivity and diagnostic effectiveness of numerous cell-based assays by maintaining consistent chemical gradients, utilizing and detecting the smallest number of analytes while being high-throughput. This review will also assist in identifying the pitfalls in current PDMS-based microfluidic systems to facilitate breakthroughs and advancements in healthcare research.
Collapse
Affiliation(s)
- Soumyabrata Banik
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Ashwini Uchil
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Tenzin Kalsang
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Md Azahar Ali
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Pornsak Srisungsitthisunti
- Department of Production Engineering, Faculty of Engineering, King Mongkut's University of Technology North Bangkok, Bangkok, Thailand
| | - Krishna Kishore Mahato
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| | - Salvatore Surdo
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Nirmal Mazumder
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, India
| |
Collapse
|
16
|
Rawat VS, Kaur J, Bhagwat S, Pandit MA, Rawat CD. Deploying Microbes as Drivers and Indicators in Ecological Restoration. Restor Ecol 2022. [DOI: 10.1111/rec.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jasleen Kaur
- Department of Botany, Dyal Singh College University of Delhi New Delhi 110003 India
| | - Sakshi Bhagwat
- Department of Biosciences Faculty of Natural Sciences, Jamia Millia Islamia New Delhi 110025 India
| | - Manisha Arora Pandit
- Department of Zoology, Kalindi College University of Delhi New Delhi 110008 India
| | - Charu Dogra Rawat
- Molecular Biology and Genomics Research Laboratory, Ramjas College University of Delhi Delhi 110007 India
- Department of Zoology, Ramjas College University of Delhi Delhi 110007 India
| |
Collapse
|
17
|
Díaz-Cruz GA, Cassone BJ. Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens. FEMS Microbiol Ecol 2022; 98:fiac022. [PMID: 35195242 DOI: 10.1093/femsec/fiac022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/20/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.
Collapse
Affiliation(s)
- Gustavo A Díaz-Cruz
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
| | - Bryan J Cassone
- Department of Biology, Brandon University, Brandon, MB, R7A 6A9, Canada
| |
Collapse
|
18
|
Ding C, Zhang W, Wang Y, Ding M, Wang X, Li A, Liang D, Su X. Study on the differences of phyllosphere microorganisms between poplar hybrid offspring and their parents. PeerJ 2022; 10:e12915. [PMID: 35310169 PMCID: PMC8932310 DOI: 10.7717/peerj.12915] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/20/2022] [Indexed: 01/11/2023] Open
Abstract
The females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microorganism of dioecious plants between parents and hybrid offspring remain largely unexplored. Here, the phyllosphere bacterial and fungal community diversity and composition of female (Populus nigra 'DH5' (PNDH5)), male (P. simonii 'DH4' (PSDH4)), and the hybrid offspring (P. simonii × P. nigra 'DH1' (PSPNDH1), P. simonii × P. nigra 'DH2' (PSPNDH2), P. simonii × P. nigra 'DH3' (PSPNDH3)) were investigated using 16S rDNA/ITS rDNA gene-based Illumina NovaSeq 6000 sequencing. There was considerable variation of plant height, diameter at breast height, leaf area, length of petioles, leaf moisture content, and starch among different samples, and PSDH2 owned the highest plant height, diameter at breast height, and length of petioles. No distinct differences of phyllosphere bacterial community diversity were observed among PSDH4, PNDH5, PSPNDH1, PSPNDH2, and PSPNDH3; while, PSPNDH2 owned the highest fungal Pielou_e index, Shannon index, and Simpson index. Firmicutes and Ascomycota were the predominant phyllosphere bacterial and fungal community at the phylum level, respectively. Bacilli and Gammaproteobacteria were the two most dominant bacterial classes regardless of parent and the hybrid offspring. The predominant phyllosphere fungal community was Dothideomycetes at the class level. The NMDS demonstrated that phyllosphere microbial community obviously differed between parents and offspring, while the phyllosphere microbial community presented some similarities under different hybrid progeny. Also, leaf characteristics contributed to the differentiation of phyllosphere bacterial and fungal communities between parents and hybrid offspring. These results highlighted the discrimination of phyllosphere microorganisms on parent and hybrid offspring, which provided clues to potential host-related species in the phyllosphere environment.
