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Gharsallah H, Ksentini I, Frikha-Gargouri O, Hadj Taieb K, Ben Gharsa H, Schuster C, Chatti-Kolsi A, Triki MA, Ksantini M, Leclerque A. Exploring Bacterial and Fungal Biodiversity in Eight Mediterranean Olive Orchards ( Olea europaea L.) in Tunisia. Microorganisms 2023; 11:microorganisms11041086. [PMID: 37110509 PMCID: PMC10145363 DOI: 10.3390/microorganisms11041086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
A wide array of bacteria and fungi are known for their association with pests that impact the health of the olive tree. The latter presents the most economically important cultivation in Tunisia. The microbial diversity associated with olive orchards in Tunisia remains unknown and undetermined. This study investigated microbial diversity to elucidate the microbial interactions that lead to olive disease, and the bio-prospects for potential microbial biocontrol agents associated with insect pests of economic relevance for olive cultivation in the Mediterranean area. Bacterial and fungal isolation was made from soil and olive tree pests. A total of 215 bacterial and fungal strains were randomly isolated from eight different biotopes situated in Sfax (Tunisia), with different management practices. 16S rRNA and ITS gene sequencing were used to identify the microbial community. The majority of the isolated bacteria, Staphylococcus, Bacillus, Alcaligenes, and Providencia, are typical of the olive ecosystem and the most common fungi are Penicillium, Aspergillus, and Cladosporium. The different olive orchards depicted distinct communities, and exhibited dissimilar amounts of bacteria and fungi with distinct ecological functions that could be considered as promising resources in biological control.
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Affiliation(s)
- Houda Gharsallah
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Ines Ksentini
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Olfa Frikha-Gargouri
- Laboratory of Biopesticides, Centre of Biotechnology of Sfax, University of Sfax, Sfax 3038, Tunisia
| | - Karama Hadj Taieb
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Haifa Ben Gharsa
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Christina Schuster
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Amel Chatti-Kolsi
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Mohamed Ali Triki
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Mohieddine Ksantini
- Laboratory of Improvement and Protection of Olive Tree Genetic Resources, Olive Tree Institute, University of Sfax, Sfax 3038, Tunisia
| | - Andreas Leclerque
- Department of Biology, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, 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
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- 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
| | - 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
| | - 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
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Cheng JE, Su P, Zhang ZH, Zheng LM, Wang ZY, Hamid MR, Dai JP, Du XH, Chen LJ, Zhai ZY, Kong XT, Liu Y, Zhang DY. Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods. PLoS One 2022; 17:e0262517. [PMID: 35834536 PMCID: PMC9282544 DOI: 10.1371/journal.pone.0262517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.
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Affiliation(s)
- Ju-E Cheng
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Pin Su
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhan-Hong Zhang
- Hunan Vegetable Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Li-Min Zheng
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Yong Wang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Muhammad Rizwan Hamid
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Jian-Ping Dai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Hua Du
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Li-Jie Chen
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Ying Zhai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Ting Kong
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - De-Yong Zhang
- Hunan Hybrid Rice Research Center, Changsha, China
- * E-mail:
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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: 61] [Impact Index Per Article: 20.3] [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.
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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
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Barraza A, Caamal-Chan MG, Castellanos T, Loera-Muro A. Bacterial community characterization of the rhizobiome of plants belonging to Solanaceae family cultivated in desert soils. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01572-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Abstract
Purpose
The plant Solanaceae family is one of the most important for global agriculture and nutrition. Within this plant family, two plant species stand out for their economic importance and for human consumption, which are tomato (Solanum lycopersicum) and chili pepper (Capsicum annuum). Moreover, those plants support diverse and characteristic microbial communities that are uniquely suited to the plant habitat and intimately connected to plant health. The main objective of this work is the bacterial community characterization in the rhizobiome of tomato and chili pepper, cultivated in arid environments.
Methods
Five crop fields located in the south of the peninsula of Baja California, Mexico, were sampled. Total DNA was extracted from rhizosphere, rhizoplane, and endophytic root compartment and sequenced by Illumina MiniSeq platform technology applied to 16S rRNA gene V3 region.
Results
We were able to obtain 1,195,426 total reads and 1,725,258 total reads for tomato and chili pepper samples, respectively. The analysis of the bacterial community structures confirmed that the two plant species showed differences in their microbial community structures. Nonetheless, the microbial community structures were directly and equally influenced by the crop field localization of each plant species. Interestingly, we determined that in both plant species, the Proteobacteria was the main phylum.
Conclusion
In conclusion, we found that several bacterial families are part of the core rhizobiome (28 OTUs) for both tomato and chili pepper, but the most abundant were the Pseudomonadaceae family and the Pseudomonas genus, which most probably play a pivotal role in the microbial ecology to benefit both crop plants.
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Yadav AN, Singh J, Rastegari AA, Yadav N. Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications. ACTA ACUST UNITED AC 2020. [PMCID: PMC7123684 DOI: 10.1007/978-3-030-38453-1_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.
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Affiliation(s)
- Ajar Nath Yadav
- Department of Biotechnology, Eternal University, Baru Sahib, Himachal Pradesh India
| | - Joginder Singh
- Department of Microbiology, Lovely Professional University, Phagwara, Punjab India
| | | | - Neelam Yadav
- Gopi Nath PG College, Veer Bahadur Singh Purvanchal University, Ghazipur, Uttar Pradesh India
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7
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Nerva L, Pagliarani C, Pugliese M, Monchiero M, Gonthier S, Gullino ML, Gambino G, Chitarra W. Grapevine Phyllosphere Community Analysis in Response to Elicitor Application against Powdery Mildew. Microorganisms 2019; 7:microorganisms7120662. [PMID: 31817902 PMCID: PMC6956034 DOI: 10.3390/microorganisms7120662] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/26/2019] [Accepted: 12/05/2019] [Indexed: 12/23/2022] Open
Abstract
The reduction of antimicrobial treatments and mainly the application of environmentally friendly compounds, such as resistance elicitors, is an impelling challenge to undertake more sustainable agriculture. We performed this research to study the effectiveness of non-conventional compounds in reducing leaf fungal attack and to investigate whether they influence the grape phyllosphere. Pathogenicity tests were conducted on potted Vitis vinifera "Nebbiolo" and "Moscato" cultivars infected with the powdery mildew agent (Erysiphe necator) and treated with three elicitors. Differences in the foliar microbial community were then evaluated by community-level physiological profiling by using BiologTM EcoPlates, high throughput sequencing of the Internal Transcribed Spacer (ITS) region, and RNA sequencing for the viral community. In both cultivars, all products were effective as they significantly reduced pathogen development. EcoPlate analysis and ITS sequencing showed that the microbial communities were not influenced by the alternative compound application, confirming their specific activity as plant defense elicitors. Nevertheless, "Moscato" plants were less susceptible to the disease and presented different phyllosphere composition, resulting in a richer viral community, when compared with the "Nebbiolo" plants. The observed effect on microbial communities pointed to the existence of distinct genotype-specific defense mechanisms independently of the elicitor application.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Correspondence: (L.N.); (W.C.); Tel.: +39-04-3845-6712 (W.C.); Fax: +39-04-3845-0773 (W.C.)
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
| | - Massimo Pugliese
- Centre of Competence for the Innovation in the Agro-Environmental Sector (AGROINNOVA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy; (M.P.); (M.L.G.)
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | | | - Solène Gonthier
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Biocomputing and Modelling Department, National Institute of Applied Sciences, INSA Lyon, 69621 Villeurbanne cedex, France
| | - Maria Lodovica Gullino
- Centre of Competence for the Innovation in the Agro-Environmental Sector (AGROINNOVA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy; (M.P.); (M.L.G.)
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, Italy
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Strada delle Cacce 73, 10135 Torino, Italy; (C.P.); (S.G.); (G.G.)
