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Correa-Delgado R, Brito-López P, Jaizme Vega MC, Laich F. Biodiversity of Trichoderma species of healthy and Fusarium wilt-infected banana rhizosphere soils in Tenerife (Canary Islands, Spain). Front Microbiol 2024; 15:1376602. [PMID: 38800760 PMCID: PMC11122028 DOI: 10.3389/fmicb.2024.1376602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Banana (Musa acuminata) is the most important crop in the Canary Islands (38.9% of the total cultivated area). The main pathogen affecting this crop is the soil fungal Fusarium oxysporum f. sp. cubense subtropical race 4 (Foc-STR4), for which there is no effective control method under field conditions. Therefore, the use of native biological control agents may be an effective and sustainable alternative. This study aims to: (i) investigate the diversity and distribution of Trichoderma species in the rhizosphere of different banana agroecosystems affected by Foc-STR4 in Tenerife (the island with the greatest bioclimatic diversity and cultivated area), (ii) develop and preserve a culture collection of native Trichoderma species, and (iii) evaluate the influence of soil chemical properties on the Trichoderma community. A total of 131 Trichoderma isolates were obtained from 84 soil samples collected from 14 farms located in different agroecosystems on the northern (cooler and wetter) and southern (warmer and drier) slopes of Tenerife. Ten Trichoderma species, including T. afroharzianum, T. asperellum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hamatum, T. harzianum, T. hirsutum, T. longibrachiatum, and T. virens, and two putative novel species, named T. aff. harzianum and T. aff. hortense, were identified based on the tef1-α sequences. Trichoderma virens (35.89% relative abundance) and T. aff. harzianum (27.48%) were the most abundant and dominant species on both slopes, while other species were observed only on one slope (north or south). Biodiversity indices (Margalef, Shannon, Simpson, and Pielou) showed that species diversity and evenness were highest in the healthy soils of the northern slope. The Spearman analysis showed significant correlations between Trichoderma species and soil chemistry parameters (mainly with phosphorus and soil pH). To the best of our knowledge, six species are reported for the first time in the Canary Islands (T. afroharzianum, T. asperellum, T. atrobrunneum, T. guizhouense, T. hamatum, T. hirsutum) and in the rhizosphere of banana soils (T. afroharzianum, T. atrobrunneum, T. gamsii, T. guizhouense, T. hirsutum, T. virens). This study provides essential information on the diversity/distribution of native Trichoderma species for the benefit of future applications in the control of Foc-STR4.
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Affiliation(s)
| | | | | | - Federico Laich
- Unidad de Protección Vegetal, Instituto Canario de Investigaciones Agrarias, Valle de Guerra, Santa Cruz de Tenerife, Canary Islands, Spain
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Ünal F. Phylogenetic analysis of Microdochium spp. associated with turfgrass and their pathogenicity in cereals. PeerJ 2024; 12:e16837. [PMID: 38304186 PMCID: PMC10832662 DOI: 10.7717/peerj.16837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Turfgrass is frequently used today in the arrangement and aesthetic beautification of grounds in parks, gardens, median strips, recreation and sports areas. In this study, surveys were conduct in turfgrass areas in the three provinces of Türkiye. As a result of isolations from the collected samples, 44 Microdochium isolates obtained belonging to five different species including M. bolleyi, M. majus, M. nivale, M. paspali and M. sorghi which have different virulences. Identification of the isolates were performed by rDNA-ITS sequence analyzes. According to the pathogenicity tests results, the most virulent species was M. nivale M62 with a disease severity value of 91.93%. This was followed by M. bolleyi M1584 and M. majus M63, with disease severity values of 91.12% and 91.08%, respectively. The virulence of M. bolleyi isolates varied among the species. Only 13 of the 31 M. bolleyi species were found to be virulent in turfgrass, M. paspali was less virulent than the others in Poa pratensis. The most virulent isolate of each Microdochium species was tested on four different cereal varieties. M. sorghi and M. paspali had low virulence values in barley and oat than the other Microdochium species, while the other three species showed high virulence in turfgrass, wheat and barley, other than oat. In the phylogenetic neighboor-joining tree belonging to 44 Microdochium isolates clearly demonstrated that the isolates were grouped into five distinct clusters. M. nivale and M. majus were considered genetically close isolates.
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Affiliation(s)
- Filiz Ünal
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Eskişehir, Odunpazarı, Türkiye
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Li J, Hou L, Zhang G, Cheng L, Liu Y. Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants. J Fungi (Basel) 2024; 10:84. [PMID: 38276030 PMCID: PMC10817651 DOI: 10.3390/jof10010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
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Affiliation(s)
- Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Gui Zhang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yujiao Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Two New Species and a New Record of Microdochium from Grasses in Yunnan Province, South-West China. J Fungi (Basel) 2022; 8:jof8121297. [PMID: 36547630 PMCID: PMC9783193 DOI: 10.3390/jof8121297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Microdochium species are frequently reported as phytopathogens on various plants and also as saprobic and soil-inhabiting organisms. As a pathogen, they mainly affect grasses and cereals, causing severe disease in economically valuable crops, resulting in reduced yield and, thus, economic loss. Numerous asexual Microdochium species have been described and reported as hyphomycetous. However, the sexual morph is not often found. The main purpose of this study was to describe and illustrate two new species and a new record of Microdochium based on morphological characterization and multi-locus phylogenetic analyses. Surveys of both asexual and sexual morph specimens were conducted from March to June 2021 in Yunnan Province, China. Here, we introduce Microdochium graminearum and M. shilinense, from dead herbaceous stems of grasses and report M. bolleyi as an endophyte of Setaria parviflora leaves. This study improves the understanding of Microdochium species on monocotyledonous flowering plants in East Asia. A summary of the morphological characteristics of the genus and detailed references are provided for use in future research.
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Effects on Capsicum annuum Plants Colonized with Trichoderma atroviride P. Karst Strains Genetically Modified in Taswo1, a Gene Coding for a Protein with Expansin-like Activity. PLANTS 2021; 10:plants10091919. [PMID: 34579451 PMCID: PMC8468806 DOI: 10.3390/plants10091919] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 12/01/2022]
Abstract
Here, we analyzed the effects on Capsicum annuum plants of Trichoderma atroviride P. Karst strains altered in the expression of SWOLLENIN (SWO1), a protein with amorphogenic activity on plant cell wall components. Strains of T. atroviride that overexpressed the Taswo1 gene were constructed as well as deletion mutants. A novel, cheap and accurate method for assessing root colonization was developed. Colonization assays showed that the Taswo1 overexpressing strains invaded the host root better than the WT, resulting in a stronger plant growth-promoting effect. The expression of plant defense marker genes for both the systemic acquired resistance and induced systemic resistance pathways was enhanced in plants inoculated with Taswo1 overexpressing strains, while inoculation with deletion mutant strains resulted in a similar level of expression to that observed upon inoculation with the wild-type strain. Response to pathogen infection was also enhanced in the plants inoculated with the Taswo1 overexpressing strains, and surprisingly, an intermediate level of protection was achieved with the mutant strains. Tolerance to abiotic stresses was also higher in plants inoculated with the Taswo1 overexpressing strains but was similar in plants inoculated with the wild-type or the mutant strains. Compatible osmolyte production in drought conditions was studied. This study may contribute to improving Trichoderma biocontrol and biofertilization abilities.
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The assembly of wheat-associated fungal community differs across growth stages. Appl Microbiol Biotechnol 2021; 105:7427-7438. [PMID: 34505913 DOI: 10.1007/s00253-021-11550-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/03/2021] [Accepted: 08/22/2021] [Indexed: 02/04/2023]
Abstract
Plant-associated fungal communities play a vital role in plant adaptations, physiological functions, and productivity. Therefore, it is important to reveal the mechanisms driving the assembly of these communities. Yet it is still not fully understood how community assembly and structure differentiate in plant compartments, growth seasons, and varieties at large geographic distances. In this study, we analyzed bulk soil and plant-associated fungal communities of five wheat varieties across two growth stages in three biogeographic sites with distances of about 324, 534, or 800 km apart between any two locations. Our results indicated that the fungal community varied primarily across the sample types (leaf endosphere, root endosphere, rhizosphere, and bulk soil), followed by growth stage. Compared with the regreening stage, lower α-diversity and more dominance by abundant species in the fungal community were observed in wheat-associated compartments (four sample types except for bulk soil) at the heading stage. Additionally, within each wheat-associated compartment across every growth stage, location had stronger effects on fungal community assembly than the wheat variety. The effects of variety on fungal community assembly were location specific as were the growth-stage patterns of varietal effects on leaf endosphere and rhizosphere fungal communities. We further detected a less diverse but abundant core fungal taxa that could be grouped into three clusters associated mainly with location. This study characterized the interplay effects between plant selection (compartment, growth stage, variety) and environment (location) on wheat-associated mycobiomes by determining drivers of fungal community assembly and core fungal taxa in field conditions. KEY POINTS: • Fungal community assembly was mainly shaped by sample type and growth stage • A lower diversity and more abundant core fungal taxa were shown at heading stage • Location had stronger effects on fungal community assembly than variety.