Collapse
Affiliation(s)
- Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yanbo Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Mi Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaojiang Wang
- Inner Mongolia Academy of Forestry Sciences, Hohhot, Inner Mongolia, China
| | - Aiping Li
- Inner Mongolia Academy of Forestry Sciences, Hohhot, Inner Mongolia, China
| | - Dejun Liang
- Liaoning Provincial Poplar Institute, Gaizhou, Liaoning, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China,Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
19
|
Longa CMO, Antonielli L, Bozza E, Sicher C, Pertot I, Perazzolli M. Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment. Microbiol Res 2022; 258:126991. [DOI: 10.1016/j.micres.2022.126991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 01/04/2023]
|
20
|
Sullam KE, Musa T. Ecological Dynamics and Microbial Treatments against Oomycete Plant Pathogens. PLANTS 2021; 10:plants10122697. [PMID: 34961168 PMCID: PMC8707103 DOI: 10.3390/plants10122697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/16/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022]
Abstract
In this review, we explore how ecological concepts may help assist with applying microbial biocontrol agents to oomycete pathogens. Oomycetes cause a variety of agricultural diseases, including potato late blight, apple replant diseases, and downy mildew of grapevine, which also can lead to significant economic damage in their respective crops. The use of microbial biocontrol agents is increasingly gaining interest due to pressure from governments and society to reduce chemical plant protection products. The success of a biocontrol agent is dependent on many ecological processes, including the establishment on the host, persistence in the environment, and expression of traits that may be dependent on the microbiome. This review examines recent literature and trends in research that incorporate ecological aspects, especially microbiome, host, and environmental interactions, into biological control development and applications. We explore ecological factors that may influence microbial biocontrol agents’ efficacy and discuss key research avenues forward.
Collapse
|
21
|
Dimopoulou A, Theologidis I, Varympopi A, Papafotis D, Mermigka G, Tzima A, Panopoulos NJ, Skandalis N. Shifting Perspectives of Translational Research in Bio-Bactericides: Reviewing the Bacillus amyloliquefaciens Paradigm. BIOLOGY 2021; 10:biology10111202. [PMID: 34827195 PMCID: PMC8614995 DOI: 10.3390/biology10111202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The continuous reduction of approved conventional microbicides, due to health concerns and the development of plant-pathogen resistance, has been urged for the use of safe alternatives in crop protection. Several beneficial bacterial species, termed biological control agents, are currently used in lieu of chemical pesticides. The approach to select such bacterial species and manufacture commercial products has been based on their biocontrol effect under optimal growth conditions, which is far from the real nutrient-limited field conditions of plant niches. It’s important to determine the complex interactions that occur among BCAs, plant host and niche microbiome to fully understand and exploit the potential of biological control agents. Furthermore, it’s crucial to acknowledge the environmental impact of their long-term use. Abstract Bacterial biological control agents (BCAs) have been increasingly used against plant diseases. The traditional approach to manufacturing such commercial products was based on the selection of bacterial species able to produce secondary metabolites that inhibit mainly fungal growth in optimal media. Such species are required to be massively produced and sustain long-term self-storage. The endpoint of this pipeline is large-scale field tests in which BCAs are handled as any other pesticide. Despite recent knowledge of the importance of BCA-host-microbiome interactions to trigger plant defenses and allow colonization, holistic approaches to maximize their potential are still in their infancy. There is a gap in scientific knowledge between experiments in controlled conditions for optimal BCA and pathogen growth and the nutrient-limited field conditions in which they face niche microbiota competition. Moreover, BCAs are considered to be safe by competent authorities and the public, with no side effects to the environment; the OneHealth impact of their application is understudied. This review summarizes the state of the art in BCA research and how current knowledge and new biotechnological tools have impacted BCA development and application. Future challenges, such as their combinational use and ability to ameliorate plant stress are also discussed. Addressing such challenges would establish their long-term use as centerfold agricultural pesticides and plant growth promoters.