- Correspondence: (L.N.); (W.C.); Tel.: +39-04-3845-6712 (W.C.); Fax: +39-04-3845-0773 (W.C.)
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Potential of Pantoea dispersa as an effective biocontrol agent for black rot in sweet potato. Sci Rep 2019; 9:16354. [PMID: 31704990 PMCID: PMC6841936 DOI: 10.1038/s41598-019-52804-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/21/2019] [Indexed: 02/06/2023] Open
Abstract
Biocontrol offers a promising alternative to synthetic fungicides for the control of a variety of pre- and post-harvest diseases of crops. Black rot, which is caused by the pathogenic fungus Ceratocytis fimbriata, is the most destructive post-harvest disease of sweet potato, but little is currently known about potential biocontrol agents for this fungus. Here, we isolated several microorganisms from the tuberous roots and shoots of field-grown sweet potato plants, and analyzed their ribosomal RNA gene sequences. The microorganisms belonging to the genus Pantoea made up a major portion of the microbes residing within the sweet potato plants, and fluorescence microscopy showed these microbes colonized the intercellular spaces of the vascular tissue in the sweet potato stems. Four P. dispersa strains strongly inhibited C. fimbriata mycelium growth and spore germination, and altered the morphology of the fungal hyphae. The detection of dead C. fimbriata cells using Evans blue staining suggested that these P. dispersa strains have fungicidal rather than fungistatic activity. Furthermore, P. dispersa strains significantly inhibited C. fimbriata growth on the leaves and tuberous roots of a susceptible sweet potato cultivar (“Yulmi”). These findings suggest that P. dispersa strains could inhibit black rot in sweet potato plants, highlighting their potential as biocontrol agents.
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Jia T, Wang RH, Chai BF. Various Phyllosphere and Soil Bacterial Communities of Natural Grasses and the Impact Factors in a Copper Tailings Dam. Curr Microbiol 2018; 76:7-14. [PMID: 30310969 DOI: 10.1007/s00284-018-1575-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/26/2018] [Indexed: 10/28/2022]
Abstract
Copper mining caused severe damage to the ecological environment of mining areas. The combination of microbe and plant remediation has an application potential in improving the absorption and transformation efficiency of heavy metals. The phyllosphere is the largest biointerface on the planet, and bacteria are the dominant microbial inhabitants of the phyllosphere, believed to be critical to plant growth and health. This study investigated the phyllospheric and soil bacteria communities using high-throughput sequencing, and endophyte infection statuses of four natural grasses by toluidine blue heparin assay. Results showed variation in phyllospheric bacterial community structure. Gammaproteobacteria were the most abundant bacterial population. Bacilli were found in the phyllosphere of Bothriochloa ischaemum and Imperata cylindrica, while Clostridia were only found in Calamagrostis epigejos. Alphaproteobacteria were the dominant bacteria in soil. In addition, bacterial communities were influenced by endophytic infection statuses. Oxalobacteraceae was associated with soil carbon and sulfur. Enterobacteriaceae had negative correlation with the ratio of soil carbon and nitrogen, and had positive correlation with Cd content. These results offer useful insights into phyllospheric bacterial community variance in four different natural grasses in a copper tailings dam.
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Affiliation(s)
- Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China.
| | - Rui-Hong Wang
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China
| | - Bao-Feng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, Shanxi, China
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10
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Scott M, Rani M, Samsatly J, Charron JB, Jabaji S. Endophytes of industrial hemp (Cannabis sativa L.) cultivars: identification of culturable bacteria and fungi in leaves, petioles, and seeds. Can J Microbiol 2018; 64:664-680. [PMID: 29911410 DOI: 10.1139/cjm-2018-0108] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant endophytes are a group of microorganisms that reside asymptomatically within the healthy living tissue. The diversity and molecular and biochemical characterization of industrial hemp-associated endophytes have not been previously studied. This study explored the abundance and diversity of culturable endophytes residing in petioles, leaves, and seeds of three industrial hemp cultivars, and examined their biochemical attributes and antifungal potential. A total of 134 bacterial and 53 fungal strains were isolated from cultivars Anka, CRS-1, and Yvonne. The number of bacterial isolates was similarly distributed among the cultivars, with the majority recovered from petiole tissue. Most fungal strains originated from leaf tissue of cultivar Anka. Molecular and phylogenetic analyses grouped the endophytes into 18 bacterial and 13 fungal taxa, respectively. The most abundant bacterial genera were Pseudomonas, Pantoea, and Bacillus, and the fungal genera were Aureobasidium, Alternaria, and Cochliobolus. The presence of siderophores, cellulase production, and phosphorus solubilization were the main biochemical traits. In proof-of-concept experiments, re-inoculation of tomato roots with some endophytes confirmed their migration to aerial tissues of the plant. Taken together, this study demonstrates that industrial hemp harbours a diversity of microbial endophytes, some of which could be used in growth promotion and (or) in biological control designed experiments.
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Affiliation(s)
- Maryanne Scott
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Mamta Rani
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jamil Samsatly
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Jean-Benoit Charron
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Suha Jabaji
- Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada.,Plant Science Department, MacDonald Campus of McGill University, 21 111 Lakeshore, Ste. Anne-de-Bellevue, QC H9X 3V9, Canada
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11
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Quambusch M, Winkelmann T. Bacterial Endophytes in Plant Tissue Culture: Mode of Action, Detection, and Control. Methods Mol Biol 2018; 1815:69-88. [PMID: 29981114 DOI: 10.1007/978-1-4939-8594-4_4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Endophytic bacteria have been increasingly in the focus of research projects during the last decade. This has changed the view on bacteria in plant tissue culture and led to the differentiation between artificially introduced contaminations and naturally occurring endophytes with neutral, negative, or positive impact on the plant propagation process. This review chapter gives an overview on recent findings about the impact that bacteria have on the plant physiology in general and during micropropagation. Additionally, methods for the detection and identification of bacteria in plant tissue are described and, finally, suggestions of how to deal with bacterial endophytes in in vitro culture are given.
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Affiliation(s)
- Mona Quambusch
- Abteilung Waldgenressourcen, Nordwestdeutsche Forstliche Versuchsanstalt, Hann. Münden, Germany.
| | - Traud Winkelmann
- Institut für Gartenbauliche Produktionssysteme, Leibniz Universität Hannover, Hannover, Germany
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Wang M, Li E, Liu C, Jousset A, Salles JF. Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession. Front Microbiol 2017; 8:2102. [PMID: 29163397 PMCID: PMC5670159 DOI: 10.3389/fmicb.2017.02102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 01/23/2023] Open
Abstract
Plant-associated bacteria are known for their high functional trait diversity, from which many are likely to play a role in primary and secondary succession, facilitating plant establishment in suboptimal soils conditions. Here we used an undisturbed salt marsh chronosequence that represents over 100 years of soil development to assess how the functional traits of plant associated bacteria respond to soil type, plant species and plant compartment. We isolated and characterized 808 bacterial colonies from the rhizosphere soil and root endosphere of two salt marsh plants, Limonium vulgare and Artemisia maritima, along the chronosequence. From these, a set of 59 strains (with unique BOX-PCR patterns, 16S rRNA sequence and unique to one of the treatments) were further screened for their plant growth promoting traits (siderophore production, IAA production, exoprotease production and biofilm formation), traits associated with bacterial fitness (antibiotic and abiotic stress resistance - pH, osmotic and oxidative stress, and salinity) and metabolic potential. An overall view of functional diversity (multivariate analysis) indicated that the distributional pattern of bacterial functional traits was driven by soil type. Samples from the late succession (Stage 105 year) showed the most restricted distribution, harboring strains with relatively low functionalities, whereas the isolates from intermediate stage (35 year) showed a broad functional profiles. However, strains with high trait performance were largely from stage 65 year. Grouping the traits according to category revealed that the functionality of plant endophytes did not vary along the succession, thus being driven by plant rather than soil type. In opposition, the functionality of rhizosphere isolates responded strongly to variations in soil type as observed for antibiotic resistance (P = 0.014). Specifically, certain Pseudomonas sp. and Serratia sp. strains revealed high resistance against abiotic stress and antibiotics and produce more siderophores, confirming the high plant-growth promoting activity of these two genera. Overall, this study contributes to a better understanding of the functional diversity and adaptation of the microbiome at typical salt marsh plant species across soil types. Specifically, soil type was influential only in the rhizosphere but not on the endosphere, indicating a strong plant-driven effect on the functionality of endophytes.