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Jin L, Yang L, Li W, Xu D, Yang N, Li G, Wan P. Diversity and Biocontrol Potential of Culturable Endophytic Fungi in Cotton. Front Microbiol 2021; 12:698930. [PMID: 34484142 PMCID: PMC8415002 DOI: 10.3389/fmicb.2021.698930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Healthy cotton samples were collected and 93 endophytic fungal strains were isolated: 23 strains from the roots and 70 strains from the stems. Morphological characterization and ITS sequence analysis were used for the identification of these isolates. The results showed that the 93 strains including 20 species were highly diverse in terms of their taxonomy. Simpson's and Shannon's diversity indices were 0.915 and 3.848, respectively. Fusarium and Alternaria were the two dominant genera, constituting 19.4% of the total strains. Then, 72 spore-producing strains were tested for the suppression of cotton Verticillium wilt (CVW) caused by Verticillium dahliae in a greenhouse. Five strains exhibited effective suppression of CVW with average efficacy values higher than 50%. One of the effective strains, namely, Fusarium proliferatum 10R-7, was selected for the investigation of the role of fusaric acid, a secondary metabolite of strain 10R-7, in the suppression of V. dahliae and CVW. The results showed that F. proliferatum 10R-7 could produce fusaric acid, and this metabolite exhibited 100% inhibition of mycelial growth of V. dahliae at concentrations higher than 20 μg/ml. However, fusaric acid at 2.5 to 80 μg/ml was not effective in the suppression of CVW, compared with the control treatment with V. dahliae alone. F. proliferatum 10R-7 was labeled with green fluorescent protein (GFP), and the GFP-tagged strain was found to be able to colonize inside the taproots of cotton, suggesting that F. proliferatum 10R-7 is a true endophyte of cotton and endophytic colonization may play a role in the suppression of infection of cotton by V. dahliae.
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Affiliation(s)
- Lirong Jin
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Integrated Pest Management Crops in Central China, Ministry of Agriculture, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Plant Protection, Soil and Fertilizer Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Long Yang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Wenjing Li
- Key Laboratory of Integrated Pest Management Crops in Central China, Ministry of Agriculture, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Plant Protection, Soil and Fertilizer Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dong Xu
- Key Laboratory of Integrated Pest Management Crops in Central China, Ministry of Agriculture, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Plant Protection, Soil and Fertilizer Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Nina Yang
- Key Laboratory of Integrated Pest Management Crops in Central China, Ministry of Agriculture, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Plant Protection, Soil and Fertilizer Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guoqing Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Peng Wan
- Key Laboratory of Integrated Pest Management Crops in Central China, Ministry of Agriculture, Hubei Academy of Agricultural Sciences, Wuhan, China.,Hubei Key Laboratory of Crop Disease, Insect Pests and Weeds Control, Plant Protection, Soil and Fertilizer Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
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The Arbuscular Mycorrhizal Fungus Glomus viscosum Improves the Tolerance to Verticillium Wilt in Artichoke by Modulating the Antioxidant Defense Systems. Cells 2021; 10:cells10081944. [PMID: 34440713 PMCID: PMC8392416 DOI: 10.3390/cells10081944] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
Verticillium wilt, caused by the fungal pathogen Verticillium dahliae, is the most severe disease that threatens artichoke (Cynara scolymus L.) plants. Arbuscular mycorrhizal fungi (AMF) may represent a useful biological control strategy against this pathogen attack, replacing chemical compounds that, up to now, have been not very effective. In this study, we evaluated the effect of the AMF Glomus viscosum Nicolson in enhancing the plant tolerance towards the pathogen V. dahliae. The role of the ascorbate-glutathione (ASC-GSH) cycle and other antioxidant systems involved in the complex network of the pathogen-fungi-plant interaction have been investigated. The results obtained showed that the AMF G. viscosum is able to enhance the defense antioxidant systems in artichoke plants affected by V. dahliae, alleviating the oxidative stress symptoms. AMF-inoculated plants exhibited significant increases in ascorbate peroxidase (APX), monodehydroascorbate reductase (MDHAR), and superoxide dismutase (SOD) activities, a higher content of ascorbate (ASC) and glutathione (GSH), and a decrease in the levels of lipid peroxidation and hydrogen peroxide (H2O2). Hence, G. viscosum may represent an effective strategy for mitigating V. dahliae pathogenicity in artichokes, enhancing the plant defense systems, and improving the nutritional values and benefit to human health.
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Peng Y, Li SJ, Yan J, Tang Y, Cheng JP, Gao AJ, Yao X, Ruan JJ, Xu BL. Research Progress on Phytopathogenic Fungi and Their Role as Biocontrol Agents. Front Microbiol 2021; 12:670135. [PMID: 34122383 PMCID: PMC8192705 DOI: 10.3389/fmicb.2021.670135] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/23/2021] [Indexed: 02/01/2023] Open
Abstract
Phytopathogenic fungi decrease crop yield and quality and cause huge losses in agricultural production. To prevent the occurrence of crop diseases and insect pests, farmers have to use many synthetic chemical pesticides. The extensive use of these pesticides has resulted in a series of environmental and ecological problems, such as the increase in resistant weed populations, soil compaction, and water pollution, which seriously affect the sustainable development of agriculture. This review discusses the main advances in research on plant-pathogenic fungi in terms of their pathogenic factors such as cell wall-degrading enzymes, toxins, growth regulators, effector proteins, and fungal viruses, as well as their application as biocontrol agents for plant pests, diseases, and weeds. Finally, further studies on plant-pathogenic fungal resources with better biocontrol effects can help find new beneficial microbial resources that can control diseases.
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Affiliation(s)
- Yan Peng
- College of Agriculture, Guizhou University, Guiyang, China
| | - Shi J Li
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
| | - Jun Yan
- Key Laboratory of Coarse Cereal Processing in Ministry of Agriculture and Rural Affairs, Schools of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yong Tang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jian P Cheng
- College of Agriculture, Guizhou University, Guiyang, China
| | - An J Gao
- College of Agriculture, Guizhou University, Guiyang, China
| | - Xin Yao
- College of Agriculture, Guizhou University, Guiyang, China
| | - Jing J Ruan
- College of Agriculture, Guizhou University, Guiyang, China
| | - Bing L Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, China
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Wang H, Narsing Rao MP, Gao Y, Li X, Gao R, Xie Y, Li Q, Li W. Insights into the endophytic bacterial community comparison and their potential role in the dimorphic seeds of halophyte Suaeda glauca. BMC Microbiol 2021; 21:143. [PMID: 33980153 PMCID: PMC8114534 DOI: 10.1186/s12866-021-02206-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Seed dimorphism has been thought to be a bet-hedging strategy that helps plants survive in the disturbed environment and has been widely studied for its ecological adaptation mechanism. Many studies showed that seed-associated microorganisms play an important role in enhancing plant fitness, but information regarding endophytic bacteria associated with dimorphic seeds is limited. This study explores the influence of seed coat structure and seed phytochemical properties on the community composition and diversity of endophytic bacteria of dimorphic seeds of Suaeda glauca. In this study, we used 16S rRNA high-throughput gene sequencing method to compare the community composition and bacterial diversity between brown and black seeds of Suaeda glauca. RESULTS A significant difference was observed in seed coat structure and phytochemical properties between brown and black seeds of S. glauca. Total 9 phyla, 13 classes, 31 orders, 53 families, 102 genera were identified in the dimorphic seeds. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteria. The results showed that seed dimorphism had little impact on the diversity and richness of endophytic bacterial communities but significantly differs in the relative abundance of the bacterial community between brown and black seeds. At the phylum level, Actinobacteria tend to be enriched significantly in brown seeds. At the genus level, Rhodococcus, Ralstonia, Pelomonas and Bradyrhizobium tend to be enriched significantly in brown seeds, while Marinilactibacillus was mainly found in black seeds. Besides, brown seeds harbored a large number of bacteria with plant-growth-promoting traits, whereas black seeds presented bacteria with enzyme activities (i.e., pectinase, cellulolytic and xylanolytic activities). CONCLUSION The endophytic bacterial community compositions were significantly different between dimorphic seeds of Suaeda glauca, and play an important role in the ecological adaptation of dimorphic seeds by performing different biological function roles. The endophytic bacterial communities of the dimorphic seeds may be influenced mainly by the seed coat structureand partly by the seed phytochemical characteristics. These findings provide valuable information for better understanding of the ecological adaptation strategy of dimorphic seeds in the disturbed environment.
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Affiliation(s)
- Hongfei Wang
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yanli Gao
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Xinyang Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China
| | - Rui Gao
- Dandong Forestry and Grassland Development Service Center, Dandong, 118000, China
| | - Yuanguo Xie
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiuli Li
- The Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, No.1 Liushu South Street, Dalian, 650081, China.
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, 510275, China. .,State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.
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12
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Shi C, Chen J, Ge Q, Sun J, Guo W, Wang J, Peng L, Xu Q, Fan G, Zhang W, Liu X. Draft Genomes and Comparative Analysis of Seven Mangrove Rhizosphere-Associated Fungi Isolated From Kandelia obovata and Acanthus ilicifolius. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:626904. [PMID: 37744136 PMCID: PMC10512393 DOI: 10.3389/ffunb.2021.626904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/16/2021] [Indexed: 09/26/2023]
Abstract
Mangroves are one of the most productive and biologically diverse ecosystems, with unique plants, animals, and microorganisms adapted to the harsh coastal environments. Although fungi are widely distributed in the mangrove ecosystem and they are playing an important role in the decomposition of organic matter, their genomic profiles are still poorly understood. In this study, we isolated seven Ascomycota fungi (Westerdykella dispersa F012, Trichoderma lixii F014, Aspergillus tubingensis F023, Penicillium brefeldianum F032, Neoroussoella solani F033, Talaromyces fuscoviridis F034, and Arthrinium marii F035) from rhizospheres of two mangroves of Kandelia obovata and Acanthus ilicifolius. We sequenced and assembled the whole genome of these fungi, resulting in size ranging from 29 to 48 Mb, while contig N50 from 112 to 833 Kb. We generated six novel fungi genomes except A. tubingensis, and the gene completeness and genome completeness of all seven genomes are higher than 94%. Comparing with non-mangrove fungi, we found Carbohydrate-Binding Modules (CBM32), a subfamily of carbohydrate active enzymes, only detected in two mangrove fungi. Another two subfamilies, Glycoside Hydrolases (GH6) and Polysaccharide Lyases (PL4), were significantly different in gene copy number between K. obovata and A. ilicifolius rhizospheres (P-value 0.041 for GH6, 0.047 for PL4). These findings may indicate an important influence of mangrove environments or hosts on the ability of decomposition in rhizosphere fungi. Secondary metabolite biosynthesis gene clusters were detected and we found the mangrove fungi averagely contain 18 Type I Polyketide (t1pks) synthase, which was significantly higher than 13 in non-mangrove fungi (P-value 0.048), suggesting their potential roles in producing bioactive compounds that important for fungi development and ecology. We reported seven mangrove-associated fungal genomes in this study and compared their carbohydrate active enzymes and secondary metabolites (SM) genes with those of non-mangrove fungi, and the results suggest that there are differences in genetic information among fungi in different habitats.
