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Gruet C, Alaoui M, Gerin F, Prigent-Combaret C, Börner A, Muller D, Moënne-Loccoz Y. Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2023; 46:3933-3948. [PMID: 37614118 DOI: 10.1111/pce.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maroua Alaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Javal M, Terblanche JS, Benoit L, Conlong DE, Lloyd JR, Smit C, Chapuis MP. Does Host Plant Drive Variation in Microbial Gut Communities in a Recently Shifted Pest? MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02100-x. [PMID: 35997797 DOI: 10.1007/s00248-022-02100-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Biotic interactions can modulate the responses of organisms to environmental stresses, including diet changes. Gut microbes have substantial effects on diverse ecological and evolutionary traits of their hosts, and microbial communities can be highly dynamic within and between individuals in space and time. Modulations of the gut microbiome composition and their potential role in the success of a species to maintain itself in a new environment have been poorly studied to date. Here we examine this question in a large wood-boring beetle Cacosceles newmannii (Cerambycidae), that was recently found thriving on a newly colonized host plant. Using 16S metabarcoding, we assessed the gut bacterial community composition of larvae collected in an infested field and in "common garden" conditions, fed under laboratory-controlled conditions on four either suspected or known hosts (sugarcane, tea tree, wattle, and eucalyptus). We analysed microbiome variation (i.e. diversity and differentiation), measured fitness-related larval growth, and studied host plant lignin and cellulose contents, since their degradation is especially challenging for wood-boring insects. We show that sugarcane seems to be a much more favourable host for larval growth. Bacterial diversity level was the highest in field-collected larvae, whereas lab-reared larvae fed on sugarcane showed a relatively low level of diversity but very specific bacterial variants. Bacterial communities were mainly dominated by Proteobacteria, but were significantly different between sugarcane-fed lab-reared larvae and any other hosts or field-collected larvae. We identified changes in the gut microbiome associated with different hosts over a short time frame, which support the hypothesis of a role of the microbiome in host switches.
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Affiliation(s)
- Marion Javal
- Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa.
- Current Address: CEFE, Univ Montpellier, CNRS, EPHE, Montpellier, IRD, France.
| | - John S Terblanche
- Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
| | - Laure Benoit
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France
| | - Desmond E Conlong
- Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
- South African Sugarcane Research Institute, Mount Edgecombe, South Africa
| | - James R Lloyd
- Institute for Plant Biotechnology, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Chantelle Smit
- Department of Conservation Ecology & Entomology, Faculty of AgriSciences, Stellenbosch University, Stellenbosch, South Africa
| | - Marie-Pierre Chapuis
- CBGP, Cirad, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France
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Vandana UK, Rajkumari J, Singha LP, Satish L, Alavilli H, Sudheer PD, Chauhan S, Ratnala R, Satturu V, Mazumder PB, Pandey P. The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion. BIOLOGY 2021; 10:101. [PMID: 33535706 PMCID: PMC7912845 DOI: 10.3390/biology10020101] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in 'omic' technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.
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Affiliation(s)
- Udaya Kumar Vandana
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Jina Rajkumari
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - L. Paikhomba Singha
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
| | - Lakkakula Satish
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the Ilse Katz Center for Meso and Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel;
- The Albert Katz International School for Desert Studies, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Hemasundar Alavilli
- Department of Biochemistry and Molecular Biology, College of Medicine, Korea Molecular Medicine and Nutrition Research Institute, Korea University, Seoul 02841, Korea;
| | - Pamidimarri D.V.N. Sudheer
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Sushma Chauhan
- Amity Institute of Biotechnology, Amity University Chhattisgarh, Raipur 493225, India; (P.D.V.N.S.); (S.C.)
| | - Rambabu Ratnala
- TATA Institute for Genetics and Society, Bangalore 560065, India;
| | - Vanisri Satturu
- Institute of Biotechnology, Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad 500030, India;
| | - Pranab Behari Mazumder
- Department of Biotechnology, Assam University Silchar, Assam 788011, India; (U.K.V.); (P.B.M.)
| | - Piyush Pandey
- Department of Microbiology, Assam University Silchar, Assam 788011, India; (J.R.); (L.P.S.)
