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Zhou H, Jia S, Gao Y, Li X, Lin Y, Yang F, Ni K. Characterization of phyllosphere endophytic lactic acid bacteria reveals a potential novel route to enhance silage fermentation quality. Commun Biol 2024; 7:117. [PMID: 38253824 PMCID: PMC10803313 DOI: 10.1038/s42003-024-05816-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The naturally attached phyllosphere microbiota play a crucial role in plant-derived fermentation, but the structure and function of phyllosphere endophytes remain largely unidentified. Here, we reveal the diversity, specificity, and functionality of phyllosphere endophytes in alfalfa (Medicago sativa L.) through combining typical microbial culture, high-throughput sequencing, and genomic comparative analysis. In comparison to phyllosphere bacteria (PB), the fermentation of alfalfa solely with endophytes (EN) enhances the fermentation characteristics, primarily due to the dominance of specific lactic acid bacteria (LAB) such as Lactiplantibacillus, Weissella, and Pediococcus. The inoculant with selected endophytic LAB strains also enhances the fermentation quality compared to epiphytic LAB treatment. Especially, one key endophytic LAB named Pediococcus pentosaceus EN5 shows enrichment of genes related to the mannose phosphotransferase system (Man-PTS) and carbohydrate-metabolizing enzymes and higher utilization of carbohydrates. Representing phyllosphere, endophytic LAB shows great potential of promoting ensiling and provides a novel direction for developing microbial inoculant.
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Affiliation(s)
- Hongzhang Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yu Gao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanli Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Compant S, Cambon MC, Vacher C, Mitter B, Samad A, Sessitsch A. The plant endosphere world - bacterial life within plants. Environ Microbiol 2020; 23:1812-1829. [PMID: 32955144 DOI: 10.1111/1462-2920.15240] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/11/2020] [Accepted: 09/16/2020] [Indexed: 12/23/2022]
Abstract
The plant endosphere is colonized by complex microbial communities and microorganisms, which colonize the plant interior at least part of their lifetime and are termed endophytes. Their functions range from mutualism to pathogenicity. All plant organs and tissues are generally colonized by bacterial endophytes and their diversity and composition depend on the plant, the plant organ and its physiological conditions, the plant growth stage as well as on the environment. Plant-associated microorganisms, and in particular endophytes, have lately received high attention, because of the increasing awareness of the importance of host-associated microbiota for the functioning and performance of their host. Some endophyte functions are known from mostly lab assays, genome prediction and few metagenome analyses; however, we have limited understanding on in planta activities, particularly considering the diversity of micro-environments and the dynamics of conditions. In our review, we present recent findings on endosphere environments, their physiological conditions and endophyte colonization. Furthermore, we discuss microbial functions, the interaction between endophytes and plants as well as methodological limitations of endophyte research. We also provide an outlook on needs of future research to improve our understanding on the role of microbiota colonizing the endosphere on plant traits and ecosystem functioning.
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Affiliation(s)
- Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | | | | | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
| | - Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, G1V4C7, Canada
| | - Angela Sessitsch
- Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, AIT Austrian Institute of Technology, Tulln, A-3430, Austria
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Liu Y, Shang L, Zhan Y, Lin M, Liu Z, Yan Y. Genome-Wide Analysis of Sugar Transporters Identifies the gtsA Gene for Glucose Transportation in Pseudomonas stutzeri A1501. Microorganisms 2020; 8:microorganisms8040592. [PMID: 32325908 PMCID: PMC7232493 DOI: 10.3390/microorganisms8040592] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/15/2020] [Accepted: 04/18/2020] [Indexed: 11/16/2022] Open
Abstract
Pseudomonas stutzeri A1501 possesses an extraordinary number of transporters which confer this rhizosphere bacterium with the sophisticated ability to metabolize various carbon sources. However, sugars are not a preferred carbon source for P. stutzeri A1501. The P. stutzeri A1501 genome has been sequenced, allowing for the homology-based in silico identification of genes potentially encoding sugar-transport systems by using established microbial sugar transporters as a template sequence. Genomic analysis revealed that there were 10 sugar transporters in P. stutzeri A1501, most of which belong to the ATP-binding cassette (ABC) family (5/10); the others belong to the phosphotransferase system (PTS), major intrinsic protein (MIP) family, major facilitator superfamily (MFS) and the sodium solute superfamily (SSS). These systems might serve for the import of glucose, galactose, fructose and other types of sugar. Growth analysis showed that the only effective medium was glucose and its corresponding metabolic system was relatively complete. Notably, the loci of glucose metabolism regulatory systems HexR, GltR/GtrS, and GntR were adjacent to the transporters ABCMalEFGK, ABCGtsABCD, and ABCMtlEFGK, respectively. Only the ABCGtsABCD expression was significantly upregulated under both glucose-sufficient and -limited conditions. The predicted structure and mutant phenotype data of the key protein GtsA provided biochemical evidence that P. stutzeri A1501 predominantly utilized the ABCGtsABCD transporter for glucose uptake. We speculate that gene absence and gene diversity in P. stutzeri A1501 was caused by sugar-deficient environmental factors and hope that this report can provide guidance for further analysis of similar bacterial lifestyles.