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Affiliation(s)
- Chengcheng Shi
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | | | - Qijin Ge
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jiahui Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Wenjie Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Jie Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, China
- BGI-Argo Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, China
| | - Ling Peng
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Qiwu Xu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | | | - Wenwei Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- BGI-Shenzhen, Shenzhen, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
- BGI-Shenzhen, Shenzhen, China
- BGI-Fuyang, BGI-Shenzhen, Fuyang, China
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13
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Schmidt CS, Mrnka L, Lovecká P, Frantík T, Fenclová M, Demnerová K, Vosátka M. Bacterial and fungal endophyte communities in healthy and diseased oilseed rape and their potential for biocontrol of Sclerotinia and Phoma disease. Sci Rep 2021; 11:3810. [PMID: 33589671 PMCID: PMC7884388 DOI: 10.1038/s41598-021-81937-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 12/23/2020] [Indexed: 11/09/2022] Open
Abstract
Phoma stem canker (caused by the ascomycetes Leptosphaeria maculans and Leptosphaeria biglobosa) is an important disease of oilseed rape. Its effect on endophyte communities in roots and shoots and the potential of endophytes to promote growth and control diseases of oilseed rape (OSR) was investigated. Phoma stem canker had a large effect especially on fungal but also on bacterial endophyte communities. Dominant bacterial genera were Pseudomonas, followed by Enterobacter, Serratia, Stenotrophomonas, Bacillus and Staphylococcus. Achromobacter, Pectobacter and Sphingobacterium were isolated only from diseased plants, though in very small numbers. The fungal genera Cladosporium, Botrytis and Torula were dominant in healthy plants whereas Alternaria, Fusarium and Basidiomycetes (Vishniacozyma, Holtermaniella, Bjerkandera/Thanatephorus) occurred exclusively in diseased plants. Remarkably, Leptosphaeria biglobosa could be isolated in large numbers from shoots of both healthy and diseased plants. Plant growth promoting properties (antioxidative activity, P-solubilisation, production of phytohormones and siderophores) were widespread in OSR endophytes. Although none of the tested bacterial endophytes (Achromobacter, Enterobacter, Pseudomonas, Serratia and Stenotrophomonas) promoted growth of oilseed rape under P-limiting conditions or controlled Phoma disease on oilseed rape cotyledons, they significantly reduced incidence of Sclerotinia disease. In the field, a combined inoculum consisting of Achromobacter piechaudii, two pseudomonads and Stenotrophomonas rhizophila tendencially increased OSR yield and reduced Phoma stem canker.
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Affiliation(s)
- C S Schmidt
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, 25243, Průhonice, Czech Republic
| | - L Mrnka
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, 25243, Průhonice, Czech Republic.
| | - P Lovecká
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6-Dejvice, Czech Republic
| | - T Frantík
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, 25243, Průhonice, Czech Republic
| | - M Fenclová
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6-Dejvice, Czech Republic
| | - K Demnerová
- University of Chemistry and Technology, Technická 5, 166 28, Prague 6-Dejvice, Czech Republic
| | - M Vosátka
- Department of Mycorrhizal Symbioses, Institute of Botany, Czech Academy of Sciences, Lesní 322, 25243, Průhonice, Czech Republic
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14
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Paecilomyces and Its Importance in the Biological Control of Agricultural Pests and Diseases. PLANTS 2020; 9:plants9121746. [PMID: 33321854 PMCID: PMC7763231 DOI: 10.3390/plants9121746] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022]
Abstract
Incorporating beneficial microorganisms in crop production is the most promising strategy for maintaining agricultural productivity and reducing the use of inorganic fertilizers, herbicides, and pesticides. Numerous microorganisms have been described in the literature as biological control agents for pests and diseases, although some have not yet been commercialised due to their lack of viability or efficacy in different crops. Paecilomyces is a cosmopolitan fungus that is mainly known for its nematophagous capacity, but it has also been reported as an insect parasite and biological control agent of several fungi and phytopathogenic bacteria through different mechanisms of action. In addition, species of this genus have recently been described as biostimulants of plant growth and crop yield. This review includes all the information on the genus Paecilomyces as a biological control agent for pests and diseases. Its growth rate and high spore production rate in numerous substrates ensures the production of viable, affordable, and efficient commercial formulations for agricultural use.
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15
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Kerdraon L, Barret M, Balesdent M, Suffert F, Laval V. Impact of a resistance gene against a fungal pathogen on the plant host residue microbiome: The case of the Leptosphaeria maculans-Brassica napus pathosystem. MOLECULAR PLANT PATHOLOGY 2020; 21:1545-1558. [PMID: 32975002 PMCID: PMC7694673 DOI: 10.1111/mpp.12994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/20/2020] [Accepted: 08/21/2020] [Indexed: 06/11/2023]
Abstract
Oilseed rape residues are a crucial determinant of stem canker epidemiology as they support the sexual reproduction of the fungal pathogen Leptosphaeria maculans. The aim of this study was to characterize the impact of a resistance gene against L. maculans infection on residue microbial communities and to identify microorganisms interacting with this pathogen during residue degradation. We used near-isogenic lines to obtain healthy and infected host plants. The microbiome associated with the two types of plant residues was characterized by metabarcoding. A combination of linear discriminant analysis and ecological network analysis was used to compare the microbial communities and to identify microorganisms interacting with L. maculans. Fungal community structure differed between the two lines at harvest, but not subsequently, suggesting that the presence/absence of the resistance gene influences the microbiome at the base of the stem whilst the plant is alive, but that this does not necessarily lead to differential colonization of the residues by fungi. Direct interactions with other members of the community involved many fungal and bacterial amplicon sequence variants (ASVs). L. maculans appeared to play a minor role in networks, whereas one ASV affiliated to Plenodomus biglobosus (synonym Leptosphaeria biglobosa) from the Leptosphaeria species complex may be considered a keystone taxon in the networks at harvest. This approach could be used to identify and promote microorganisms with beneficial effects against residue-borne pathogens and, more broadly, to decipher the complex interactions between multispecies pathosystems and other microbial components in crop residues.
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Affiliation(s)
- Lydie Kerdraon
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
| | | | | | | | - Valérie Laval
- Université Paris‐SaclayINRAE, UMR BIOGERThiverval‐GrignonFrance
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16
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Tao X, Zhang H, Gao M, Li M, Zhao T, Guan X. Pseudomonas species isolated via high-throughput screening significantly protect cotton plants against verticillium wilt. AMB Express 2020; 10:193. [PMID: 33118043 PMCID: PMC7593376 DOI: 10.1186/s13568-020-01132-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/18/2020] [Indexed: 12/15/2022] Open
Abstract
Verticillium wilt (VW) caused by Verticillium dahliae is a devastating soil-borne disease that causes severe yield losses in cotton and other major crops worldwide. Here we conducted a high-throughput screening of isolates recovered from 886 plant rhizosphere samples taken from the three main cotton-producing areas of China. Fifteen isolates distributed in different genera of bacteria that showed inhibitory activity against V. dahliae were screened out. Of these, two Pseudomonas strains, P. protegens XY2F4 and P. donghuensis 22G5, showed significant inhibitory action against V. dahliae. Additional comparative genomic analyses and phenotypical assays confirmed that P. protegens XY2F4 and P. donghuensis 22G5 were the strains most efficient at protecting cotton plants against VW due to specific biological control products they produced. Importantly, we identified a significant efficacy of the natural tropolone compound 7-hydroxytropolone (7-HT) against VW. By phenotypical assay using the wild-type 22G5 and its mutant strain in 7-HT production, we revealed that the 7-HT produced by P. donghuensis is the major substance protecting cotton against VW. This study reveals that Pseudomonas specifically has gene clusters that allow the production of effective antipathogenic metabolites that can now be used as new agents in the biocontrol of VW.