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Valadares RV, Costa MD, Neves JCL, Vieira Netto JAF, Silva IRD, Moro E, Alves MR, Fernandes LA. Rhizosphere microbiological processes and eucalypt nutrition: Synthesis and conceptualization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:141305. [PMID: 32771762 DOI: 10.1016/j.scitotenv.2020.141305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/15/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
In this review, we present the state of art regarding rhizosphere effects on eucalypt plantations. It provides a greater understanding of carbon (C) and nitrogen (N) turnover in forest soils. P organic hydrolysis, soil mineral solubilization, indoleacetic acid, gibberellin, resistance factors, and production of siderophores by rhizosphere microbial populations help to explain the tolerance of Eucalyptus plants to biotic and abiotic stresses and the apparent steady-state condition of C and N soil stocks in many planted forests. This work aims to present the main findings on Eucalyptus rhizosphere processes and highlights their importance for trees nutrition, especially for N mineralization triggered by microbial activation or microbial community structure changes regarding the so-called rhizosphere priming effect and N fixation. Furthermore, we present an explanatory conceptual model of the steady-state condition for soil organic matter (SOM) stocks and its relation with fertilization based on a nutrient balance model. This review also considers the main experimental and modeling studies that demonstrate the quantitative importance of rhizosphere processes to Eucalyptus genus and their shortcomings. This provides a framework for process modeling under scenarios of global climate change. A better understanding of rhizosphere microbiological processes may allow improvements in Eucalyptus nutrition and production, as well as in accurate long-term estimates of SOM stocks and C-CO2 exchanges between forest soils and the atmosphere.
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Affiliation(s)
- Rafael V Valadares
- Universidade Federal de Viçosa, Departamento de Solos, Viçosa, Minas Gerais CEP: 36570-900, Brazil.
| | - Maurício D Costa
- Universidade Federal de Viçosa, Departamento de Microbiologia, Viçosa, Minas Gerais CEP: 36570-900, Brazil; Bolsista Pesquisador do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
| | - Júlio César L Neves
- Universidade Federal de Viçosa, Departamento de Solos, Viçosa, Minas Gerais CEP: 36570-900, Brazil
| | - João A F Vieira Netto
- Universidade Federal de Viçosa, Departamento de Microbiologia, Viçosa, Minas Gerais CEP: 36570-900, Brazil
| | - Ivo Ribeiro da Silva
- Universidade Federal de Viçosa, Departamento de Solos, Viçosa, Minas Gerais CEP: 36570-900, Brazil
| | - Edemar Moro
- Universidade do Oeste Paulista, Presidente Prudente, São Paulo CEP: 19050-920, Brazil
| | - Marcelo Rodrigo Alves
- Universidade do Oeste Paulista, Presidente Prudente, São Paulo CEP: 19050-920, Brazil
| | - Luiz Arnaldo Fernandes
- Universidade Federal de Minas Gerais, Instituto de Ciências Agrárias, Montes Claros CEP: 39404-547, Brazil; Bolsista Pesquisador do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
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Li Y, Kong Y, Teng D, Zhang X, He X, Zhang Y, Lv G. Rhizobacterial communities of five co-occurring desert halophytes. PeerJ 2018; 6:e5508. [PMID: 30186688 PMCID: PMC6119601 DOI: 10.7717/peerj.5508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/02/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Recently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas. METHODS Five halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3-V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed. RESULTS Significant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity of Halostachys caspica, Halocnemum strobilaceum and Kalidium foliatum associated bacterial communities was lower than that of Limonium gmelinii and Lycium ruthenicum communities. Furthermore, the composition of the bacterial communities of Halostachys caspica and Halocnemum strobilaceum was very different from those of Limonium gmelinii and Lycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients. DISCUSSION Halophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.