Collapse
Affiliation(s)
- Anastasia Dimopoulou
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Heraklion, Greece; (A.D.); (G.M.)
| | - Ioannis Theologidis
- Laboratory of Pesticides’ Toxicology, Benaki Phytopathological Institute, 14561 Athens, Greece;
| | - Adamantia Varympopi
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (A.V.); (D.P.)
| | - Dimitris Papafotis
- Enzyme and Microbial Biotechnology Unit, Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece; (A.V.); (D.P.)
| | - Glykeria Mermigka
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Heraklion, Greece; (A.D.); (G.M.)
| | - Aliki Tzima
- Laboratory of Plant Pathology, Department of Crop Production, School of Agricultural Production Infrastructure and Environment, Faculty of Crop Science, Agricultural University of Athens, 11855 Athens, Greece;
| | - Nick J. Panopoulos
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA;
| | - Nicholas Skandalis
- Health Sciences Campus, Keck School of Medicine, University of Southern California, 1441 Eastlake Ave, Los Angeles, CA 90033, USA
- Correspondence:
| |
Collapse
|
22
|
Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
Collapse
Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | | |
Collapse
|
23
|
Tao J, Cao P, Xiao Y, Wang Z, Huang Z, Jin J, Liu Y, Yin H, Liu T, Zhou Z. Distribution of the potential pathogenic Alternaria on plant leaves determines foliar fungal communities around the disease spot. ENVIRONMENTAL RESEARCH 2021; 200:111715. [PMID: 34297933 DOI: 10.1016/j.envres.2021.111715] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/14/2021] [Accepted: 07/14/2021] [Indexed: 06/13/2023]
Abstract
Plant leaves are colonized by a remarkably diverse fungal microbiome, which contributes to host plant growth and health. However, responses of foliar fungal community to phytopathogen invasion and measures of the fungal community taken to resist or assist pathogens remain elusive. By utilizing high-throughput sequencing of internal transcribed spacer (ITS) amplicons, we studied the relationships between the foliar fungal community around the disease spot and the pathogen of brown spot disease. The pathogenic Alternaria was found to follow a dramatically decreased trend from the disease spot to its surrounding fungal communities, whose community structure also diverged substantially away from the disease spot community. With the increase of pathogenic Alternaria, diversity indexes, including Shannon, Pielou and Simpson, showed a trend of increasing first and then decreasing. Total network links and the average path distance exhibited strong negative and positive correlations with Alternaria, respectively. Five keystone members showed direct interactions with pathogenic Alternaria. Members of Botryosphaeria, Paraphoma and Plectosphaerella might act as key 'pathogen facilitators' to increase the severity and development of brown spot disease, while Pleospora and Ochrocladosporium might be important 'pathogen antagonists' to suppress the expansion of pathogenic Alternaria. Our study provides new insights in developing new strategies for leaf disease prediction or prevention.
Collapse
Affiliation(s)
- Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China; School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yansong Xiao
- Chenzhou Tobacco Company of Hunan Province, Chenzhou, 423000, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, 427000, China
| | - Zhihua Huang
- Yuxi Tobacco Company of Yunnan Province, Yuxi, 653100, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, China
| | - Yongjun Liu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, 410083, China
| | - Tianbo Liu
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China; College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.
| | - Zhicheng Zhou
- Central South Agricultural Experiment Station of China Tobacco, Changsha, 410004, China.