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Affiliation(s)
- Miao Wang
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Erqin Li
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Chen Liu
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Joana F. Salles
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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Secondary metabolite genes encoded by potato rhizosphere microbiomes in the Andean highlands are diverse and vary with sampling site and vegetation stage. Sci Rep 2017; 7:2330. [PMID: 28539610 PMCID: PMC5443786 DOI: 10.1038/s41598-017-02314-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/10/2017] [Indexed: 12/26/2022] Open
Abstract
Potato (Solanum tuberosum) is an important staple crop worldwide, it has been cultivated in the Andean Altiplano under low-input farming practices at high altitudes and under harsh environment for centuries. We analyzed secondary metabolite (SM) gene diversity encoded in the potato rhizosphere microbiome during plant growth at three distinct sites located in the Andes at high altitudes by 454-pyrosequencing of non-ribosomal peptide and polyketide biosynthetic genes. Phylogenetic analysis indicated that the majority of rhizosphere SM-encoding sequences differed from previously known sequences and may have distinct ancestors. In particular, actinobacterial methyl-malonyl-CoA transferase and acyl carrier protein from Firmicutes, both involved in the synthesis of SMs, showed widespread distribution of clades which were clearly distinct from sequences deposited in public databases, and only 11% of these sequences could be linked to the production of specific classes of SMs. Although the same cultivar was analyzed, SM gene composition radically differed among plant growth stages and across sites, suggesting a distinct repertoire of SM genes that likely encode diverse SM structures. Also, great diversity of non-ribosomal peptide and polyketide biosynthetic pathways in potato-associated microbiomes in the Andean highlands may represent a rich source of novel natural products.
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Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench]. Antonie van Leeuwenhoek 2017; 110:925-943. [PMID: 28353092 DOI: 10.1007/s10482-017-0864-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 03/21/2017] [Indexed: 10/19/2022]
Abstract
A diverse group of bacteria colonize the exo- and endo-rhizospheres of sorghum and play a critical role in its tolerance to drought and other abiotic stresses. Two hundred and eighty endophytic bacteria were isolated from the surface-sterilized roots of four sorghum cultivars that were grown on three soil types at three different phenological stages of growth. The isolates were subjected to in vitro screening for their plant growth promoting traits. Out of 280 isolates, 70 could produce Indole 3-Acetic Acid (IAA), 28 showed N-fixation, 28 could solubilize phosphate, 24 had ACC deaminase activity and 13 isolates were able to produce siderophores. Functional diversity grouping of the isolates indicated one isolate having five PGP traits and two isolates having four PGP traits; two and 29 isolates having three and two PGP traits, respectively. Among the thirty-four isolates that possessed multiple PGP traits, 19 and 17 isolates were able to produce significant quantities of IAA in the presence and absence of L-tryptophan, an inducer. Eight isolates possessed high levels of ACC deaminase activity. PCR-RFLP of the 16Sr RNA gene revealed a distinct clustering and considerable genetic diversity among these functionally characterized isolates. The 16S rRNA gene based identification of the isolates of single and multiple PGP traits revealed phylogenetic dominance of Firmicutes; Acinetobacter, Bacillus, Enterobacter, Geobacillus, Lysinibacillus, Microbacterium, Ochrobactrum, Paenibacillus and Pseudomonas were the major genera present in the endo-rhizosphere of sorghum. Results of this study are constructive in selection of effective rhizobacterial endophytes or consortia for drought stress alleviation in sorghum.
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Pfeiffer S, Mitter B, Oswald A, Schloter-Hai B, Schloter M, Declerck S, Sessitsch A. Rhizosphere microbiomes of potato cultivated in the High Andes show stable and dynamic core microbiomes with different responses to plant development. FEMS Microbiol Ecol 2016; 93:fiw242. [PMID: 27940644 DOI: 10.1093/femsec/fiw242] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 12/04/2016] [Indexed: 11/13/2022] Open
Abstract
The rhizosphere hosts a rich microflora supporting plant nutrition and health. We examined bacterial rhizosphere microbiota of Solanum tuberosum grown in its center of origin, the Central Andean Highlands, at different vegetation stages and sites at altitudes ranging from 3245 to 4070 m.a.s.l., differing in soil characteristics, climate and the agricultural practices by 454 sequence analysis of 16S rRNA genes. We observed that the taxonomic composition of bacteria repeatedly occurring at particular stages of plant development was almost unaffected by highly diverse environmental conditions. A detailed statistical analysis on the operational taxonomic unit (OTU) level, representing bacterial species, revealed a complex community structure of the rhizosphere. We identified an opportunistic microbiome which comprises OTUs that occur randomly or under specific environmental conditions. In contrast, core microbiome members were found at all sites. The 'stable' component of the core microbiome consisted of few ubiquitous OTUs that were continuously abundant in all samples and vegetation stages, whereas the 'dynamic' component comprised OTUs that were enriched at specific vegetation stages.
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Affiliation(s)
- Stefan Pfeiffer
- AIT Austrian Institute of Technology GmbH, Department of Health and Environment, Bioresources Unit, Konrad-Lorenz Straße 24, A-3430 Tulln, Austria
| | - Birgit Mitter
- AIT Austrian Institute of Technology GmbH, Department of Health and Environment, Bioresources Unit, Konrad-Lorenz Straße 24, A-3430 Tulln, Austria
| | - Andreas Oswald
- Integrated Crop Management Division, International Potato Center (CIP), La Molina, Lima, Peru.,Agroforestry and Sustainable Agriculture Program, CATIE, Turrialba, 30501 Costa Rica
| | - Brigitte Schloter-Hai
- Research Unit Environmental Genomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Michael Schloter
- Research Unit Environmental Genomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, D-85764 Neuherberg, Germany
| | - Stéphane Declerck
- Earth and Life Institute, Applied Microbiology, Mycology, Université catholique de Louvain, Croix du Sud 2, 1348 Louvain-la-Neuve, Belgium
| | - Angela Sessitsch
- AIT Austrian Institute of Technology GmbH, Department of Health and Environment, Bioresources Unit, Konrad-Lorenz Straße 24, A-3430 Tulln, Austria
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Kang SA, Han JW, Kim BS. Community structures and antagonistic activities of the bacteria associated with surface-sterilized pepper plants grown in different field soils. Arch Microbiol 2016; 198:1027-1034. [PMID: 27577932 DOI: 10.1007/s00203-016-1282-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 05/11/2016] [Accepted: 08/22/2016] [Indexed: 11/27/2022]
Abstract
Endophytic bacteria may act individually or in consortia in controlling certain plant diseases. In this study, pepper plants (Capsicum annuum L. cv. Nokkwang) were cultivated in glasshouse conditions using field soils collected from two different geographic locations, Deokso (DS) and Gwangyang (GY) in Korea. Community structure and antifungal activity of pepper endophytic bacteria were analyzed using culture-independent (PCR-DGGE) and culture-dependent (plating) methods, respectively. Dissimilarities were observed between DGGE profiles of DS and GY samples at all plant tissues. However, sequencing of the major DGGE bands revealed an enrichment of Firmicutes in the leaves of plants propagated in either soil. Similar results were observed with the culturable assays. Firmicutes dominated the isolates from both leaf samples, DS leaf (100 %) and GY leaf (83.3 %), although the genus compositions of DS leaf and GY leaf isolates were different. We assessed the antifungal activity of each isolate recovered to better understand the potential role that these endophytic bacteria may play. Of the 27 representative isolates from DS plant samples, 17 isolates (63.0 %) had antagonistic activity against at least one of the fungi tested. Seventeen isolates from GY plant samples (58.6 %) displayed antagonistic properties. The results show that the endophytic communities differ in the same plant species when propagated in different soils. Exploring the internal tissues of plants growing in diverse soil environments could be a way to find potential candidates for biocontrol agents.