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Affiliation(s)
- Yan Li
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, China
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
- Ecology Post-doctoral Research Station, Xinjiang University, Urumqi, Xinjiang, China
| | - Yan Kong
- School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, China
- SJTU-Yale Joint Center for Biostistics, Shanghai Jiaotong University, Shanghai, China
| | - Dexiong Teng
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
| | - Xueni Zhang
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, China
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
| | - Xuemin He
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, China
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
| | - Yang Zhang
- College of Resource and Environment Sciences, Xinjiang University, Urumqi, Xinjiang, China
| | - Guanghui Lv
- Key Laboratory of Oasis Ecology of Education Ministry, Xinjiang University, Urumqi, Xinjiang, China
- Institute of Arid Ecology and Environment, Xinjiang University, Urumqi, Xinjiang, China
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Oh SY, Fong JJ, Park MS, Lim YW. Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil. PLoS One 2016; 11:e0168573. [PMID: 27977803 PMCID: PMC5158061 DOI: 10.1371/journal.pone.0168573] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/03/2016] [Indexed: 02/01/2023] Open
Abstract
Tricholoma matsutake, the pine mushroom, is a valuable forest product with high economic value in Asia, and plays an important ecological role as an ectomycorrhizal fungus. Around the host tree, T. matsutake hyphae generate a distinctive soil aggregating environment called a fairy ring, where fruiting bodies form. Because T. matsutake hyphae dominate the soil near the fairy ring, this species has the potential to influence the microbial community. To explore the influence of T. matsutake on the microbial communities, we compared the microbial community and predicted bacterial function between two different soil types-T. matsutake dominant and T. matsutake minor. DNA sequence analyses showed that fungal and bacterial diversity were lower in the T. matsutake dominant soil compared to T. matsutake minor soil. Some microbial taxa were significantly more common in the T. matsutake dominant soil across geographic locations, many of which were previously identified as mycophillic or mycorrhiza helper bacteria. Between the two soil types, the predicted bacterial functional profiles (using PICRUSt) had significantly distinct KEGG modules. Modules for amino acid uptake, carbohydrate metabolism, and the type III secretion system were higher in the T. matsutake dominant soil than in the T. matsutake minor soil. Overall, similar microbial diversity, community structure, and bacterial functional profiles of the T. matsutake dominant soil across geographic locations suggest that T. matsutake may generate a dominance effect.
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Affiliation(s)
- Seung-Yoon Oh
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jonathan J. Fong
- Science Unit, Lingnan University, Tuen Mun, New Territories, Hong Kong
| | - Myung Soo Park
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
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Identification and characterization of endophytic bacteria isolated from in vitro cultures of peach and pear rootstocks. 3 Biotech 2016; 6:120. [PMID: 28330195 PMCID: PMC4909027 DOI: 10.1007/s13205-016-0442-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/25/2016] [Indexed: 11/16/2022] Open
Abstract
Endophytes are microorganisms which live symbiotically with almost all varieties of plant and in turn helping the plant in a number of ways. Instead of satisfactory surface sterilization approaches, repeatedly occurring bacterial growth on in vitro rootstock cultures of peach and pear was identified and isolated as endophytic bacteria in our present study. Five different isolates from peach rootstocks were molecularly identified by 16S rRNA gene sequencing as Brevundimonas diminuta, Leifsonia shinshuensis, Sphingomonas parapaucimobilis Brevundimonas vesicularis, Agrobacterium tumefaciens while two endophytic isolates of pear were identified as Pseudoxanthomonas mexicana, and Stenotrophomonas rhizophilia. Identified endophytes were also screened for their potential of plant growth promotion according to indoleacetic acid (IAA) production, nitrogen fixation, solubilization of phosphate and production of siderophore. All seven endophytic isolates have shown positive results for IAA, nitrogen fixation and phosphate solubilization tests. However, two out of seven isolates showed positive results for siderophore production. On the basis of these growth promoting competences, isolated endophytes can be presumed to have significant influence on the growth of host plants. Future studies required to determine the antimicrobial susceptibility profile and potential application of these isolates in biological control, microbial biofertilizers and degradative enzyme production.