| |
Collapse
|
24
|
Liu T, Gu Y, Zhou Z, Liu Z, Yin H, Qin C, Yi T, Tao J. Ecological strategies of biological and chemical control agents on wildfire disease of tobacco (Nicotiana tabacum L.). BMC Microbiol 2021; 21:184. [PMID: 34139992 PMCID: PMC8212473 DOI: 10.1186/s12866-021-02237-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/19/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND To investigate the ecological effects of chemical and biological control methods on tobacco wildfire disease, a plot field experiment was conducted to compare the control efficiency and mechanisms of a chemical pesticide (kasugamycin wettable powder, KWP) and a biological control agent (BCA) through high-throughput sequencing of bacterial 16S rRNA genes. RESULTS The results showed that the BCA displayed better performance in decreasing the disease index and morbidity of tobacco than the chemical pesticide. By monitoring the endophytic community within tobacco leaves, it was found that the control effects of these two methods might be mediated by different changes in the endophytic bacterial communities and community assembly patterns. The application of either method decreased the taxonomic diversity of the leaf endophytic community. Compared to the BCA, KWP showed a more significant effect on the endophytic community structure, while the endophytic community treated with the BCA was able to return to the original state, which presented much lower disease infection. The disease control efficiency of KWP and BCA treatments might be achieved by increasing the abundance of Sphingomonas and Streptophyta, respectively. Furthermore, an analysis of the ecological processes in community assembly indicated that the BCA strengthened the homogeneous and variable selection, while KWP enhanced ecological drift. CONCLUSIONS The results suggested different control mechanisms between KWP and BCA treatments, which will help in developing diverse ecological strategies for plant disease control.
Collapse
Affiliation(s)
- Tianbo Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Central South Agricultural Experiment Station of China Tobacco, Changsha, China
| | - Yabing Gu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Zhicheng Zhou
- Central South Agricultural Experiment Station of China Tobacco, Changsha, China
| | - Zhenghua Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Chong Qin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Tuyong Yi
- College of Plant Protection, Hunan Agricultural University, Changsha, China.
| | - Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China.
| |
Collapse
|
25
|
Chaudhry V, Runge P, Sengupta P, Doehlemann G, Parker JE, Kemen E. Shaping the leaf microbiota: plant-microbe-microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:36-56. [PMID: 32910810 PMCID: PMC8210630 DOI: 10.1093/jxb/eraa417] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/07/2020] [Indexed: 05/28/2023]
Abstract
The aerial portion of a plant, namely the leaf, is inhabited by pathogenic and non-pathogenic microbes. The leaf's physical and chemical properties, combined with fluctuating and often challenging environmental factors, create surfaces that require a high degree of adaptation for microbial colonization. As a consequence, specific interactive processes have evolved to establish a plant leaf niche. Little is known about the impact of the host immune system on phyllosphere colonization by non-pathogenic microbes. These organisms can trigger plant basal defenses and benefit the host by priming for enhanced resistance to pathogens. In most disease resistance responses, microbial signals are recognized by extra- or intracellular receptors. The interactions tend to be species specific and it is unclear how they shape leaf microbial communities. In natural habitats, microbe-microbe interactions are also important for shaping leaf communities. To protect resources, plant colonizers have developed direct antagonistic or host manipulation strategies to fight competitors. Phyllosphere-colonizing microbes respond to abiotic and biotic fluctuations and are therefore an important resource for adaptive and protective traits. Understanding the complex regulatory host-microbe-microbe networks is needed to transfer current knowledge to biotechnological applications such as plant-protective probiotics.
