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Wei Y, Chen S, Zhou X, Ding D, Song J, Yang S. Endophytic Microorganisms in Tomato Roots, Changes in the Structure and Function of the Community at Different Growing Stages. Microorganisms 2024; 12:1251. [PMID: 38930633 PMCID: PMC11206058 DOI: 10.3390/microorganisms12061251] [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: 04/23/2024] [Revised: 05/20/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
This study analyzed flower bud differentiation and fruiting stages to investigate how the structure of the plant endophytic microbial community in the roots of tomatoes changes with plant senescence. Based on high-throughput sequencing technology, the diversity and relative abundance of endophytic microorganisms (bacteria and fungi) in tomato stems at different growth stages were analyzed. At the same time, based on LEfSe analysis, the differences in endophytic microorganisms in tomato stems at different growth stages were studied. Based on PICRUSt2 function prediction and FUNGuild, we predicted the functions of endophytic bacterial and fungal communities in tomato stems at different growth stages to explore potential microbial functional traits. The results demonstrated that not only different unique bacterial genera but also unique fungal genera could be found colonizing tomato roots at different growth stages. In tomato seedlings, flower bud differentiation, and fruiting stages, the functions of colonizing endophytes in tomato roots could primarily contribute to the promotion of plant growth, stress resistance, and improvement in nutrient cycling, respectively. These results also suggest that different functional endophytes colonize tomato roots at different growth stages.
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Affiliation(s)
- Yufei Wei
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Siyu Chen
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Xinyan Zhou
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Diancao Ding
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
| | - Jingjing Song
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535011, China
| | - Shangdong Yang
- Guangxi Key Laboratory of Agro-Environment and Agro-Products Safety, National Demonstration Center for Experimental Plant Science Education, Guangxi Agricultural College, Guangxi University, Nanning 530004, China; (Y.W.); (S.C.); (X.Z.); (D.D.)
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Vergine M, Vita F, Casati P, Passera A, Ricciardi L, Pavan S, Aprile A, Sabella E, De Bellis L, Luvisi A. Characterization of the olive endophytic community in genotypes displaying a contrasting response to Xylella fastidiosa. BMC PLANT BIOLOGY 2024; 24:337. [PMID: 38664617 PMCID: PMC11044560 DOI: 10.1186/s12870-024-04980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
Abstract
BACKGROUND Endophytes mediate the interactions between plants and other microorganisms, and the functional aspects of interactions between endophytes and their host that support plant-growth promotion and tolerance to stresses signify the ecological relevance of the endosphere microbiome. In this work, we studied the bacterial and fungal endophytic communities of olive tree (Olea europaea L.) asymptomatic or low symptomatic genotypes sampled in groves heavily compromised by Xylella fastidiosa subsp. pauca, aiming to characterize microbiota in genotypes displaying differential response to the pathogen. RESULTS The relationships between bacterial and fungal genera were analyzed both separately and together, in order to investigate the intricate correlations between the identified Operational Taxonomic Units (OTUs). Results suggested a dominant role of the fungal endophytic community compared to the bacterial one, and highlighted specific microbial taxa only associated with asymptomatic or low symptomatic genotypes. In addition, they indicated the occurrence of well-adapted genetic resources surviving after years of pathogen pressure in association with microorganisms such as Burkholderia, Quambalaria, Phaffia and Rhodotorula. CONCLUSIONS This is the first study to overview endophytic communities associated with several putatively resistant olive genotypes in areas under high X. fastidiosa inoculum pressure. Identifying these negatively correlated genera can offer valuable insights into the potential antagonistic microbial resources and their possible development as biocontrol agents.
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Affiliation(s)
- Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Federico Vita
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.
| | - Paola Casati
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences, Production, Landscape, Agroenergy, University of Milan, Milano, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Bari, Italy
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Fu X, Ma Y, Wang D, Zhan L, Guo Z, Fan K, Yang T, Chu H. Long-term chemical fertilization results in a loss of temporal dynamics of diazotrophic communities in the wheat rhizosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162663. [PMID: 36894087 DOI: 10.1016/j.scitotenv.2023.162663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Diazotrophs are potential bacterial biofertilizers with efficacy for plant nutrition, which convert atmospheric N2 into plant available nitrogen. Although they are known to respond strongly to fertilization, little is known about the temporal dynamics of diazotrophic communities throughout plant developmental under different fertilization regimes. In this study, we investigated diazotrophic communities in the wheat rhizosphere at four developmental stages under three long-term fertilization regimes: no fertilizer (Control), chemical NPK fertilizer only (NPK), and NPK fertilizer plus cow manure (NPKM). Fertilization regime had greater effect (explained of 54.9 %) on diazotrophic community structure than developmental stage (explained of 4.8 %). NPK fertilization decreased the diazotrophic diversity and abundance to one-third of the Control, although this was largely recovered by the addition of manure. Meanwhile, Control treatment resulted in significant variation in diazotrophic abundance, diversity, and community structure (P = 0.001) depending on the developmental stage, while the NPK fertilization resulted in the loss of temporal dynamics of the diazotrophic community (P = 0.330), which could be largely recovered by the addition of manure (P = 0.011). Keystone species identified in this study were quite different among the four developmental stages under Control and NPKM treatment but were similar among stages under NPK treatment. These findings suggest that long-term chemical fertilization not only reduces diazotrophic diversity and abundance, but also results in a loss of temporal dynamics of rhizosphere diazotrophic communities.