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Communities of endophytic microorganisms in different developmental stages from a local variety as well as transgenic and conventional isogenic hybrids of maize. World J Microbiol Biotechnol 2016; 32:189. [PMID: 27696288 DOI: 10.1007/s11274-016-2149-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 09/24/2016] [Indexed: 01/06/2023]
Abstract
The diversity of endophytic microorganisms may change due to the genotype of the host plant and its phenological stage. In this study we evaluated the effect of phenological stage, transgenes and genetic composition of maize on endophytic bacterial and fungal communities. The maize populations were composed of a local variety named Rosado (RS) and three isogenic hybrids. One isogenic hybrid was not genetically modified (NGM). Another hybrid (Hx) contained the transgenes cry1F and pat (T1507 event), which provide resistance to insects of the order Lepidoptera and tolerance to the glufosinate-ammonium herbicide, respectively. The third hybrid (Hxrr) contained the transgene cp4 epsps (NK603 event) combined with the transgenes cry1F and pat (T1507 event), which allow tolerance to the Roundup Ready herbicide, besides the characteristics of Hx. Evaluation of the foliar tissue was done through PCR-DGGE analysis, with specific primers for bacteria and fungi within four phenological stages of maize. The endophytic bacteria were only clustered by phenological stages; the structure of the fungal community was clustered by maize genotypes in each phenological stage. The fungal community from the local variety RS was different from the three hybrids (NGM, Hx and Hxrr) within the four evaluated stages. In the reproductive stage, the fungal community from the two transgenic hybrids (Hx and Hxrr) were separated, and the Hxrr was different from NGM, in the two field experiments. This research study showed that the genetic composition of the maize populations, especially the presence of transgenes, is the determining factor for the changes detected in the endophytic fungal community of maize leaves.
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Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage. World J Microbiol Biotechnol 2015; 31:1737-46. [PMID: 26377625 DOI: 10.1007/s11274-015-1924-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
Micropropagation has been applied in the recovery and rejuvenation of adult trees, which is achieved by various subcultures in the multiplication phase. This strategy has brought questions about the endophytic microbiota associated with these plants along its manipulation. Therefore, the aim of this study was to evaluate the composition of the endophytic bacterial communities associated with two explants sources [the canopy branches (CB) and the trunk base of the tree (TB)] under prolonged in vitro cultivation. In addition we analyzed the bacterial community dynamic along the subcultures in different micropropagation phases. Bacterial DNA was extracted from samples of mini-stumps (in vivo) from CB and TB and in micro-stumps produced by in vitro cultivations of these explants sources--both originated from one single matrix plant of Eucalyptus benthamii. In vitro establishment occurred in two dates and the evaluation of endophytic bacterial communities was made in vivo and in vitro samples (on 10th, 13th and 16th subcultures), when elongated shoots and roots were analyzed. Analysis was performed by PCR-DGGE based on the V6 region of ribosomal gene 16S rDNA. Bands profiles showed differences in communities between in vivo and in vitro samples, and also distinctions of communities assessed in the subcultures, elongated and rooted samples. Distinctions in the composition of endophytic bacterial communities were greater in CB micro-stumps. These results indicate a differential colonization of explants by endophytic bacteria, with predominance of common (ever-present) endophytes in TB samples and casual, here named opportunistic, in CB samples.