Collapse
Affiliation(s)
- Vasvi Chaudhry
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| | - Paul Runge
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Priyamedha Sengupta
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Gunther Doehlemann
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Jane E Parker
- Max Planck Institute for Plant Breeding Research, Köln, Germany
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences
(CEPLAS), University of Cologne, Center for Molecular Biosciences, Cologne,
Germany
| | - Eric Kemen
- Department of Microbial Interactions, IMIT/ZMBP, University of
Tübingen, Tübingen, Germany
| |
Collapse
|
26
|
Chen X, Wicaksono WA, Berg G, Cernava T. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141799. [PMID: 32889475 DOI: 10.1016/j.scitotenv.2020.141799] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well as whole ecosystems. However, such effects remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning and host health. We analysed bacterial communities by sequencing 16S rRNA gene fragment amplicons following spray application of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide on Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized by Proteobacteria, with Alphaproteobacteria accounting for up to 33.8% of the indigenous bacterial community. Bioinformatic analyses indicated that pesticide applications had an effect on the core microbiome as well as the rare microbiome. Moreover, the interference of the pesticide with phyllosphere bacteria was found to be selective. We have identified four positive responders including an ASV assigned to the genus Acinetobacter and 12 negative responders mainly assigned to bacterial genera known for beneficial plant-microbe interactions, including Stenotrophomonas, Sphingomonas, Flavobacterium and Serratia. Complementary inference of bacterial functioning on community level indicated that microbes with distinct stress response systems were likely enriched in the conducted treatments. The overall findings confirmed that pesticide treatments can induce measureable shifts in non-target bacterial communities colonizing the plant phyllosphere. They also indicate that potentially beneficial bacteria, which are known for their intrinsic association with plants, are among the most sensitive responders to the employed fungicide and thus highlight the importance of off-target studies in the context of the plant microbiome.
Collapse
Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 550025 Guiyang, China; College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China; Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| |
Collapse
|
27
|
Costa D, Tavares RM, Baptista P, Lino-Neto T. Cork Oak Endophytic Fungi as Potential Biocontrol Agents against Biscogniauxia mediterranea and Diplodia corticola. J Fungi (Basel) 2020; 6:E287. [PMID: 33202643 PMCID: PMC7711870 DOI: 10.3390/jof6040287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 01/06/2023] Open
Abstract
An increase in cork oak diseases caused by Biscogniauxia mediterranea and Diplodia corticola has been reported in the last decade. Due to the high socio-economic and ecologic importance of this plant species in the Mediterranean Basin, the search for preventive or treatment measures to control these diseases is an urgent need. Fungal endophytes were recovered from cork oak trees with different disease severity levels, using culture-dependent methods. The results showed a higher number of potential pathogens than beneficial fungi such as cork oak endophytes, even in healthy plants. The antagonist potential of a selection of eight cork oak fungal endophytes was tested against B. mediterranea and D. corticola by dual-plate assays. The tested endophytes were more efficient in inhibiting D. corticola than B. mediterranea growth, but Simplicillium aogashimaense, Fimetariella rabenhorstii, Chaetomium sp. and Alternaria alternata revealed a high potential to inhibit the growth of both. Simplicillium aogashimaense caused macroscopic and microscopic mycelial/hyphal deformations and presented promising results in controlling both phytopathogens' growth in vitro. The evaluation of the antagonistic potential of non-volatile and volatile compounds also revealed that A. alternata compounds could be further explored for inhibiting both pathogens. These findings provide valuable knowledge that can be further explored in in vivo assays to find a suitable biocontrol agent for these cork oak diseases.
Collapse
Affiliation(s)
- Daniela Costa
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (D.C.); (R.M.T.)
| | - Rui M. Tavares
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (D.C.); (R.M.T.)
| | - Paula Baptista
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
| | - Teresa Lino-Neto
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal; (D.C.); (R.M.T.)
| |
Collapse
|
28
|
Moitinho MA, Souza DT, Chiaramonte JB, Bononi L, Melo IS, Taketani RG. The unexplored bacterial lifestyle on leaf surface. Braz J Microbiol 2020; 51:1233-1240. [PMID: 32363565 PMCID: PMC7455623 DOI: 10.1007/s42770-020-00287-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 04/25/2020] [Indexed: 01/19/2023] Open
Abstract
Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.