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Affiliation(s)
- Yaqun Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Liguo Shang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Yuhua Zhan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
| | - Zhu Liu
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570100, China;
- Correspondence: (Z.L.); (Y.Y.)
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (L.S.); (Y.Z.); (M.L.)
- Correspondence: (Z.L.); (Y.Y.)
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Mahmood A, Takagi K, Ito K, Kataoka R. Changes in endophytic bacterial communities during different growth stages of cucumber (Cucumis sativus L.). World J Microbiol Biotechnol 2019; 35:104. [PMID: 31236765 DOI: 10.1007/s11274-019-2676-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/15/2019] [Indexed: 10/26/2022]
Abstract
Endophytic bacterial diversity in plants presents the level of interaction between culturable and non-culturable endophytic bacteria, thereby providing an appropriate insight into the endophytic environment. This study was conducted to determine the trend of culturable and non-culturable endophytic bacteria at two different sites encompassing four consecutive growth stages. For culturable endophytic bacteria, isolation was carried out using the dilution plate technique, and the obtained colonies were compared using PCR-restriction fragment length polymorphism (RFLP). Different RFLP-types were identified to their nearest neighbour using 16S rRNA sequencing. The non-culturable endophytic bacterial diversity was obtained by next generation sequencing. Results suggested a similar trend among the culturable and non-culturable bacteria for observed operational taxonomic units and diversity indices. It is noticeable that the endophytic bacteria inhabiting in stage 1 disappeared, and instead, different endophytic bacteria appeared. Moreover, the temporal persistence of certain culturable and non-culturable bacteria was also observed. In conclusion, the endophytic bacterial diversity in cucumber initially increased with the plant growth and then decreased at a later stage. Furthermore, it was suggested that plants regulate the number and diversity of endophytes throughout the lifecycle of plants.
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Affiliation(s)
- Ahmad Mahmood
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda, Kofu, Yamanashi, Japan
| | - Kazuhiro Takagi
- NARO Division of Hazardous Chemicals, Institute for Agro-Environmental Sciences, Kannondai, Tsukuba, Ibaraki, Japan
| | - Koji Ito
- NARO Division of Hazardous Chemicals, Institute for Agro-Environmental Sciences, Kannondai, Tsukuba, Ibaraki, Japan
| | - Ryota Kataoka
- Department of Environmental Sciences, Faculty of Life and Environmental Sciences, University of Yamanashi, Takeda, Kofu, Yamanashi, Japan.
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Mercado-Blanco J, Alós E, Rey MD, Prieto P. Pseudomonas fluorescens PICF7 displays an endophytic lifestyle in cultivated cereals and enhances yield in barley. FEMS Microbiol Ecol 2016; 92:fiw092. [PMID: 27130938 DOI: 10.1093/femsec/fiw092] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2016] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas fluorescens PICF7, an indigenous inhabitant of olive roots, displays an endophytic lifestyle in this woody crop and exerts biocontrol against the fungal phytopathogen Verticillium dahliae Here we report microscopy evidence that the strain PICF7 is also able to colonize and persist on or in wheat and barley root tissues. Root colonization of both cereal species followed a similar pattern to that previously reported in olive, including inner colonization of the root hairs. This demonstrates that strain PICF7 can colonize root systems of distant botanical species. Barley plants germinated from PICF7-treated seeds showed enhanced vegetative growth. Moreover, significant increases in the number of grains (up to 19.5%) and grain weight (up to 20.5%) per plant were scored in this species. In contrast, growth and yield were not significantly affected in wheat plants by the presence of PICF7. Proteomics analysis of the root systems revealed that different proteins were exclusively found depending on the presence or absence of PICF7 and only one protein with hydrogen ion transmembrane transporter activity was exclusively found in both PICF7-inoculated barley and wheat plants but not in the controls.
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Affiliation(s)
- Jesús Mercado-Blanco
- Departments of Crop Protection, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda Menéndez Pidal s/n, Campus Alameda del Obispo s/n, E-14004 Córdoba, Spain
| | - Enriqueta Alós
- Plant Breeding, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda Menéndez Pidal s/n, Campus Alameda del Obispo s/n, E-14004 Córdoba, Spain
| | - María Dolores Rey
- Plant Breeding, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda Menéndez Pidal s/n, Campus Alameda del Obispo s/n, E-14004 Córdoba, Spain
| | - Pilar Prieto
- Plant Breeding, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Avda Menéndez Pidal s/n, Campus Alameda del Obispo s/n, E-14004 Córdoba, Spain
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Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TYS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 2015; 6:1118. [PMID: 26528266 PMCID: PMC4604316 DOI: 10.3389/fmicb.2015.01118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
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Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Alisha G Campbell
- Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA
| | - Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Se-Ran Jun
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Rebecca E Parales
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Watumesa A Tan
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - David W Ussery
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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