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Affiliation(s)
- Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Daozhong Wang
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Linchuan Zhan
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Zhibin Guo
- Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province, Soil and Fertilizer Research Institute, Anhui Academy of Agricultural Sciences, 40 South Nongke Road, Hefei 230001, China
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Pino AFS, Espinosa ZYD, Cabrera EVR. Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau. BMC PLANT BIOLOGY 2023; 23:217. [PMID: 37098489 PMCID: PMC10127060 DOI: 10.1186/s12870-023-04182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The microbial biodiversity and the role of microorganisms in the fermentation of washed coffee in Colombia were investigated using the Bourbon and Castillo coffee varieties. DNA sequencing was used to evaluate the soil microbial biota and their contribution to fermentation. The potential benefits of these microorganisms were analyzed, including increased productivity and the need to understand the rhizospheric bacterial species to optimize these benefits. METHODS This study used coffee beans for DNA extraction and 16 S rRNA sequencing. The beans were pulped, samples were stored at 4ºC, and the fermentation process was at 19.5ºC and 24ºC. The fermented mucilage and root-soil samples were collected in duplicate at 0, 12, and 24 h. DNA was extracted from the samples at a concentration of 20 ng/µl per sample, and the data obtained were analyzed using the Mothur platform. RESULTS The study demonstrates that the coffee rhizosphere is a diverse ecosystem composed primarily of microorganisms that cannot be cultured in the laboratory. This suggests that the microbial community may vary depending on the coffee variety and play an essential role in fermentation and overall coffee quality. CONCLUSIONS The study highlights the importance of understanding and optimizing the microbial diversity in coffee production, which could have implications for the sustainability and success of coffee production. DNA sequencing techniques can help characterize the structure of the soil microbial biota and evaluate its contribution to coffee fermentation. Finally, further research is needed to fully understand the biodiversity of coffee rhizospheric bacteria and their role.
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Affiliation(s)
- Andrés Felipe Solis Pino
- Corporación Universitaria Comfacauca - Unicomfacauca, Cl. 4 N. 8-30, Popayán, Cauca, 190001, Colombia.
| | | | - Efren Venancio Ramos Cabrera
- Corporación Universitaria Comfacauca - Unicomfacauca, Cl. 4 N. 8-30, Popayán, Cauca, 190001, Colombia
- Universidad Nacional Abierta y a Distancia - UNAD, Calle 5 # 46N -67, Popayán, Cauca, 190001, Colombia
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Al-Zahrani HS, Moussa TAA, Alsamadany H, Hafez RM, Fuller MP. Phylogenetic and Expression Studies of Small GTP-Binding Proteins in Solanum lycopersicum Super Strain B. PLANTS 2022; 11:plants11050641. [PMID: 35270112 PMCID: PMC8912273 DOI: 10.3390/plants11050641] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 11/16/2022]
Abstract
This investigation involved a comparative analysis of the small GTPase superfamily in S. lycopersicum super strain B compared to their analogues in leguminous and other non-leguminous species. The small GTPases superfamily members were recognized by tBLASTn searches. The sequences of amino acid were aligned using Clustal Omega and the analysis of phylogeny was performed with the MEGA7 package. Protein alignments were applied for all studied species. Three-dimensional models of RABA2, ROP9, and ROP10 from Solanum lycopersicum “Super strain B” were performed. The levels of mRNA of the Rab, Arf, Rop, and Ran subfamilies were detected in aerial tissues vs. roots. Significant divergences were found in the number of members and groups comprising each subfamily of the small GTPases and Glycine max had the highest count. High expression of Rab and Arf proteins was shown in the roots of legumes whilst in non-legume plants, the highest values were recorded in aerial tissues. S. lycopersicum super strain B had the highest expression of Rab and Arf proteins in its aerial tissues, which may indicate that diazotroph strains have supreme activities in the aerial tissues of strain B and act as associated N-fixing bacteria. The phylogenies of the small GTPase superfamily of the studied plants did not reveal asymmetric evolution of the Ra, Arf, Rop, and Ran subfamilies. Multiple sequence alignments derived from each of the Rab, Arf, and Rop proteins of S. lycopersicum super strain B showed a low frequency of substitutions in their domains. GTPases superfamily members have definite functions during infection, delivery, and maintenance of N2-fixing diazotroph but show some alterations in their function among S. lycopersicum super strain B, and other species.
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Affiliation(s)
- Hassan S. Al-Zahrani
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.S.A.-Z.); (H.A.)
| | - Tarek A. A. Moussa
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.S.A.-Z.); (H.A.)
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
- Correspondence: ; Tel.: +20-1001531738
| | - Hameed Alsamadany
- Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.S.A.-Z.); (H.A.)
| | - Rehab M. Hafez
- Botany and Microbiology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
| | - Michael P. Fuller
- School of Biological and Marine Sciences, Faculty of Science and Engineering, University of Plymouth, Drake Circus, Plymouth PL4 8AA, UK;
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Beltran-Garcia MJ, Martínez-Rodríguez A, Olmos-Arriaga I, Valdes-Salas B, Di Mascio P, White JF. Nitrogen fertilization and stress factors drive shifts in microbial diversity in soils and plants. Symbiosis 2021. [DOI: 10.1007/s13199-021-00787-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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