Collapse
Affiliation(s)
- Marta A Moitinho
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Danilo T Souza
- Laboratory of Mass Spectrometry Applied Natural Products Chemistry; Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Av. Bandeirantes, 3900, Monte Alegre, Ribeirão Preto, São Paulo, 14040-901, Brazil
| | - Josiane B Chiaramonte
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Laura Bononi
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil
| | - Itamar S Melo
- Laboratory of Environmental Microbiology, EMBRAPA Environment, Brazilian Agricultural Research Corporation, SP 340, Km 127.5, Jaguariúna, São Paulo, 13820-000, Brazil
| | - Rodrigo G Taketani
- College of Agriculture Luiz de Queiroz, University of São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, 13418-900, Brazil.
- CETEM, Centre for Mineral Technology, MCTIC Ministry of Science, Technology, Innovation and Communication, Av. Pedro Calmon, 900, Cidade Universitária, Ilha do Fundão, Rio de Janeiro, 21941-908, Brazil.
| |
Collapse
|
29
|
In Silico and In Vitro Analyses of Glucosamine and Indole Acetaldehyde Inhibit Pathogenic Regulator Gene phcA of Ralstonia solanacearum, a Causative Agent of Bacterial Wilt of Tomato. Appl Biochem Biotechnol 2020; 192:230-242. [DOI: 10.1007/s12010-020-03328-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
|
30
|
Islam MN, Ali MS, Choi SJ, Park YI, Baek KH. Salicylic Acid-Producing Endophytic Bacteria Increase Nicotine Accumulation and Resistance against Wildfire Disease in Tobacco Plants. Microorganisms 2019; 8:E31. [PMID: 31877906 PMCID: PMC7022923 DOI: 10.3390/microorganisms8010031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/25/2022] Open
Abstract
Endophytic bacteria (EB) are both a novel source of bioactive compounds that confer phytopathogen resistance and inducers of secondary metabolites in host plants. Twenty-seven EB isolated from various parts of Metasequoia glyptostroboides, Ginkgo biloba, Taxus brevifolia, Pinus densiflora, Salix babylonica, and S. chaenomeloides could produce salicylic acid (SA). The highest producers were isolates EB-44 and EB-47, identified as Pseudomonas tremae and Curtobacterium herbarum, respectively. Nicotiana benthamiana grown from EB-44-soaked seeds exhibited a 2.3-fold higher endogenous SA concentration and increased resistance against P. syringae pv. tabaci, the causative agent of tobacco wildfire disease, than plants grown from water-soaked seeds. N benthamiana and N. tabacum grown from EB-44-treated seeds developed 33% and 54% disease lesions, respectively, when infected with P. syringae pv. tabaci, and showed increased height and weight, in addition to 4.6 and 1.4-fold increases in nicotine accumulation, respectively. The results suggest that SA-producing EB-44 can successfully colonize Nicotiana spp., leading to increased endogenous SA production and resistance to tobacco wildfire disease. The newly isolated EB can offer an efficient and eco-friendly solution for controlling wildfire disease and nicotine accumulation in Nicotiana, with additional application for other important crops to increase both productivity and the generation of bioactive compounds.
Collapse
Affiliation(s)
- Md. Nurul Islam
- Soil Resource Development Institute, Regional Office, Rajshahi 6000, Bangladesh;
| | - Md. Sarafat Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea;
| | - Seong-Jin Choi
- Department of Biotechnology, Catholic University of Daegu, Gyeongsan 38430, Korea;
| | - Youn-Il Park
- College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon 34134, Korea;
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea;
| |
Collapse
|
31
|
Leveau JH. A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome. Curr Opin Microbiol 2019; 49:41-49. [PMID: 31707206 DOI: 10.1016/j.mib.2019.10.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023]
Abstract
The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.
Collapse
Affiliation(s)
- Johan Hj Leveau
- Department of Plant Pathology, University of California, Davis, CA 95616, USA.
| |
Collapse
|