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Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hailin Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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17
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Park MS, Lee JW, Kim SH, Park JH, You YH, Lim YW. Penicillium from Rhizosphere Soil in Terrestrial and Coastal Environments in South Korea. MYCOBIOLOGY 2020; 48:431-442. [PMID: 33312010 PMCID: PMC7717687 DOI: 10.1080/12298093.2020.1823611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 05/20/2023]
Abstract
Penicillium, the most common genus plays an important ecological role in various terrestrial and marine environments. However, only a few species have been reported from rhizosphere soil. As part of a project to excavate Korean indigenous fungi, we investigated rhizosphere soil of six plants in the forest (terrestrial habitat) and sand dunes (coastal habitat) and focused on discovering Penicillium species. A total of 64 strains were isolated and identified as 26 Penicillium species in nine sections based on morphological characteristics and the sequence analysis of β-tubulin and calmodulin. Although this is a small-scale study in a limited rhizosphere soil, eight unrecorded species and four potential new species have been identified. In addition, most Penicillium species from rhizosphere soil were unique to each plant. Penicillium halotolerans, P. scabrosum, P. samsonianum, P. jejuense, and P. janczewskii were commonly isolated from rhizosphere soil. Eight Penicillium species, P. aurantioviolaceum, P. bissettii, P. cairnsense, P. halotolerans, P. kananaskense, P. ortum, P. radiatolobatum, and P. verhagenii were recorded for the first time in Korea. Here, we provide the detailed morphological description of these unrecorded species.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Jun Won Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Sung Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Ji-Hyun Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Young-Hyun You
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
- CONTACT Young Woon Lim
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18
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Glaeser SP, Gabur I, Haghighi H, Bartz JO, Kämpfer P, Snowdon R, Obermeier C. Endophytic bacterial communities of oilseed rape associate with genotype-specific resistance against Verticillium longisporum. FEMS Microbiol Ecol 2020; 96:5643882. [PMID: 31769797 DOI: 10.1093/femsec/fiz188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/25/2019] [Indexed: 01/23/2023] Open
Abstract
Associations of endophytic bacterial community composition of oilseed rape (Brassica napus L.) with quantitative resistance against the soil-borne fungal pathogen Verticillium longisporum was assessed by 16S rRNA gene amplicon sequencing in roots and hypocotyls of four plant lines with contrasting genetic composition in regard to quantitative resistance reactions. The plant compartment was found to be the dominating driving factor for the specificity of bacterial communities in healthy plants. Furthermore, V. longisporum infection triggered a stabilization of phylogenetic group abundance in replicated samples suggesting a host genotype-specific selection. Genotype-specific associations with bacterial phylogenetic group abundance were identified by comparison of plant genotype groups (resistant versus susceptible) and treatment groups (healthy versus V. longisporum-infected) allowing dissection into constitutive and induced directional association patterns. Relative abundance of Flavobacteria, Pseudomonas, Rhizobium and Cellvibrio was associated with resistance/susceptibility. Relative abundance of Flavobacteria and Cellvibrio was increased in resistant genotypes according to their known ecological functions. In contrast, a higher relative abundance of Pseudomonas and Rhizobium, which are known to harbor many species with antagonistic properties to fungal pathogens, was found to be associated with susceptibility, indicating that these groups do not play a major role in genetically controlled resistance of oilseed rape against V. longisporum.
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Affiliation(s)
- Stefanie P Glaeser
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Hossein Haghighi
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany.,Department of Life Sciences, University of Modena and Reggio Emilia, Via Kenedy 17/I, 42124 Reggio Emilia, Italy
| | - Jens-Ole Bartz
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Rod Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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19
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Köberl M, Wagner P, Müller H, Matzer R, Unterfrauner H, Cernava T, Berg G. Unraveling the Complexity of Soil Microbiomes in a Large-Scale Study Subjected to Different Agricultural Management in Styria. Front Microbiol 2020; 11:1052. [PMID: 32523580 PMCID: PMC7261914 DOI: 10.3389/fmicb.2020.01052] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/28/2020] [Indexed: 12/31/2022] Open
Abstract
Healthy soil microbiomes are crucial for achieving high productivity in combination with crop quality, but our understanding of microbial diversity is still limited. In a large-scale study including 116 composite samples from vineyards, orchards and other crops from all over Styria (south-east Austria), agricultural management as well as distinct soil parameters were identified as drivers of the indigenous microbial communities in agricultural soils. The analysis of the soil microbiota based on microbial profiling of prokaryotic 16S rRNA gene fragments and fungal ITS regions revealed high bacterial and fungal diversity within Styrian agricultural soils; 206,596 prokaryotic and 53,710 fungal OTUs. Vineyards revealed a significantly higher diversity and distinct composition of soil fungi over orchards and other agricultural soils, whereas the prokaryotic diversity was unaffected. Soil pH was identified as one of the most important edaphic modulators of microbial community structure in both, vineyard and orchard soils. In general, the acid-base balance, disorders in the soil sorption complex, content and quality of organic substance as well as individual nutrients were identified as important drivers of the microbial community structure of Styrian vineyard and orchard soils. However, responses to distinct parameters differed in orchards and vineyards, and prokaryotic and fungal community responded differently to the same abiotic factor. In comparison to orchards, the microbiome of vineyard soils maintained a higher stability when herbicides were applied. Orchard soils exhibited drastic shifts within community composition; herbicides seem to have a substantial impact on the bacterial order Chthoniobacterales as well as potential plant growth promoters and antagonists of phytopathogens (Flavobacterium, Monographella), with a decreased abundance in herbicide-treated soils. Moreover, soils of herbicide-treated orchards revealed a significantly higher presence of potential apple pathogenic fungi (Nectria, Thelonectria). These findings provide the basis to adapt soil management practices in the future in order to maintain a healthy microbiome in agricultural soils.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Philipp Wagner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Robert Matzer
- ARGE obst.wein, Association of Weinbauverband Steiermark and Verband Steirischer Erwerbsobstbauern, Graz, Austria
| | | | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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20
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Sharma R, Gal L, Garmyn D, Bisaria VS, Sharma S, Piveteau P. Evidence of Biocontrol Activity of Bioinoculants Against a Human Pathogen, Listeria monocytogenes. Front Microbiol 2020; 11:350. [PMID: 32218775 PMCID: PMC7078112 DOI: 10.3389/fmicb.2020.00350] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/17/2020] [Indexed: 11/13/2022] Open
Abstract
Due to rhizodeposits and various microbial interactions, the rhizosphere is an extremely dynamic system, which provides a conductive niche not only for bacteria beneficial to plants but also for those that might pose a potential threat to humans. The importance of bioinoculants as biocontrol agents to combat phytopathogens has been widely recognized. However, little information exists with respect to their role in inhibiting human pathogens in the rhizosphere. The present study is an attempt to understand the impact of an established bacterial consortium, Azotobacter chroococcum, Bacillus megaterium, and Pseudomonas fluorescens, on the survivability of Listeria monocytogenes in the rhizosphere of Cajanus cajan and Festuca arundinacea. An experiment conducted in Hoagland's medium in the presence of C. cajan demonstrated that the presence of bioinoculants impaired growth of L. monocytogenes compared to that observed in their absence. On the other hand, in the presence of F. arundinacea, no significant differences were observed in the population dynamics of L. monocytogenes in the presence or absence of the bioinoculants. Agar plate assay through cross streak method revealed the inhibition of L. monocytogenes by bioinoculants. Potential bioactive compounds were identified by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). These results suggest that agricultural amendments can act as protective agents against human pathogens while enforcing plant growth promotion.
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Affiliation(s)
- Richa Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Laurent Gal
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - Dominique Garmyn
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
| | - V. S. Bisaria
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique, Université Bourgogne – Franche-Comté, Dijon, France
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21
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Liu J, Ridgway HJ, Jones EE. Apple endophyte community is shaped by tissue type, cultivar and site and has members with biocontrol potential against Neonectria ditissima. J Appl Microbiol 2020; 128:1735-1753. [PMID: 31981438 DOI: 10.1111/jam.14587] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/15/2020] [Accepted: 01/17/2020] [Indexed: 11/29/2022]
Abstract
AIMS This research aimed to identify factors influencing endophyte community structure in apple shoots and the bioactivity of cultured representatives against the fungal pathogen Neonectria ditissima. METHODS AND RESULTS The endophyte community in leaves and stems of the apple cultivars 'Royal Gala' and 'Braeburn' were analysed by a cultivation-independent method (PCR-DGGE) which showed that tissue type, cultivar and site were determinant factors, with the endophyte taxa in 'Royal Gala' more variable than that in 'Braeburn', with leaf endophyte communities typically differing from stems in both cultivars. Seasonal (spring vs autumn) and regional (Nelson vs Hawke's Bay) variations were not obvious in woody stems. A collection of 783 bacterial and 87 fungal endophytes were recovered from leaves and stems of 'Royal Gala', 'Braeburn', 'Scilate' and/or 'Scifresh' from Nelson (nine sites) and Hawke's Bay (five sites) in spring and from Nelson (three sites) in autumn. A dual culture plating assay was used to test their ability to inhibit the mycelial growth of N. ditissima. Thirteen bacterial (mean of percent inhibition ≥20%) and 17 fungal isolates were antagonistic towards N. ditissima. These isolates belonged to the bacterial genera Bacillus and Pseudomonas, and fungal genera Chaetomium, Epicoccum, Biscogniauxia, Penicillium, Diaporthe, Phlyctema and two unidentified fungal isolates. CONCLUSIONS Endophyte communities in apple shoots were determined by tissue type, cultivar and site. Endophytic bacterial and fungal isolates inhibiting N. ditissima growth in vitro were found. SIGNIFICANCE AND IMPACT OF THE STUDY These results provided new evidence of factors influencing apple endophyte community in New Zealand. Endophytes with potential to reduce N. ditissima infection were identified, with the potential to be developed into a biocontrol strategy for European canker.