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Affiliation(s)
- Sin Ae Kang
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
| | - Jae Woo Han
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea
| | - Beom Seok Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 136-713, Republic of Korea.
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17
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Musyoki MK, Cadisch G, Zimmermann J, Wainwright H, Beed F, Rasche F. Soil properties, seasonality and crop growth stage exert a stronger effect on rhizosphere prokaryotes than the fungal biocontrol agent Fusarium oxysporum f.sp. strigae. APPLIED SOIL ECOLOGY : A SECTION OF AGRICULTURE, ECOSYSTEMS & ENVIRONMENT 2016; 105:126-136. [PMID: 31007391 PMCID: PMC6472298 DOI: 10.1016/j.apsoil.2016.03.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Fusarium oxysporum f.sp. strigae (Fos) is an effective biocontrol agent (BCA) against the parasitic weed Striga hermonthica. It acts in the rhizosphere of several tropical cereals, where it may interfere with indigenous microbial populations. To test this impact, we assessed in a 2-season field experiment at two contrasting tropical agro-ecological sites the response of nitrifying and total indigenous prokaryotic communities in the rhizosphere of maize to the exposure of the Fos-BCA "Foxy-2". At early leaf development (EC30), flowering (EC60) and senescence (EC90) stage of maize, rhizosphere samples were obtained and subjected to community analysis of bacterial and archaeal amoA (ammonia monooxigenase) (AOB, AOA) and 16S rRNA genes. Abundance and community composition of all studied genes were predominantly influenced by soil type, crop growth stage and seasonality. No major effect of "Foxy-2" was found. Notably, total archaeal community relative to bacteria dominated in the clayey soil which was linked to its strong soil organic carbon (SOC) background. Compared to bacterial nitrifiers, domination of nitrifying archaea increased towards senescence stage which was explained by biochemical differences in organic resource availability between the crop growth stages. During the short rain season, the higher archaeal abundance was mainly driven by increased availability of organic substrates, i.e., extractable organic carbon. Our findings suggested that archaea had greater rhizosphere competence than "Foxy-2" in soils with higher clay and SOC contents. We verified that "Foxy-2" in maize rhizospheres is compatible with nitrifying prokaryotes under the given environments, in particular in clayey soils dominated by archaea.
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Affiliation(s)
- Mary K. Musyoki
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Georg Cadisch
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Judith Zimmermann
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
| | - Henry Wainwright
- The Real IPM Company, P.O. Box 4001-01002, Madaraka, Thika, Kenya
| | - Fen Beed
- AVRDC—The World Vegetable Center, East and Southeast Asia, P.O. Box 1010 (Kasetsart), Bangkok 10903, Thailand
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, Germany
- Corresponding author.
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18
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Metabarcoding of Bacteria Associated with the Acute Oak Decline Syndrome in England. FORESTS 2016. [DOI: 10.3390/f7050095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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19
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Bogas AC, Ferreira AJ, Araújo WL, Astolfi-Filho S, Kitajima EW, Lacava PT, Azevedo JL. Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose. SPRINGERPLUS 2015; 4:258. [PMID: 26090305 PMCID: PMC4467821 DOI: 10.1186/s40064-015-1037-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 05/13/2015] [Indexed: 12/17/2022]
Abstract
Endophytes colonize an ecological niche similar to that of phytopathogens, which make them candidate for disease suppression. Anthracnose is a disease caused by Colletotrichum spp., a phytopathogen that can infect guarana (Paullinia cupana), an important commercial crop in the Brazilian Amazon. We investigated the diversity of endophytic bacteria inhabiting the phyllosphere of asymptomatic and symptomatic anthracnose guarana plants. The PCR-denaturation gradient gel electrophoresis (PCR-DGGE) fingerprints revealed differences in the structure of the evaluated communities. Detailed analysis of endophytic bacteria composition using culture-dependent and 16S rRNA clone libraries revealed the presence of Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, and Acidobacteria phyla. Firmicutes comprised the majority of isolates in asymptomatic plants (2.40E(-4)). However, cloning and sequencing of 16S rRNA revealed differences at the genus level for Neisseria (1.4E(-4)), Haemophilus (2.1E(-3)) and Arsenophonus (3.6E(-5)) in asymptomatic plants, Aquicella (3.5E(-3)) in symptomatic anthracnose plants, and Pseudomonas (1.1E(-3)), which was mainly identified in asymptomatic plants. In cross-comparisons of the endophytic bacterial communities as a whole, symptomatic anthracnose plants contained higher diversity, as reflected in the Shannon-Weaver and Simpson indices estimation (P < 0.05). Similarly, comparisons using LIBSHUFF and heatmap analysis for the relative abundance of operational taxonomic units (OTUs) showed differences between endophytic bacterial communities. These data are in agreement with the NMSD and ANOSIM analysis of DGGE profiles. Our results suggest that anthracnose can restructure endophytic bacterial communities by selecting certain strains in the phyllosphere of P. cupana. The understanding of these interactions is important for the development of strategies of biocontrol for Colletotrichum.
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Affiliation(s)
- Andréa Cristina Bogas
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av. Pádua Dias 11, PO BOX 83, Piracicaba, SP 13400-970 Brazil
| | - Almir José Ferreira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, São Paulo, SP 05508-900 Brazil
| | - Welington Luiz Araújo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes, 1374-Ed. Biomédicas II, Cidade Universitária, São Paulo, SP 05508-900 Brazil
| | - Spartaco Astolfi-Filho
- Molecular Diagnostic Laboratory, Biotechnology Division, Federal University of Amazon, Av. Gal. Rodrigo Octávio Jordão, 3000, Manaus, AM 69.077-000 Brazil
| | - Elliot Watanabe Kitajima
- Department of Plant Pathology and Nematology, ''Luiz de Queiroz'' College of Agriculture, University of São Paulo, Av. Pádua Dias 11, Piracicaba, SP 13418-900 Brazil
| | - Paulo Teixeira Lacava
- Center of Biological Sciences and Health, Federal University of São Carlos, Via Washington Luís km 235, PO BOX 676, São Carlos, SP 13565-905 Brazil
| | - João Lúcio Azevedo
- Department of Genetics, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Av. Pádua Dias 11, PO BOX 83, Piracicaba, SP 13400-970 Brazil
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20
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Shen SY, Fulthorpe R. Seasonal variation of bacterial endophytes in urban trees. Front Microbiol 2015; 6:427. [PMID: 26042095 PMCID: PMC4437045 DOI: 10.3389/fmicb.2015.00427] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/22/2015] [Indexed: 02/01/2023] Open
Abstract
Bacterial endophytes, non-pathogenic bacteria residing within plants, contribute to the growth and development of plants and their ability to adapt to adverse conditions. In order to fully exploit the capabilities of these bacteria, it is necessary to understand the extent to which endophytic communities vary between species and over time. The endophytes of Acer negundo, Ulmus pumila, and Ulmus parvifolia were sampled over three seasons and analyzed using culture dependent and independent methods (culture on two media, terminal restriction fragment length polymorphism, and tagged pyrosequencing of 16S ribosomal amplicons). The majority of culturable endophytes isolated were Actinobacteria, and all the samples harbored Bacillus, Curtobacterium, Frigoribacterium, Methylobacterium, Paenibacilllus, and Sphingomonas species. Regardless of culture medium used, only the culturable communities obtained in the winter for A. negundo could be distinguished from those of Ulmus spp. In contrast, the nonculturable communities were dominated by Proteobacteria and Actinobacteria, particularly Erwinia, Ralstonia, and Sanguibacter spp. The presence and abundance of various bacterial classes and phyla changed with the changing seasons. Multivariate analysis on the culture independent data revealed significant community differences between the endophytic communities of A. negundo and Ulmus spp., but overall season was the main determinant of endophytic community structure. This study suggests studies on endophytic populations of urban trees should expect to find significant seasonal and species-specific community differences and sampling should proceed accordingly.