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Bacterial communities in the rhizosphere of Vitis vinifera L. cultivated under distinct agricultural practices in Argentina. Antonie van Leeuwenhoek 2014; 107:575-88. [PMID: 25527391 DOI: 10.1007/s10482-014-0353-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 12/08/2014] [Indexed: 10/24/2022]
Abstract
Plants interact with a myriad of microbial cells in the rhizosphere, an environment that is considered to be important for plant development. However, the differential structuring of rhizosphere microbial communities due to plant cultivation under differential agricultural practices remains to be described for most plant species. Here we describe the rhizosphere microbiome of grapevine cultivated under conventional and organic practices, using a combination of cultivation-independent approaches. The quantification of bacterial 16S rRNA and nifH genes, by quantitative PCR (qPCR), revealed similar amounts of these genes in the rhizosphere in both vineyards. PCR-DGGE was used to detect differences in the structure of bacterial communities, including both the complete whole communities and specific fractions, such as Alphaproteobacteria, Betaproteobacteria, Actinobacteria, and those harboring the nitrogen-fixing related gene nifH. When analyzed by a multivariate approach (redundancy analysis), the shifts observed in the bacterial communities were poorly explained by variations in the physical and chemical characteristics of the rhizosphere. These approaches were complemented by high-throughput sequencing (67,830 sequences) based on the V6 region of the 16S rRNA gene, identifying the major bacterial groups present in the rhizosphere of grapevines: Proteobacteria, Actinobacteria, Firmicutes, Bacteriodetes, Acidobacteria, Cloroflexi, Verrucomicrobia and Planctomycetes, which occur in distinct proportions in the rhizosphere from each vineyard. The differences might be related to the selection of plant metabolism upon distinct reservoirs of microbial cells found in each vineyard. The results fill a gap in the knowledge of the rhizosphere of grapevines and also show distinctions in these bacterial communities due to agricultural practices.
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Characterization of rhizosphere and endophytic bacterial communities from leaves, stems and roots of medicinal Stellera chamaejasme L. Syst Appl Microbiol 2014; 37:376-85. [PMID: 24958606 DOI: 10.1016/j.syapm.2014.05.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/22/2022]
Abstract
A diverse array of bacteria that inhabit the rhizosphere and different plant organs play a crucial role in plant health and growth. Therefore, a general understanding of these bacterial communities and their diversity is necessary. Using the 16S rRNA gene clone library technique, the bacterial community structure and diversity of the rhizosphere and endophytic bacteria in Stellera chamaejasme compartments were compared and clarified for the first time. Grouping of the sequences obtained showed that members of the Proteobacteria (43.2%), Firmicutes (36.5%) and Actinobacteria (14.1%) were dominant in both samples. Other groups that were consistently found, albeit at lower abundance, were Bacteroidetes (2.1%), Chloroflexi (1.9%), and Cyanobacteria (1.7%). The habitats (rhizosphere vs endophytes) and organs (leaf, stem and root) structured the community, since the Wilcoxon signed rank test indicated that more varied bacteria inhabited the rhizosphere compared to the organs of the plant. In addition, correspondence analysis also showed that differences were apparent in the bacterial communities associated with these distinct habitats. Moreover, principal component analysis revealed that the profiles obtained from the rhizosphere and roots were similar, whereas leaf and stem samples clustered together on the opposite side of the plot from the rhizosphere and roots. Taken together, these results suggested that, although the communities associated with the rhizosphere and organs shared some bacterial species, the associated communities differed in structure and diversity.
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de Melo Pereira GV, Magalhães KT, Lorenzetii ER, Souza TP, Schwan RF. A multiphasic approach for the identification of endophytic bacterial in strawberry fruit and their potential for plant growth promotion. MICROBIAL ECOLOGY 2012; 63:405-17. [PMID: 21837472 DOI: 10.1007/s00248-011-9919-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 07/18/2011] [Indexed: 05/12/2023]
Abstract
This study used a multiphasic approach, characterized by the simultaneous use of culture-dependent and culture-independent methods, to investigate endophytic bacterial communities in strawberry (Fragaria ananassa) fruit. A total of 92 bacterial endophytes were isolated and initially grouped by their repetitive extragenic palindromic (rep)-PCR banding pattern and biochemical features. Phylogenetic analysis of the 16S rRNA gene sequences of 45 representatives showed that the isolates belonged to the species Bacillus subtilis (eight isolates), Bacillus sp. (seven isolates), Enterobacter sp. (seven isolates), Enterobacter ludwigii (six isolates), Lactobacillus plantarum (six isolates), Pseudomonas sp. (five isolates), Pantoea punctata (three isolates), and Curtobacterium citreum (three isolates). Nucleic acids were extracted from the strawberry fruit and subjected to 16S rRNA gene directed polymerase chain reaction denaturing gradient gel electrophoresis (16S rRNA PCR-DGGE). The species B. subtilis, Enterobacter sp., and Pseudomonas sp. were detected both by isolation and DGGE. The DGGE fingerprints of total bacterial DNA did not exhibit bands corresponding to several of the representative species isolated in the extinction dilution (L. plantarum, C. citreum, and P. punctata). In contrast, bands in the DGGE profile that were identified as relatives of Arthrobacter sp. and one uncultivable Erythrobacter sp. were not recovered by cultivation techniques. After isolation, the nitrogen fixation ability and the in vitro production of indole-3-acetic acid (IAA) equivalents and siderophores were evaluated. A high percentage of isolates were found to possess the ability to produce siderophores and IAA equivalents; however, only a few isolates belonging to the genera Pseudomonas and Enterobacter showed the ability to fix nitrogen. Plant growth promotion was evaluated under greenhouse conditions and revealed the ability of the Bacillus strains to enhance the number of leaves, shoot length, root dry weight, and shoot dry weight. The activity of the bacterial isolate identified as B. subtilis NA-108 exerted the greatest influence on strawberry growth and showed a 42.8% increase in number of leaves, 15.26% for high shoot, 43.5% increase in root dry weight, and a 77% increase in shoot dry weight when compared with untreated controls.