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Affiliation(s)
- J Liu
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
| | - H J Ridgway
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand.,The New Zealand Institute for Plant and Food Research Ltd, Christchurch, New Zealand
| | - E E Jones
- Department of Pest-management and Conservation, Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, Canterbury, New Zealand
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Dagher DJ, de la Providencia IE, Pitre FE, St-Arnaud M, Hijri M. Plant Identity Shaped Rhizospheric Microbial Communities More Strongly Than Bacterial Bioaugmentation in Petroleum Hydrocarbon-Polluted Sediments. Front Microbiol 2019; 10:2144. [PMID: 31572347 PMCID: PMC6753587 DOI: 10.3389/fmicb.2019.02144] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 08/30/2019] [Indexed: 01/21/2023] Open
Abstract
Manipulating the plant-root microbiota has the potential to reduce plant stress and promote their growth and production in harsh conditions. Community composition and activity of plant-roots microbiota can be either beneficial or deleterious to plant health. Shifting this equilibrium could then strongly affect plant productivity in anthropized areas. In this study, we tested whether repeated bioaugmentation with Proteobacteria influenced plant productivity and the microbial communities associated with the rhizosphere of four plant species growing in sediments contaminated with petroleum hydrocarbons (PHCs). A mesocosm experiment was performed in randomized block design with two factors: (1) presence or absence of four plants species collected from a sedimentation basin of a former petrochemical plant, and (2) bioaugmentation or not with a bacterial consortium composed of ten isolates of Proteobacteria. Plants were grown in a greenhouse over 4 months. MiSeq amplicon sequencing, targeting the bacterial 16S rRNA gene and the fungal ITS, was used to assess microbial community structures of sediments from planted or unplanted microcosms. Our results showed that while bioaugmentation caused a significant shift in microbial communities, presence of plant and their species identity had a stronger influence on the structure of the microbiome in PHCs contaminated sediments. The outcome of this study provides knowledge on the diversity and behavior of rhizosphere microbes associated with indigenous plants following repeated bioaugmentation, underlining the importance of plant selection in order to facilitate their efficient management, in order to accelerate processes of land reclamation.
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Affiliation(s)
- Dimitri J. Dagher
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | | | - Frédéric E. Pitre
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
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23
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Secondary metabolites from the Aspergillus sp. in the rhizosphere soil of Phoenix dactylifera (Palm tree). BMC Chem 2019; 13:103. [PMID: 31410414 PMCID: PMC6686371 DOI: 10.1186/s13065-019-0624-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 07/31/2019] [Indexed: 12/03/2022] Open
Abstract
The soil-derived fungus Aspergillus sp. isolated from the rhizospheric soil of Phoenix dactylifera (Date palm tree) and cultured on the large scale solid rice medium yielded a novel compound 1-(4-hydroxy-2,6-dimethoxy-3,5-dimethylphenyl)-2-methyl-1-butanone (1) and four known compounds; citricin (2), dihydrocitrinone (3), 2, 3, 4-trimethyl-5, 7-dihydroxy-2, 3-dihydrobenzofuran (4) and oricinol (5). The structures of the isolated compounds were elucidated by MS, 1H, 13C and 2D NMR spectra. Compound (1) exhibited potent antimicrobial activities against Staphylococcus aureus with MIC values of 2.3 μg mL−1 and significant growth inhibitions of 82.3 ± 3.3 against Candida albicans and of 79.2 ± 2.6 against Candida parapsilosis. This is the first report to isolate metabolites from the fungus Aspergillus found in temperate region date plant rhizospheres.![]()
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24
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Qian X, Li H, Wang Y, Wu B, Wu M, Chen L, Li X, Zhang Y, Wang X, Shi M, Zheng Y, Guo L, Zhang D. Leaf and Root Endospheres Harbor Lower Fungal Diversity and Less Complex Fungal Co-occurrence Patterns Than Rhizosphere. Front Microbiol 2019; 10:1015. [PMID: 31143169 PMCID: PMC6521803 DOI: 10.3389/fmicb.2019.01015] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/24/2019] [Indexed: 12/21/2022] Open
Abstract
Plant-associated microbiomes are key determinants of host-plant fitness, productivity, and function. However, compared to bacterial community, we still lack fundamental knowledge concerning the variation in the fungal microbiome at the plant niche level. In this study, we quantified the fungal communities in the rhizosphere soil, as well as leaf and root endosphere compartments of a subtropical island shrub, Mussaenda kwangtungensis, using high-throughput DNA sequencing. We found that fungal microbiomes varied significantly across different plant compartments. Rhizosphere soil exhibited the highest level of fungal diversity, whereas the lowest level was found in the leaf endosphere. Further, the fungal communities inhabiting the root endosphere shared a greater proportion of fungal operational taxonomic units (OTUs) with rhizosphere communities than with leaf fungal endophyte communities, despite significant separation in community structure between the two belowground compartments. The fungal co-occurrence networks in the three compartments of M. kwangtungensis showed scale-free features and non-random co-occurrence patterns and matched the topological properties of small-world and evidently modular structure. Additionally, the rhizosphere network was more complex and showed higher centrality and connectedness than the leaf and root endosphere networks. Overall, our findings provide comprehensive insights into the structural variability, niche differentiation, and co-occurrence patterns in the plant associated fungal microbiome.
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Affiliation(s)
- Xin Qian
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hanzhou Li
- Biomarker Technologies Corporation, Beijing, China
| | - Yonglong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Binwei Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mingsong Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liang Chen
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingchun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ying Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiangping Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yong Zheng
- Key Laboratory of Humid Subtropical Eco-geographical Process of Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Liangdong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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25
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Microbial Consortia versus Single-Strain Inoculants: An Advantage in PGPM-Assisted Tomato Production? AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9020105] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The use of biostimulants with plant growth-promoting properties, but without significant input of nutrients, is discussed as a strategy to increase stress resistance and nutrient use efficiency of crops. However, limited reproducibility under real production conditions remains a major challenge. The use of combination products based on microbial and non-microbial biostimulants or microbial consortia, with the aim to exploit complementary or synergistic interactions and increase the flexibility of responses under different environmental conditions, is discussed as a potential strategy to overcome this problem. This study aimed at comparing the efficiency of selected microbial single-strain inoculants with proven plant-growth promoting potential versus consortium products under real production conditions in large-scale tomato cultivation systems, exposed to different environmental challenges. In a protected greenhouse production system at Timisoara, Romania, with composted cow manure, guano, hair-, and feather-meals as major fertilizers, different fungal and bacterial single-strain inoculants, as well as microbial consortium products, showed very similar beneficial responses. Nursery performance, fruit setting, fruit size distribution, seasonal yield share, and cumulative yield (39–84% as compared to the control) were significantly improved over two growing periods. By contrast, superior performance of the microbial consortia products (MCPs) was recorded under more challenging environmental conditions in an open-field drip-fertigated tomato production system in the Negev desert, Israel with mineral fertilization on a high pH (7.9), low fertility, and sandy soil. This was reflected by improved phosphate (P) acquisition, a stimulation of vegetative shoot biomass production and increased final fruit yield under conditions of limited P supply. Moreover, MCP inoculation was associated with selective changes of the rhizosphere-bacterial community structure particularly with respect to Sphingobacteriia and Flavobacteria, reported as salinity indicators and drought stress protectants. Phosphate limitation reduced the diversity of bacterial populations at the root surface (rhizoplane) and this effect was reverted by MCP inoculation, reflecting the improved P status of the plants. The results support the hypothesis that the use of microbial consortia can increase the efficiency and reproducibility of BS-assisted strategies for crop production, particularly under challenging environmental conditions.
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26
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Oni FE, Geudens N, Omoboye OO, Bertier L, Hua HGK, Adiobo A, Sinnaeve D, Martins JC, Höfte M. Fluorescent Pseudomonas and cyclic lipopeptide diversity in the rhizosphere of cocoyam (Xanthosoma sagittifolium). Environ Microbiol 2019; 21:1019-1034. [PMID: 30623562 DOI: 10.1111/1462-2920.14520] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/21/2022]
Abstract
Cocoyam (Xanthosoma sagittifolium (L.)), an important tuber crop in the tropics, is severely affected by the cocoyam root rot disease (CRRD) caused by Pythium myriotylum. The white cocoyam genotype is very susceptible while the red cocoyam has some field tolerance to CRRD. Fluorescent Pseudomonas isolates obtained from the rhizosphere of healthy red and white cocoyams from three different fields in Cameroon were taxonomically characterized. The cocoyam rhizosphere was enriched with P. fluorescens complex and P. putida isolates independent of the plant genotype. LC-MS and NMR analyses revealed that 50% of the Pseudomonas isolates produced cyclic lipopeptides (CLPs) including entolysin, lokisin, WLIP, putisolvin and xantholysin together with eight novel CLPs. In general, CLP types were linked to specific taxonomic groups within the fluorescent pseudomonads. Representative CLP-producing bacteria showed effective control against CRRD while purified CLPs caused hyphal branching or hyphal leakage in P. myriotylum. The structure of cocoyamide A, a CLP which is predominantly produced by P. koreensis group isolates within the P. fluorescens complex is described. Compared with the white cocoyam, the red cocoyam rhizosphere appeared to support a more diverse CLP spectrum. It remains to be investigated whether this contributes to the field tolerance displayed by the red cocoyam.
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Affiliation(s)
- Feyisara Eyiwumi Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Niels Geudens
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Olumide Owolabi Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Lien Bertier
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Hoang Gia Khuong Hua
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute for Agricultural Research for Development (IRAD), Ekona, P.M.B 25, Buea, Cameroon
| | - Davy Sinnaeve
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - José C Martins
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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27
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Dehghani Bidgoli R, Azarnezhad N, Akhbari M, Ghorbani M. Salinity stress and PGPR effects on essential oil changes in Rosmarinus officinalis L. ACTA ACUST UNITED AC 2019. [DOI: 10.1186/s40066-018-0246-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Singh D, Geat N, Rajawat MVS, Prasanna R, Kar A, Singh AM, Saxena AK. Prospecting endophytes from different Fe or Zn accumulating wheat genotypes for their influence as inoculants on plant growth, yield, and micronutrient content. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1388-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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29
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Mahnert A, Ortega RA, Berg C, Grube M, Berg G. Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi. Front Microbiol 2018; 9:2343. [PMID: 30327646 PMCID: PMC6174238 DOI: 10.3389/fmicb.2018.02343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/12/2018] [Indexed: 12/18/2022] Open
Abstract
Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.