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Affiliation(s)
- Shu Yi Shen
- Department of Physical and Environmental Sciences, University of Toronto Scarborough Toronto, ON, Canada
| | - Roberta Fulthorpe
- Department of Physical and Environmental Sciences, University of Toronto Scarborough Toronto, ON, Canada
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21
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Microbial Life on Green Biomass and Their Use for Production of Platform Chemicals. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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22
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Naveed M, Mubeen S, Khan S, Ahmed I, Khalid N, Suleria HAR, Bano A, Mumtaz AS. Identification and characterization of rhizospheric microbial diversity by 16S ribosomal RNA gene sequencing. Braz J Microbiol 2014; 45:985-93. [PMID: 25477935 PMCID: PMC4204986 DOI: 10.1590/s1517-83822014000300031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 12/13/2013] [Indexed: 01/16/2024] Open
Abstract
In the present study, samples of rhizosphere and root nodules were collected from different areas of Pakistan to isolate plant growth promoting rhizobacteria. Identification of bacterial isolates was made by 16S rRNA gene sequence analysis and taxonomical confirmation on EzTaxon Server. The identified bacterial strains were belonged to 5 genera i.e. Ensifer, Bacillus, Pseudomona, Leclercia and Rhizobium. Phylogenetic analysis inferred from 16S rRNA gene sequences showed the evolutionary relationship of bacterial strains with the respective genera. Based on phylogenetic analysis, some candidate novel species were also identified. The bacterial strains were also characterized for morphological, physiological, biochemical tests and glucose dehydrogenase (gdh) gene that involved in the phosphate solublization using cofactor pyrroloquinolone quinone (PQQ). Seven rhizoshperic and 3 root nodulating stains are positive for gdh gene. Furthermore, this study confirms a novel association between microbes and their hosts like field grown crops, leguminous and non-leguminous plants. It was concluded that a diverse group of bacterial population exist in the rhizosphere and root nodules that might be useful in evaluating the mechanisms behind plant microbial interactions and strains QAU-63 and QAU-68 have sequence similarity of 97 and 95% which might be declared as novel after further taxonomic characterization.
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Affiliation(s)
- Muhammad Naveed
- Plant Genomics Laboratory Department of Plant Sciences Quaid-i-Azam University Islamabad Pakistan Plant Genomics Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Samavia Mubeen
- Plant Genomics Laboratory Department of Plant Sciences Quaid-i-Azam University Islamabad Pakistan Plant Genomics Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - SamiUllah Khan
- Plant Genomics Laboratory Department of Plant Sciences Quaid-i-Azam University Islamabad Pakistan Plant Genomics Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iftikhar Ahmed
- National Institute for Genomics & Advanced Biotechnology National Agricultural Research Centre Islamabad Pakistan National Institute for Genomics & Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Nauman Khalid
- Graduate School of Agricultural and Life Sciences The University of Tokyo Yayoi, Bunkyo-kuTokyo Japan Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Hafiz Ansar Rasul Suleria
- School of Agriculture and Food Sciences The University of Queensland Brisbane Australia School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Australia
| | - Asghari Bano
- Plant Genomics Laboratory Department of Plant Sciences Quaid-i-Azam University Islamabad Pakistan Plant Genomics Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abdul Samad Mumtaz
- Plant Genomics Laboratory Department of Plant Sciences Quaid-i-Azam University Islamabad Pakistan Plant Genomics Laboratory, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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23
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Bodenhausen N, Bortfeld-Miller M, Ackermann M, Vorholt JA. A synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet 2014; 10:e1004283. [PMID: 24743269 PMCID: PMC3990490 DOI: 10.1371/journal.pgen.1004283] [Citation(s) in RCA: 238] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 02/18/2014] [Indexed: 12/12/2022] Open
Abstract
The identity of plant host genetic factors controlling the composition of the plant microbiota and the extent to which plant genes affect associated microbial populations is currently unknown. Here, we use a candidate gene approach to investigate host effects on the phyllosphere community composition and abundance. To reduce the environmental factors that might mask genetic factors, the model plant Arabidopsis thaliana was used in a gnotobiotic system and inoculated with a reduced complexity synthetic bacterial community composed of seven strains representing the most abundant phyla in the phyllosphere. From a panel of 55 plant mutants with alterations in the surface structure, cell wall, defense signaling, secondary metabolism, and pathogen recognition, a small number of single host mutations displayed an altered microbiota composition and/or abundance. Host alleles that resulted in the strongest perturbation of the microbiota relative to the wild-type were lacs2 and pec1. These mutants affect cuticle formation and led to changes in community composition and an increased bacterial abundance relative to the wild-type plants, suggesting that different bacteria can benefit from a modified cuticle to different extents. Moreover, we identified ein2, which is involved in ethylene signaling, as a host factor modulating the community's composition. Finally, we found that different Arabidopsis accessions exhibited different communities, indicating that plant host genetic factors shape the associated microbiota, thus harboring significant potential for the identification of novel plant factors affecting the microbiota of the communities. The leaves of plants are inhabited by a diverse community of microorganisms. These leaf inhabitants influence their hosts with respect to growth and resistance to abiotic and biotic stresses. Recent studies revealed that the bacterial communities associated with leaves undergo selection, resulting in conserved microbial communities. However, the factors that are involved in structuring of bacterial communities are not well understood. In order to uncover host genetic factors that determine the community composition and to exclude confounding environmental effects, we inoculated Arabidopsis thaliana with a synthetic bacterial community under controlled conditions We screened a panel of Arabidopsis mutants defective in various traits for alterations in community structure and abundance and were able to show that cuticle synthesis and ethylene perception affect the bacterial community. In addition, we identified plant ecotypes with drastic differences in the community composition. Our system can thus be used to identify additional host genes and to broaden insights into plant microbe interactions, potentially providing a basis for applied plant protection through the identification of traits that enhance growth of plant probiotic bacteria.
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Affiliation(s)
| | | | - Martin Ackermann
- Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland
- Department of Environmental Microbiology, Eawag, Dubendorf, Switzerland
| | - Julia A. Vorholt
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
- * E-mail:
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Macarisin D, Patel J, Bauchan G, Giron JA, Ravishankar S. Effect of spinach cultivar and bacterial adherence factors on survival of Escherichia coli O157:H7 on spinach leaves. J Food Prot 2013; 76:1829-37. [PMID: 24215684 DOI: 10.4315/0362-028x.jfp-12-556] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Similar to phytopathogens, human bacterial pathogens have been shown to colonize the plant phylloplane. In addition to environmental factors, such as temperature, UV, relative humidity, etc., the plant cultivar and, specifically, the leaf blade morphological characteristics may affect the persistence of enteropathogens on leafy greens. This study was conducted to evaluate the effect of cultivar-dependent leaf topography and the role of strain phenotypic characteristics on Escherichia coli O157:H7 persistence on organic spinach. Spinach cultivars Emilia, Lazio, Space, and Waitiki were experimentally inoculated with the foodborne E. coli O157:H7 isolate EDL933 and its isogenic mutants deficient in cellulose, curli, or both curli and cellulose production. Leaves of 6-week-old plants were inoculated with 6.5 log CFU per leaf in a biosafety level 2 growth chamber. At 0, 1, 7, and 14 days, E. coli O157:H7 populations were determined by plating on selective medium and verified by laser scanning confocal microscopy. Leaf morphology (blade roughness and stoma density) was evaluated by low-temperature and variable-pressure scanning electron microscopy. E. coli O157:H7 persistence on spinach was significantly affected by cultivar and strain phenotypic characteristics, specifically, the expression of curli. Leaf blade roughness and stoma density influenced the persistence of E. coli O157:H7 on spinach. Cultivar Waitiki, which had the greatest leaf roughness, supported significantly higher E. coli O157:H7 populations than the other cultivars. These two morphological characteristics of spinach cultivars should be taken into consideration in developing intervention strategies to enhance the microbial safety of leafy greens.