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Vieira PDDS, Motta CMDS, Lima D, Torres JB, Quecine MC, Azevedo JL, Oliveira NTD. Endophytic fungi associated with transgenic and non-transgenic cotton. Mycology 2011. [DOI: 10.1080/21501203.2011.584390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
| | | | - Débora Lima
- a Department of Mycology , Federal University of Pernambuco (UFPE) , Recife, Brazil
| | - Jorge Braz Torres
- b Departament of Agronomy , Federal Rural University of Pernambuco (UFRPE) , Recife, Brazil
| | - Maria Carolina Quecine
- c Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz” , University of São Paulo , Piracicaba, Brazil
| | - João Lúcio Azevedo
- c Departament of Genetics, Escola Superior de Agricultura “Luiz de Queiroz” , University of São Paulo , Piracicaba, Brazil
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Effect of bacterial inoculation, plant genotype and developmental stage on root-associated and endophytic bacterial communities in potato (Solanum tuberosum). Antonie van Leeuwenhoek 2010; 97:389-99. [PMID: 20352404 PMCID: PMC2847171 DOI: 10.1007/s10482-010-9421-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/08/2010] [Indexed: 11/21/2022]
Abstract
Beneficial bacteria interact with plants by colonizing the rhizosphere and roots followed by further spread through the inner tissues, resulting in endophytic colonization. The major factors contributing to these interactions are not always well understood for most bacterial and plant species. It is believed that specific bacterial functions are required for plant colonization, but also from the plant side specific features are needed, such as plant genotype (cultivar) and developmental stage. Via multivariate analysis we present a quantification of the roles of these components on the composition of root-associated and endophytic bacterial communities in potato plants, by weighing the effects of bacterial inoculation, plant genotype and developmental stage. Spontaneous rifampicin resistant mutants of two bacterial endophytes, Paenibacillus sp. strain E119 and Methylobacterium mesophilicum strain SR1.6/6, were introduced into potato plants of three different cultivars (Eersteling, Robijn and Karnico). Densities of both strains in, or attached to potato plants were measured by selective plating, while the effects of bacterial inoculation, plant genotype and developmental stage on the composition of bacterial, Alphaproteobacterial and Paenibacillus species were determined by PCR-denaturing gradient gel-electrophoresis (DGGE). Multivariate analyses revealed that the composition of bacterial communities was mainly driven by cultivar type and plant developmental stage, while Alphaproteobacterial and Paenibacillus communities were mainly influenced by bacterial inoculation. These results are important for better understanding the effects of bacterial inoculations to plants and their possible effects on the indigenous bacterial communities in relation with other plant factors such as genotype and growth stage.
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Abreu-Tarazi MF, Navarrete AA, Andreote FD, Almeida CV, Tsai SM, Almeida M. Endophytic bacteria in long-term in vitro cultivated “axenic” pineapple microplants revealed by PCR–DGGE. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0191-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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