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Affiliation(s)
- Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Rocel Amor Ortega
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Department of Biology, College of Science, University of the Philippines Baguio, Baguio, Philippines
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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30
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Yergeau E, Tremblay J, Joly S, Labrecque M, Maynard C, Pitre FE, St-Arnaud M, Greer CW. Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. THE ISME JOURNAL 2018; 12:869-884. [PMID: 29330533 PMCID: PMC5864237 DOI: 10.1038/s41396-017-0018-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/10/2017] [Accepted: 11/03/2017] [Indexed: 11/09/2022]
Abstract
Phytoremediation using willows is thought to be a sustainable alternative to traditional remediation techniques involving excavation, transport, and landfilling. However, the complexity of the interaction between the willow and its associated highly diverse microbial communities makes the optimization of phytoremediation very difficult. Here, we have sequenced the rhizosphere metatranscriptome of four willow species and the plant root metatranscriptome for two willow species growing in petroleum hydrocarbon-contaminated and non-contaminated soils on a former petroleum refinery site. Significant differences in the abundance of transcripts related to different bacterial and fungal taxa were observed between willow species, mostly in contaminated soils. When comparing transcript abundance in contaminated vs. non-contaminated soil for each willow species individually, transcripts for many microbial taxa and functions were significantly more abundant in contaminated rhizosphere soil for Salix eriocephala, S. miyabeana and S. purpurea, in contrast to what was observed in the rhizosphere of S. caprea. This agrees with the previously reported sensitivity of S. caprea to contamination, and the superior tolerance of S. miyabeana and S. purpurea to soil contamination at that site. The root metatranscriptomes of two species were compared and revealed that plants transcripts are mainly influenced by willow species, while microbial transcripts mainly responded to contamination. A comparison of the rhizosphere and root metatranscriptomes in the S. purpurea species revealed a complete reorganization of the linkages between root and rhizosphere pathways when comparing willows growing in contaminated and non-contaminated soils, mainly because of large shifts in the rhizosphere metatranscriptome.
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Affiliation(s)
- Etienne Yergeau
- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, QC, Canada.
| | - Julien Tremblay
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Michel Labrecque
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Christine Maynard
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
| | - Frederic E Pitre
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Jardin botanique de Montréal et Université de Montréal, Montréal, QC, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, Montréal, QC, Canada
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31
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Dhar Purkayastha G, Mangar P, Saha A, Saha D. Evaluation of the biocontrol efficacy of a Serratia marcescens strain indigenous to tea rhizosphere for the management of root rot disease in tea. PLoS One 2018; 13:e0191761. [PMID: 29466418 PMCID: PMC5821441 DOI: 10.1371/journal.pone.0191761] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 01/10/2018] [Indexed: 11/19/2022] Open
Abstract
The aim of the present study is to evaluate plant growth promoting and biocontrol efficacy of a Serratia marcescens strain ETR17 isolated from tea rhizosphere for the effective management of root rot disease in tea. Isolated bacterial culture ETR17 showed significant level of in vitro antagonism against nine different foliar and root pathogens of tea. The phenotypic and molecular characterization of ETR17 revealed the identity of the bacterium as Serratia marcescens. The bacterium was found to produce several hydrolytic enzymes like chitinase, protease, lipase, cellulase and plant growth promoting metabolites like IAA and siderophore. Scanning electron microscopic studies on the interaction zone between pathogen and antagonistic bacterial isolate revealed severe deformities in the fungal mycelia. Spectral analyses (LC-ESI-MS, UV-VIS spectrophotometry and HPLC) and TLC indicated the presence of the antibiotics pyrrolnitrin and prodigiosin in the extracellular bacterial culture extracts. Biofilm formation by ETR17 on polystyrene surface was also observed. In vivo application of talc-based formulations prepared with the isolate ETR17 in tea plantlets under green house conditions revealed effective reduction of root-rot disease as well as plant growth promotion to a considerable extent. Viability studies with the ETR17 talc formulation showed the survivability of the isolate up to six months at room temperature. The sustenance of ETR17 (concentration of 8-9x108 cfu g-1) in the soil after the application of talc formulation was recorded by ELISA. Safety studies revealed that ETR17 did not produce hemolysin as observed in pathogenic Serratia strains. The biocontrol strain reported in this study can be used for field application in order to minimize the use of chemical fungicides for disease control in tea gardens.
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Affiliation(s)
| | - Preeti Mangar
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - Aniruddha Saha
- Department of Botany, University of North Bengal, Siliguri, West Bengal, India
| | - Dipanwita Saha
- Department of Biotechnology, University of North Bengal, Siliguri, West Bengal, India
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32
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Yim B, Nitt H, Wrede A, Jacquiod S, Sørensen SJ, Winkelmann T, Smalla K. Effects of Soil Pre-Treatment with Basamid® Granules, Brassica juncea, Raphanus sativus, and Tagetes patula on Bacterial and Fungal Communities at Two Apple Replant Disease Sites. Front Microbiol 2017; 8:1604. [PMID: 28919882 PMCID: PMC5586068 DOI: 10.3389/fmicb.2017.01604] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/07/2017] [Indexed: 12/04/2022] Open
Abstract
Nurseries producing apple and rose rootstock plants, apple orchards as well as rose production often experience replanting problems after several cultivations at the same site when a chemical soil disinfectant is not applied. The etiology of apple and rose replanting problems is most likely caused by soil-borne pathogen complex, defined as "replant disease (RD)". Symptoms typical of RD are reduced shoot and root growth, a smaller leaf area, a significant decrease in plant biomass, yield and fruit quality and a shorter life span. In our previous study, we showed that RD symptoms were reduced when apple rootstock M106 were grown in RD soils treated either with the soil fumigant Basamid or after biofumigation by incorporating Brassica juncea or Raphanus sativus or by growing Tagetes under field conditions compared to untreated control soil. The present study aimed at identifying potential bacterial and fungal taxa that were affected by different soil treatments and linking bacterial and fungal responders to plant performance. Miseq® Illumina® sequencing of 16S rRNA gene fragments (bacteria) and ITS regions (fungi) amplified from total community DNA extracted from soil samples taken 4 weeks after treatments were performed. Soil properties and culture history of the two RD sites greatly influenced soil microbiomes. Several bacterial genera were identified that significantly increased in treated soils such as Arthrobacter (R. sativus, both sites), Curtobacterium (Basamid, both sites), Terrimonas (Basamid and R. sativus, site A) and Ferruginibacter (B. juncea, site K and R. sativus, site A) that were also significantly and positively correlated with growth of apple M106 plants. Only few fungal genera, such as Podospora, Monographella and Mucor, were significantly promoted in soils treated with B. juncea and R. sativus (both sites). The least pronounced changes were recorded for bacterial as well as fungal communities in the RD soils planted with Tagetes. The detection of bacterial and fungal genera that were significantly increased in relative abundance in response to the treatments and that were positively correlated with plant growth suggests that management of the soil microbial community could contribute to overcome the apple RD encountered at affected sites.
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Affiliation(s)
- Bunlong Yim
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
- Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen DiagnosticsBraunschweig, Germany
| | - Heike Nitt
- Department of Plant Production, Plant Protection, Environment, Landwirtschaftskammer Schleswig-HolsteinEllerhoop, Germany
| | - Andreas Wrede
- Department of Horticulture, Landwirtschaftskammer Schleswig-HolsteinEllerhoop, Germany
| | - Samuel Jacquiod
- Section of Microbiology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Søren J. Sørensen
- Section of Microbiology, Department of Biology, University of CopenhagenCopenhagen, Denmark
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Kornelia Smalla
- Federal Research Centre for Cultivated Plants (JKI), Institute for Epidemiology and Pathogen DiagnosticsBraunschweig, Germany
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33
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Ambardar S, Singh HR, Gowda M, Vakhlu J. Comparative Metagenomics Reveal Phylum Level Temporal and Spatial Changes in Mycobiome of Belowground Parts of Crocus sativus. PLoS One 2016; 11:e0163300. [PMID: 27685092 PMCID: PMC5042540 DOI: 10.1371/journal.pone.0163300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/07/2016] [Indexed: 11/27/2022] Open
Abstract
Plant-fungal associations have been explored by routine cultivation based approaches and cultivation based approaches cannot catalogue more than 5% of fungal diversity associated with any niche. In the present study, an attempt has been made to catalogue fungal diversity associated with belowground parts i.e. rhizosphere and cormosphere, of Crocus sativus (an economically important herb) during two growth stages, using cultivation independent ITS gene targeted approach, taking bulk soil as reference. The 454 pyrosequencing sequence data analysis suggests that the fungal diversity was niche and growth stage specific. Fungi diversity, in the present case, was not only different between the two organs (roots and corm) but the dominance pattern varies between the cormosphere during two growth stages. Zygomycota was dominant fungal phylum in the rhizosphere whereas Basidiomycota was dominant in cormosphere during flowering stage. However in cormosphere though Basidiomycota was dominant phylum during flowering stage but Zygomycota was dominant during dormant stage. Interestingly, in cormosphere, the phyla which was dominant at dormant stage was rare at flowering stage and vice-versa (Basidiomycota: Flowering = 93.2% Dormant = 0.05% and Zygomycota: Flowering = 0.8% Dormant = 99.7%). At genus level, Rhizopus was dominant in dormant stage but was rare in flowering stage (Rhizopus: Dormant = 99.7% Flowering = 0.55%). This dynamics is not followed by the bulk soil fungi which was dominated by Ascomycota during both stages under study. The genus Fusarium, whose species F. oxysporum causes corm rot in C. sativus, was present during both stages with slightly higher abundance in roots. Interestingly, the abundance of Rhizopus varied a great deal in two stages in cormosphere but the abundance of Fusarium was comparable in two growth stages (Bulk soil Flowering = 0.05%, Rhizosphere Flowering = 1.4%, Cormosphere Flowering = 0.06%, Bulk soil Dormant = 2.47% and cormosphere dormant = 0.05%). This is the first report on the fungal diversity associated with the root of Crocus sativus and first report on the fungi associated with corm of any plant with the temporal and spatial variation in the fungal community structure.