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Affiliation(s)
- Dumitru Macarisin
- U.S. Department of Agriculture, Agricultural Research Service, Environmental Microbial & Food Safety Laboratory, 10300 Baltimore Avenue, Building 201, Beltsville Agricultural Research Center East, Beltsville, Maryland 20705, USA
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Bodenhausen N, Horton MW, Bergelson J. Bacterial communities associated with the leaves and the roots of Arabidopsis thaliana. PLoS One 2013; 8:e56329. [PMID: 23457551 PMCID: PMC3574144 DOI: 10.1371/journal.pone.0056329] [Citation(s) in RCA: 410] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 01/08/2013] [Indexed: 11/18/2022] Open
Abstract
Diverse communities of bacteria inhabit plant leaves and roots and those bacteria play a crucial role for plant health and growth. Arabidopsis thaliana is an important model to study plant pathogen interactions, but little is known about its associated bacterial community under natural conditions. We used 454 pyrosequencing to characterize the bacterial communities associated with the roots and the leaves of wild A. thaliana collected at 4 sites; we further compared communities on the outside of the plants with communities in the endophytic compartments. We found that the most heavily sequenced bacteria in A. thaliana associated community are related to culturable species. Proteobacteria, Actinobacteria, and Bacteroidetes are the most abundant phyla in both leaf and root samples. At the genus level, sequences of Massilia and Flavobacterium are prevalent in both samples. Organ (leaf vs root) and habitat (epiphytes vs endophytes) structure the community. In the roots, richness is higher in the epiphytic communities compared to the endophytic compartment (P = 0.024), while the reverse is true for the leaves (P = 0.032). Interestingly, leaf and root endophytic compartments do not differ in richness, diversity and evenness, while they differ in community composition (P = 0.001). The results show that although the communities associated with leaves and roots share many bacterial species, the associated communities differ in structure.
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Affiliation(s)
- Natacha Bodenhausen
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew W. Horton
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Mitter B, Brader G, Afzal M, Compant S, Naveed M, Trognitz F, Sessitsch A. Advances in Elucidating Beneficial Interactions Between Plants, Soil, and Bacteria. ADVANCES IN AGRONOMY 2013:381-445. [PMID: 0 DOI: 10.1016/b978-0-12-407685-3.00007-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
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Marasco R, Rolli E, Ettoumi B, Vigani G, Mapelli F, Borin S, Abou-Hadid AF, El-Behairy UA, Sorlini C, Cherif A, Zocchi G, Daffonchio D. A drought resistance-promoting microbiome is selected by root system under desert farming. PLoS One 2012; 7:e48479. [PMID: 23119032 PMCID: PMC3485337 DOI: 10.1371/journal.pone.0048479] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/02/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Traditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of "reverse desertification". Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress. METHODOLOGY/PRINCIPAL FINDINGS We assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuum rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress. CONCLUSIONS/SIGNIFICANCE Crop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a "resource island" able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.
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Affiliation(s)
- Ramona Marasco
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Eleonora Rolli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Besma Ettoumi
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, Tunis, Tunisia and Laboratoire Biotechnologie et Valorisation des Bio-Géo Ressources, Institut Supérieur de Biotechnologie, Université de La Manouba, Sidi Thabet, Ariana, Tunisia
| | - Gianpiero Vigani
- Dipartimento di Scienze Agrarie e Alimentari- Produzione, Territorio, Agroenergia; Università degli Studi di Milano, Milan, Italy
| | - Francesca Mapelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Sara Borin
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
| | | | | | - Claudia Sorlini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
| | - Ameur Cherif
- Laboratoire Microorganismes et Biomolécules Actives, Université Tunis El Manar, Tunis, Tunisia and Laboratoire Biotechnologie et Valorisation des Bio-Géo Ressources, Institut Supérieur de Biotechnologie, Université de La Manouba, Sidi Thabet, Ariana, Tunisia
| | - Graziano Zocchi
- Dipartimento di Scienze Agrarie e Alimentari- Produzione, Territorio, Agroenergia; Università degli Studi di Milano, Milan, Italy
| | - Daniele Daffonchio
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente, Università degli Studi di Milano, Milan, Italy
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Khan Z, Guelich G, Phan H, Redman R, Doty S. Bacterial and Yeast Endophytes from Poplar and Willow Promote Growth in Crop Plants and Grasses. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/890280] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Endophytic associations with plants have a beneficial effect for many different plant species with some of them being host specific. Several endophytes isolated from poplar and willow were screened for their effects on commercially important crops including corn, tomato, pepper, squash, sunflower, and grasses. Most of these endophytes produce growth hormones such as indoleacetic acid (IAA) and have the nitrogenase gene required for nitrogen fixation. The effects of these isolates on plant growth and yield were evaluated under greenhouse conditions. We found that inoculated plants not only had better viability and earlier flowering and fruiting, they also had increased plant growth and fruit yields when grown in nitrogen-limited soil. In a particular variety of perennial rye grass, the endophytes increased the total nitrogen content of the plants, indicative of nitrogen fixation, in addition to promoting plant growth. The use of specific endophytes may be preferable to the use of chemical fertilizers because of the monetary and environmental costs, contributing to more sustainable agricultural systems.
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Affiliation(s)
- Zareen Khan
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Grant Guelich
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Ha Phan
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Regina Redman
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
| | - Sharon Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA 98195-2100, USA
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Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, Ainuddin AN, Chun J, Adams JM. Distinctive phyllosphere bacterial communities in tropical trees. MICROBIAL ECOLOGY 2012; 63:674-681. [PMID: 21990015 DOI: 10.1007/s00248-011-9953-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 09/23/2011] [Indexed: 05/27/2023]
Abstract
Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.
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Affiliation(s)
- Mincheol Kim
- School of Biological Sciences, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea
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Ferrando L, Fernández Mañay J, Fernández Scavino A. Molecular and culture-dependent analyses revealed similarities in the endophytic bacterial community composition of leaves from three rice (Oryza sativa) varieties. FEMS Microbiol Ecol 2012; 80:696-708. [PMID: 22375835 DOI: 10.1111/j.1574-6941.2012.01339.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 12/27/2011] [Accepted: 02/18/2012] [Indexed: 12/01/2022] Open
Abstract
The endophytic bacterial communities of the three most important rice varieties cultivated in Uruguay were compared by a multiphasic approach. Leaves of mature plants grown in field experiments for two consecutive crop seasons were studied. No significant differences were found in the heterotrophic bacterial density for the three varieties. Pantoea ananatis and Pseudomonas syringae constituted 51% of the total of the isolates. These species were always present regardless of the variety or the season. Molecular analysis based on the 16S rRNA gene was performed by terminal restriction fragment length polymorphism (T-RFLP) and cloning. T-RFLP analysis revealed that bacterial communities grouped according to the variety, although the three varieties presented communities that showed 74% or higher similarities. Brevundimonas, the dominant genus in the clone library (18% of the clones), which might be present in all varieties according to T-RFLP profiles, was not recovered by cultivation. Conversely, bacteria from the genus Pseudomonas were not detected in the clone library. These results indicate that communities established in leaves of physiologically different rice varieties were highly similar and composed by a reduced group of strongly associated and persistent bacteria that were partially recovered by cultivation.
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Affiliation(s)
- Lucía Ferrando
- Cátedra de Microbiología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo, Uruguay.
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Isolation and Characterization of Nodule-Associated Exiguobacterium sp. from the Root Nodules of Fenugreek (Trigonella foenum-graecum) and Their Possible Role in Plant Growth Promotion. Int J Microbiol 2012; 2012:693982. [PMID: 22518149 PMCID: PMC3299478 DOI: 10.1155/2012/693982] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 09/20/2011] [Accepted: 10/23/2011] [Indexed: 11/24/2022] Open
Abstract
One of the ways to increase the competitive survivability of rhizobial biofertilizers and thus achieve better plant growth under such conditions is by modifying the rhizospheric environment or community by addition of nonrhizobial nodule-associated bacteria (NAB) that cause better nodulation and plant growth when coinoculated with rhizobia. A study was performed to investigate the most commonly associated nodule-associated bacteria and the rhizospheric microorganisms associated with the Fenugreek (Trigonella foenum-graecum) plant. Isolation of nonrhizobial isolates from root nodules of Fenugreek was carried out along with the rhizospheric isolates. About 64.7% isolates obtained from Fenugreek nodules were gram-negative coccobacilli, 29.41% were gram-positive bacilli, and all rhizospheric isolates except one were gram-positive bacilli. All the isolates were characterized for their plant growth promoting (PGP) activities. Two of the NAB isolates M2N2c and B1N2b (Exiguobacterium sp.) showed maximum positive PGP features. Those NAB isolates when coinoculated with rhizobial strain—S. meliloti, showed plant growth promotion with respect to increase in plant's root and shoot length, chlorophyll content, nodulation efficiency, and nodule dry weight.
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Ringelberg D, Foley K, Reynolds CM. Bacterial endophyte communities of two wheatgrass varieties following propagation in different growing media. Can J Microbiol 2012; 58:67-80. [PMID: 22220581 DOI: 10.1139/w11-122] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bacterial endophyte communities of two wheatgrass varieties currently being used in the revegetation of military training ranges were studied. Culturable and direct 16S rDNA PCR amplification techniques were used to describe bacterial communities present in Siberian and slender wheatgrass seeds, leaf tissues, and root tissues following propagation in either sand or a peat-based growing mix. Our hypothesis was that the resulting plant endophytic communities would be distinct, showing not only the presence of endophytes originating from the seed but also the characteristics of growth in the two different growing media. Both culture and culture-independent assays showed the likely translocation of Actinobacteria, Firmicutes, and Gammaproteobacteria from seed to mature plant tissues as well as subsequent colonization by exogenous organisms. Statistical analysis of 16S terminal restriction fragment profiles identified growing media as having a greater significant effect on the formation of the endpoint endophytic communities than either plant tissue or wheatgrass variety. In silico digests of the ribosomal database produced putative identifications indicating an increase in overall species diversity and increased relative abundances of Firmicutes and Cyanobacteria following propagation in sand and Betaproteobacteria following propagation in the peat-based growing mix. Results indicated a substantial translocation of endophytes from seed to mature plant tissues for both growing media and that growing medium was a dominant determinant of the final taxonomy of the endpoint plant endophytic communities.
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Affiliation(s)
- D Ringelberg
- US Army Cold Regions Research and Engineering Laboratory, Hanover, NH 03755, USA.
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Phyllopshere Bacterial Community Structure of Spinach (Spinacia oleracea) as Affected by Cultivar and Environmental Conditions at Time of Harvest. DIVERSITY-BASEL 2011. [DOI: 10.3390/d3040721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Nikolic B, Schwab H, Sessitsch A. Metagenomic analysis of the 1-aminocyclopropane-1-carboxylate deaminase gene (acdS) operon of an uncultured bacterial endophyte colonizing Solanum tuberosum L. Arch Microbiol 2011; 193:665-76. [PMID: 21523387 DOI: 10.1007/s00203-011-0703-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Revised: 02/16/2011] [Accepted: 03/29/2011] [Indexed: 01/08/2023]
Abstract
Deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is a key plant-beneficial trait found in many plant growth-promoting bacteria. In this study, we analysed ACC deaminase genes (acdS) of bacterial endophytes colonizing field-grown potato plants. PCR analysis revealed the presence of two types of acdS genes, the dominant one showing high homology to an acdS gene derived from Pseudomonas fluorescens. Construction, functional screening and sequence analysis of metagenomic libraries revealed clones containing the acdS gene identified in the PCR library. Sequence analysis of one metagenomic clone identified the entire acdS operon of an uncultivated endophyte and revealed that the acdS gene is coupled upstream with an acdR transcriptional regulator gene as previously found in P. putida strain UW4 (Grichko and Glick 2000). However, in-silico analysis of 195 fully sequenced, acdS-containing bacterial genomes revealed that the majority of strains, including numerous strains belonging to the genus Pseudomonas, do not contain an acdR regulatory gene in the vicinity of the acdS gene or elsewhere in the genome. The acdR (+)-acdS (+) operon was exclusively found in several Alpha- and Betaproteobacteria most prominently in the genus Burkholderia.
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Hunter PJ, Hand P, Pink D, Whipps JM, Bending GD. Both leaf properties and microbe-microbe interactions influence within-species variation in bacterial population diversity and structure in the lettuce (Lactuca Species) phyllosphere. Appl Environ Microbiol 2010; 76:8117-25. [PMID: 20952648 PMCID: PMC3008232 DOI: 10.1128/aem.01321-10] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 10/07/2010] [Indexed: 11/20/2022] Open
Abstract
Morphological and chemical differences between plant genera influence phyllosphere microbial populations, but the factors driving within-species variation in phyllosphere populations are poorly understood. Twenty-six lettuce accessions were used to investigate factors controlling within-species variation in phyllosphere bacterial populations. Morphological and physiochemical characteristics of the plants were compared, and bacterial community structure and diversity were investigated using terminal restriction fragment length polymorphism (T-RFLP) profiling and 16S rRNA gene clone libraries. Plant morphology and levels of soluble carbohydrates, calcium, and phenolic compounds (which have long been associated with plant responses to biotic stress) were found to significantly influence bacterial community structure. Clone libraries from three representative accessions were found to be significantly different in terms of both sequence differences and the bacterial genera represented. All three libraries were dominated by Pseudomonas species and the Enterobacteriaceae family. Significant differences in the relative proportions of genera in the Enterobacteriaceae were detected between lettuce accessions. Two such genera (Erwinia and Enterobacter) showed significant variation between the accessions and revealed microbe-microbe interactions. We conclude that both leaf surface properties and microbial interactions are important in determining the structure and diversity of the phyllosphere bacterial community.
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Affiliation(s)
- Paul J Hunter
- Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, United Kingdom.
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Knief C, Frances L, Vorholt JA. Competitiveness of diverse Methylobacterium strains in the phyllosphere of Arabidopsis thaliana and identification of representative models, including M. extorquens PA1. MICROBIAL ECOLOGY 2010; 60:440-452. [PMID: 20700590 DOI: 10.1007/s00248-010-9725-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 07/11/2010] [Indexed: 05/29/2023]
Abstract
Facultative methylotrophic bacteria of the genus Methylobacterium are consistently found in association with plants, particularly in the phyllosphere. To gain a better understanding of the mechanisms underlying the dispersal and occurrence of Methylobacterium on plants, diverse strains were isolated, identified, and studied with regard to their competitiveness on the model plant Arabidopsis thaliana. As a basis for this study a comprehensive collection of Methylobacterium isolates was established. Isolates were obtained from five different naturally grown A. thaliana populations and diverse other plant genera at these and further sites. They were classified using automated ribosomal internal spacer analysis (ARISA) and a representative subset was identified based on 16S rRNA gene sequence analysis. A comparison of their ARISA patterns with those generated based on a cultivation-independent approach from the same sampling material confirmed that the isolates were abundant colonizers of the studied plants. In competition experiments, colonization efficiency of the strains was found to be linked to phylogeny, rather than to the geographical origin or plant genus from which they were isolated. The most competitive colonizers were related to the species Methylobacterium tardum and Methylobacterium extorquens. Higher cell numbers were observed in the phyllosphere of A. thaliana when a mixture of different strains was applied relative to inoculation with only one strain, suggesting partial niche heterogeneity. Based on the results of the competition experiments, representative strains with different colonization efficiencies were selected, which will serve as models in future studies aiming at a better understanding of plant colonization by this bacterial genus. Among them is the meanwhile genome-sequenced strain M. extorquens PA1, which represents a competitive species of plant colonizers with a broad dispersal. This strain was characterized in more detail including physiological, morphological, and chemotaxonomical properties.