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Affiliation(s)
- Sheetal Ambardar
- School of Biotechnology, University of Jammu, Jammu, India
- Next Generation Genomics Facility, C-CAMP, NCBS, Bangalore, India
| | | | - Malali Gowda
- Next Generation Genomics Facility, C-CAMP, NCBS, Bangalore, India
| | - Jyoti Vakhlu
- School of Biotechnology, University of Jammu, Jammu, India
- * E-mail:
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Tardif S, Yergeau É, Tremblay J, Legendre P, Whyte LG, Greer CW. The Willow Microbiome Is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects. Front Microbiol 2016; 7:1363. [PMID: 27660624 PMCID: PMC5015464 DOI: 10.3389/fmicb.2016.01363] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Abstract
The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.
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Affiliation(s)
- Stacie Tardif
- Department of Natural Resource Sciences, McGill UniversitySainte-Anne-de-Bellevue, QC, Canada; Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagen, Denmark
| | - Étienne Yergeau
- Energy, Mining, and Environment, National Research Council CanadaMontréal, QC, Canada; Centre INRS-Institut Armand-Frappier, Institut national de la recherche scientifiqueLaval, QC, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment, National Research Council Canada Montréal, QC, Canada
| | - Pierre Legendre
- Département de Sciences Biologiques, Université de Montréal Montréal, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University Sainte-Anne-de-Bellevue, QC, Canada
| | - Charles W Greer
- Department of Natural Resource Sciences, McGill UniversitySainte-Anne-de-Bellevue, QC, Canada; Energy, Mining, and Environment, National Research Council CanadaMontréal, QC, Canada
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Lu D, Jin H, Yang X, Zhang D, Yan Z, Li X, Zhao Y, Han R, Qin B. Characterization of rhizosphere and endophytic fungal communities from roots of Stipa purpurea in alpine steppe around Qinghai Lake. Can J Microbiol 2016; 62:643-56. [PMID: 27348421 DOI: 10.1139/cjm-2015-0857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stipa purpurea is among constructive endemic species in the alpine steppe on the Qinghai-Xizang Plateau. To reveal the fungal community structure and diversity in the rhizosphere and roots of this important grass and to analyze the potential influence of different habitats on the structure of fungal communities, we explored the root endophyte and the directly associated rhizosphere communities of S. purpurea by using internal transcribed spacer rRNA cloning and sequencing methods. We found that the roots of S. purpurea are associated with a diverse consortium of Basidiomycota (59.8%) and Ascomycota (38.5%). Most fungi obtained from rhizosphere soil in S. purpurea have been identified as Ascomycetes, while the high proportion detected in roots were basidiomycetous endophytes. The species richness, diversity, and evenness of fungal assemblages were higher in roots than in the rhizosphere soil. Fungi inhabiting the rhizosphere and roots of S. purpurea are significantly different, and the rhizosphere and endophyte communities are largely independent with little overlap in the dominant phyla or operational taxonomic units. Taken together, these results suggested that a wide variety of fungal communities are associated with the roots and rhizosphere soil of S. purpurea and that the fungal assemblages are strongly influenced by different habitats.
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Affiliation(s)
- Dengxue Lu
- a Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Hui Jin
- b Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Xiaoyan Yang
- b Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Denghong Zhang
- c College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Centers for Grazing land Ecosystem Sustainability, Gansu Agricultural University, Lanzhou 730070, People's Republic of China
| | - Zhiqiang Yan
- b Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Xiuzhuang Li
- b Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Yuhui Zhao
- a Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Rongbing Han
- a Institute of Biology, Gansu Academy of Sciences, Lanzhou 730000, People's Republic of China
| | - Bo Qin
- b Key Laboratory of Chemistry of Northwestern Plant Resources and Key Laboratory for Natural Medicine of Gansu Province, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000, People's Republic of China
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Zachow C, Berg C, Müller H, Monk J, Berg G. Endemic plants harbour specific Trichoderma communities with an exceptional potential for biocontrol of phytopathogens. J Biotechnol 2016; 235:162-70. [PMID: 27039271 DOI: 10.1016/j.jbiotec.2016.03.049] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/26/2016] [Accepted: 03/29/2016] [Indexed: 10/22/2022]
Abstract
Trichoderma strains exhibit enormous potential for applications in biotechnology, in particular as biocontrol agents against pathogens. However, little is known about the diversity of plant-associated Trichoderma communities at a global scale and their antagonistic spectrum. In order to gather information about structure and function, we compared Trichoderma biomes of endemic (Aeonium, Diospyros, Hebe, Rhododendron) and cosmopolitan plants (Zea mays) in a global study encompassing the area Northwest Africa to New Zealand via the European Alps and Madagascar. At the quantitative level we found no differences between cosmopolitan and endemic plants. Statistically significant differences were detected at the qualitative level: Trichoderma populations of endemic plants were highly specific and diverse with hot spots appearing in Madagascar and New Zealand. By contrast, maize plants from all sites shared the majority of Trichoderma species (65.5%). Interestingly, the high above ground biodiversity in ecosystems containing endemic plants was confirmed by a high below ground Trichoderma diversity. Despite the differences, we found a global Trichoderma core community shared by all analysed plants, which was dominated by T. koningii and T. koningiopsis. Amplicon-based network analyses revealed a high similarity between maize Trichoderma grown world-wide and distinct populations of endemic plants. Furthermore, Trichoderma strains from endemic plants showed a higher antagonistic activity against fungal pathogens compared to maize-associated strains. Our results showed that endemic plants are associated with a specific Trichoderma microbiome which possesses a high antagonistic activity indicating that it has potential to be used for biocontrol purposes.
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Affiliation(s)
- Christin Zachow
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, 8010 Graz, Austria.
| | - Christian Berg
- Karl-Franzens-University of Graz, Institute of Plant Sciences, Holteigasse 6, 8010 Graz, Austria
| | - Henry Müller
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria
| | - Jana Monk
- AgResearch Limited, 4749 Private Bag, 8140 Christchurch, New Zealand
| | - Gabriele Berg
- Graz University of Technology, Institute of Environmental Biotechnology, Petersgasse 12, 8010 Graz, Austria
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Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils. Fungal Biol 2016; 120:862-72. [PMID: 27268246 DOI: 10.1016/j.funbio.2016.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 03/10/2016] [Accepted: 03/21/2016] [Indexed: 12/19/2022]
Abstract
Rhizosphere and root-associated microbiota are crucial in determining plant health and in increasing productivity of agricultural crops. To date, research has mainly focused on the bacterial dimension of the microbiota. However, interest in the mycobiota is increasing, since fungi play a key role in soil ecosystems. We examined the effect of plant genotype, soil, and of Fusarium oxysporum f. sp. lycopersici (Fol) on the cultivable component of rhizosphere and root-associated mycobiota of tomato. Resistant and susceptible varieties were cultivated on two different soils (A and B), under glasshouse conditions. Isolated fungi were identified by morphological and molecular approaches. Differences were found between the rhizosphere and the roots, which in general displayed a lower number of species. The structure of the mycobiota was significantly affected by the soil type in the rhizosphere as well as by the plant genotype within the roots (NPERMANOVA, p < 0.05). The addition of Fol changed the community structure, particularly in soil A, where Penicillium spp. and Fusarium spp. were the dominant responding fungi. Overall, the results indicated that i) soil type and plant genotype affect the fungal communities; ii) plant roots select few species from the rhizosphere; and iii) the fungal community structure is influenced by Fol.
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Elucidating the Diversity of Aquatic Microdochium and Trichoderma Species and Their Activity against the Fish Pathogen Saprolegnia diclina. Int J Mol Sci 2016; 17:ijms17010140. [PMID: 26805821 PMCID: PMC4730379 DOI: 10.3390/ijms17010140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 12/25/2015] [Accepted: 01/12/2016] [Indexed: 11/17/2022] Open
Abstract
Animals and plants are increasingly threatened by emerging fungal and oomycete diseases. Amongst oomycetes, Saprolegnia species cause population declines in aquatic animals, especially fish and amphibians, resulting in significant perturbation in biodiversity, ecological balance and food security. Due to the prohibition of several chemical control agents, novel sustainable measures are required to control Saprolegnia infections in aquaculture. Previously, fungal community analysis by terminal restriction fragment length polymorphism (T-RFLP) revealed that the Ascomycota, specifically the genus Microdochium, was an abundant fungal phylum associated with salmon eggs from a commercial fish farm. Here, phylogenetic analyses showed that most fungal isolates obtained from salmon eggs were closely related to Microdochium lycopodinum/Microdochium phragmitis and Trichoderma viride species. Phylogenetic and quantitative PCR analyses showed both a quantitative and qualitative difference in Trichoderma population between diseased and healthy salmon eggs, which was not the case for the Microdochium population. In vitro antagonistic activity of the fungi against Saprolegnia diclina was isolate-dependent; for most Trichoderma isolates, the typical mycoparasitic coiling around and/or formation of papilla-like structures on S. diclina hyphae were observed. These results suggest that among the fungal community associated with salmon eggs, Trichoderma species may play a role in Saprolegnia suppression in aquaculture.