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Affiliation(s)
- Claudia Knief
- Institute of Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
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Magnani GS, Didonet CM, Cruz LM, Picheth CF, Pedrosa FO, Souza EM. Diversity of endophytic bacteria in Brazilian sugarcane. GENETICS AND MOLECULAR RESEARCH 2010; 9:250-8. [PMID: 20198580 DOI: 10.4238/vol9-1gmr703] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Endophytic bacteria live inside plant tissues without causing disease. Studies of endophytes in sugarcane have focused on the isolation of diazotrophic bacteria. We examined the diversity of endophytic bacteria in the internal tissues of sugarcane stems and leaves, using molecular and biochemical methods. Potato-agar medium was used to cultivate the endophytes; 32 isolates were selected for analysis. DNA was extracted and the 16S rRNA gene was partially sequenced and used for molecular identification. Gram staining, catalase and oxidase tests, and the API-20E system were used to characterize the isolates. The strains were divided into five groups, based on the 16S rRNA sequences. Group I comprised 14 representatives of the Enterobacteriaceae; group II was composed of Bacilli; group III contained one representative, Curtobacterium sp; group IV contained representatives of the Pseudomonadaceae family, and group V had one isolate with an uncultured bacterium. Four isolates were able to reduce acetylene to ethylene. Most of the bacteria isolated from the sugarcane stem and leaf tissues belonged to Enterobacteriaceae and Pseudomonaceae, respectively, demonstrating niche specificity. Overall, we found the endophytic bacteria in sugarcane to be more diverse than previously reported.
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Affiliation(s)
- G S Magnani
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Ikeda S, Kaneko T, Okubo T, Rallos LEE, Eda S, Mitsui H, Sato S, Nakamura Y, Tabata S, Minamisawa K. Development of a bacterial cell enrichment method and its application to the community analysis in soybean stems. MICROBIAL ECOLOGY 2009; 58:703-14. [PMID: 19662454 DOI: 10.1007/s00248-009-9566-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2009] [Accepted: 07/06/2009] [Indexed: 05/06/2023]
Abstract
A method was developed for enriching bacterial cells from soybean stems which was recalcitrant for a culture-independent analysis of bacterial community due to the interference with plant DNA. Stem homogenates were fractionated by a series of differential centrifugations followed by a Nycodenz density gradient centrifugation. The efficiency of bacterial cell enrichment was assessed by ribosomal intergenic spacer analysis (RISA). The intensity and the number of bacterial amplicons of RISA were markedly increased in the DNA extracted from the enriched bacterial cells compared to that in the DNA directly extracted from soybean stems. The phylogenetic diversity of the enriched bacterial cells was evaluated by analyzing a clone library of 16S rRNA gene in comparison with those of the culturable fractions of the enriched and non-enriched stem-associated bacteria, endophytic bacteria, and epiphytic bacteria. The results indicated that the method was able to enrich both endophytic and epiphytic bacteria from soybean stems, and was useful to assess the bacterial diversity based on a 16S rRNA gene clone library. When the sequence data from all clones (1,332 sequences) were combined, 72 operational taxonomic units were affiliated with Proteobacteria (Alpha-, Beta-, and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes, which also provided the most comprehensive set of data on the bacterial diversity in the aerial parts of soybeans.
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Affiliation(s)
- Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi, 980-8577, Japan.
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Whipps J, Hand P, Pink D, Bending G. Phyllosphere microbiology with special reference to diversity and plant genotype. J Appl Microbiol 2008; 105:1744-55. [DOI: 10.1111/j.1365-2672.2008.03906.x] [Citation(s) in RCA: 332] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Cultivation-independent characterization of methylobacterium populations in the plant phyllosphere by automated ribosomal intergenic spacer analysis. Appl Environ Microbiol 2008; 74:2218-28. [PMID: 18263752 DOI: 10.1128/aem.02532-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Bacteria of the genus Methylobacterium are widespread in the environment, but their ecological role in ecosystems, such as the plant phyllosphere, is not very well understood. To gain better insight into the distribution of different Methylobacterium species in diverse ecosystems, a rapid and specific cultivation-independent method for detection of these organisms and analysis of their community structure is needed. Therefore, 16S rRNA gene-targeted primers specific for this genus were designed and evaluated. These primers were used in PCR in combination with a reverse primer that binds to the tRNA(Ala) gene, which is located upstream of the 23S rRNA gene in the 16S-23S intergenic spacer (IGS). PCR products that were of different lengths were obtained due to the length heterogeneity of the IGS of different Methylobacterium species. This length variation allowed generation of fingerprints of Methylobacterium communities in environmental samples by automated ribosomal intergenic spacer analysis. The Methylobacterium communities on leaves of different plant species in a natural field were compared using this method. The new method allows rapid comparisons of Methylobacterium communities and is thus a useful tool to study Methylobacterium communities in different ecosystems.
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Sziderics AH, Rasche F, Trognitz F, Sessitsch A, Wilhelm E. Bacterial endophytes contribute to abiotic stress adaptation in pepper plants (Capsicum annuumL.). Can J Microbiol 2007; 53:1195-202. [DOI: 10.1139/w07-082] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Endophytes are nonpathogenic plant-associated bacteria that can play an important role in plant vitality and may confer resistance to abiotic or biotic stress. The effects of 5 endophytic bacterial strains isolated from pepper plants showing 1-aminocyclopropane-1-carboxylate deaminase activity were studied in sweet pepper under in vitro conditions. Four of the strains tested showed production of indole acetic acid. Plant growth, osmotic potential, free proline content, and gene expression were monitored in leaves and roots under control and mild osmotic stress conditions. All indole acetate producers promoted growth in Capsicum annuum L. ‘Ziegenhorn Bello’, from which they were isolated. Osmotic stress caused an increase in the content of free proline in the leaves of both inoculated and noninoculated plants. Inoculated control plants also revealed higher proline levels in comparison with noninoculated control plants. Differential gene expression patterns of CaACCO, CaLTPI, CaSAR82A, and putative P5CR and P5CS genes during moderate stress were observed, depending on the bacterium applied. Inoculation with 2 bacterial strains, EZB4 and EZB8 ( Arthrobacter sp. and Bacillus sp., respectively), resulted in a significantly reduced upregulation or even downregulation of the stress-inducible genes CaACCO and CaLTPI, as compared with the gene expression in noninoculated plants. This indicates that both strains reduced abiotic stress in pepper under the conditions tested.
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Affiliation(s)
- A. H. Sziderics
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf A-2444, Austria
| | - F. Rasche
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf A-2444, Austria
| | - F. Trognitz
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf A-2444, Austria
| | - A. Sessitsch
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf A-2444, Austria
| | - E. Wilhelm
- Austrian Research Centers GmbH, Department of Bioresources, Seibersdorf A-2444, Austria
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Saito A, Ikeda S, Ezura H, Minamisawa K. Microbial Community Analysis of the Phytosphere Using Culture-Independent Methodologies. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.93] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Asami Saito
- Graduate School of Life Sciences, Tohoku University
| | - Seishi Ikeda
- Graduate School of Life Sciences, Tohoku University
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