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Matyjaszczyk E. Products containing microorganisms as a tool in integrated pest management and the rules of their market placement in the European Union. PEST MANAGEMENT SCIENCE 2015; 71:1201-1206. [PMID: 25652108 DOI: 10.1002/ps.3986] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 11/20/2014] [Accepted: 01/27/2015] [Indexed: 05/29/2023]
Abstract
Products containing microorganisms (bacteria, fungi and viruses) can be used in plant production as an intervention as well as a prevention method for pest control. Their utilisation is strictly in line with the principles of integrated pest management, provided that they are effective and safe. The rules of registration of microorganisms for crop production in the European Union differ, depending on whether they are placed on the market as plant protection products or not. For over 20 years, uniform rules for registration of plant protection products have been in force. Currently, 36 microorganisms marked up to the strain are approved for use in pest control in the Community. The decision concerning market placement of plant protection products containing approved microorganisms is issued for each member state separately. The approaches to market placement of other products with microorganisms differ within the EU, ranging from a complete lack of requirements to long and costly registration procedures.
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Affiliation(s)
- Ewa Matyjaszczyk
- Plant Protection Institute - National Research Institute, Poznań, Poland
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40
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Sundram S, Meon S, Seman IA, Othman R. Application of arbuscular mycorrhizal fungi with Pseudomonas aeruginosa UPMP3 reduces the development of Ganoderma basal stem rot disease in oil palm seedlings. MYCORRHIZA 2015; 25:387-97. [PMID: 25492807 DOI: 10.1007/s00572-014-0620-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/18/2014] [Indexed: 05/16/2023]
Abstract
The effect of arbuscular mycorrhizal fungi (AMF) in combination with endophytic bacteria (EB) in reducing development of basal stem rot (BSR) disease in oil palm (Elaeis guineensis) was investigated. BSR caused by Ganoderma boninense leads to devastating economic loss and the oil palm industry is struggling to control the disease. The application of two AMF with two EB as biocontrol agents was assessed in the nursery and subsequently, repeated in the field using bait seedlings. Seedlings pre-inoculated with a combination of Glomus intraradices UT126, Glomus clarum BR152B and Pseudomonas aeruginosa UPMP3 significantly reduced disease development measured as the area under disease progression curve (AUDPC) and the epidemic rate (R L) of disease in the nursery. A 20-month field trial using similar treatments evaluated disease development in bait seedlings based on the rotting area/advancement assessed in cross-sections of the seedling base. Data show that application of Glomus intraradices UT126 singly reduced disease development of BSR, but that combination of the two AMF with P. aeruginosa UPMP3 significantly improved biocontrol efficacy in both nursery and fields reducing BSR disease to 57 and 80%, respectively. The successful use of bait seedlings in the natural environment to study BSR development represents a promising alternative to nursery trial testing in the field with shorter temporal assessment.
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Affiliation(s)
- Shamala Sundram
- Ganoderma and Diseases Research of Oil Palm Unit, Malaysian Palm Oil Board, No. 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia,
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Xu X, Passey T, Wei F, Saville R, Harrison RJ. Amplicon-based metagenomics identified candidate organisms in soils that caused yield decline in strawberry. HORTICULTURE RESEARCH 2015; 2:15022. [PMID: 26504572 PMCID: PMC4595980 DOI: 10.1038/hortres.2015.22] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 05/25/2023]
Abstract
A phenomenon of yield decline due to weak plant growth in strawberry was recently observed in non-chemo-fumigated soils, which was not associated with the soil fungal pathogen Verticillium dahliae, the main target of fumigation. Amplicon-based metagenomics was used to profile soil microbiota in order to identify microbial organisms that may have caused the yield decline. A total of 36 soil samples were obtained in 2013 and 2014 from four sites for metagenomic studies; two of the four sites had a yield-decline problem, the other two did not. More than 2000 fungal or bacterial operational taxonomy units (OTUs) were found in these samples. Relative abundance of individual OTUs was statistically compared for differences between samples from sites with or without yield decline. A total of 721 individual comparisons were statistically significant - involving 366 unique bacterial and 44 unique fungal OTUs. Based on further selection criteria, we focused on 34 bacterial and 17 fungal OTUs and found that yield decline resulted probably from one or more of the following four factors: (1) low abundance of Bacillus and Pseudomonas populations, which are well known for their ability of supressing pathogen development and/or promoting plant growth; (2) lack of the nematophagous fungus (Paecilomyces species); (3) a high level of two non-specific fungal root rot pathogens; and (4) wet soil conditions. This study demonstrated the usefulness of an amplicon-based metagenomics approach to profile soil microbiota and to detect differential abundance in microbes.
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Affiliation(s)
- Xiangming Xu
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Thomas Passey
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Feng Wei
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
| | - Robert Saville
- East Malling Research, East Malling, West Malling, Kent, ME19 6BJ, UK
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Vandenkoornhuyse P, Quaiser A, Duhamel M, Le Van A, Dufresne A. The importance of the microbiome of the plant holobiont. THE NEW PHYTOLOGIST 2015; 206:1196-206. [PMID: 25655016 DOI: 10.1111/nph.13312] [Citation(s) in RCA: 873] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
Plants can no longer be considered as standalone entities and a more holistic perception is needed. Indeed, plants harbor a wide diversity of microorganisms both inside and outside their tissues, in the endosphere and ectosphere, respectively. These microorganisms, which mostly belong to Bacteria and Fungi, are involved in major functions such as plant nutrition and plant resistance to biotic and abiotic stresses. Hence, the microbiota impact plant growth and survival, two key components of fitness. Plant fitness is therefore a consequence of the plant per se and its microbiota, which collectively form a holobiont. Complementary to the reductionist perception of evolutionary pressures acting on plant or symbiotic compartments, the plant holobiont concept requires a novel perception of evolution. The interlinkages between the plant holobiont components are explored here in the light of current ecological and evolutionary theories. Microbiome complexity and the rules of microbiotic community assemblage are not yet fully understood. It is suggested that the plant can modulate its microbiota to dynamically adjust to its environment. To better understand the level of plant dependence on the microbiotic components, the core microbiota need to be determined at different hierarchical scales of ecology while pan-microbiome analyses would improve characterization of the functions displayed.
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Affiliation(s)
| | - Achim Quaiser
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Marie Duhamel
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Amandine Le Van
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
| | - Alexis Dufresne
- CNRS, UMR 6553 Ecobio, Université de Rennes 1, Campus Beaulieu, 35000, Rennes, France
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Sheoran N, Valiya Nadakkakath A, Munjal V, Kundu A, Subaharan K, Venugopal V, Rajamma S, Eapen SJ, Kumar A. Genetic analysis of plant endophytic Pseudomonas putida BP25 and chemo-profiling of its antimicrobial volatile organic compounds. Microbiol Res 2015; 173:66-78. [PMID: 25801973 DOI: 10.1016/j.micres.2015.02.001] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/31/2015] [Accepted: 02/07/2015] [Indexed: 11/19/2022]
Abstract
Black pepper associated bacterium BP25 was isolated from root endosphere of apparently healthy cultivar Panniyur-5 that protected black pepper against Phytophthora capsici and Radopholus similis - the major production constraints. The bacterium was characterized and mechanisms of its antagonistic action against major pathogens are elucidated. The polyphasic phenotypic analysis revealed its identity as Pseudomonas putida. Multi locus sequence typing revealed that the bacterium shared gene sequences with several other isolates representing diverse habitats. Tissue localization assays exploiting green fluorescence protein expression clearly indicated that PpBP25 endophytically colonized not only its host plant - black pepper, but also other distantly related plants such as ginger and arabidopsis. PpBP25 colonies could be enumerated from internal tissues of plants four weeks post inoculation indicated its stable establishment and persistence in the plant system. The bacterium inhibited broad range of pathogens such as Phytophthora capsici, Pythium myriotylum, Giberella moniliformis, Rhizoctonia solani, Athelia rolfsii, Colletotrichum gloeosporioides and plant parasitic nematode, Radopholus similis by its volatile substances. GC/MS based chemical profiling revealed presence of Heneicosane; Tetratetracontane; Pyrrolo [1,2-a] pyrazine-1,4-dione, hexahydro-3-(2-methylpropyl); Tetracosyl heptafluorobutyrate; 1-3-Eicosene, (E)-; 1-Heneicosanol; Octadecyl trifluoroacetate and 1-Pentadecene in PpBP25 metabolite. Dynamic head space GC/MS analysis of airborne volatiles indicated the presence of aromatic compounds such as 1-Undecene;Disulfide dimethyl; Pyrazine, methyl-Pyrazine, 2,5-dimethyl-; Isoamyl alcohol; Pyrazine, methyl-; Dimethyl trisulfide, etc. The work paved way for profiling of broad spectrum antimicrobial VOCs in endophytic PpBP25 for crop protection.
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Affiliation(s)
- Neelam Sheoran
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | | | - Vibhuti Munjal
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Aditi Kundu
- Division of Agricultural Chemicals, ICAR - Indian Agricultural Research Institute, New Delhi, India
| | - Kesavan Subaharan
- Division of Crop Protection, ICAR - Central Plantation Crops Research Institute, Kasaragod, India
| | - Vibina Venugopal
- Division of Crop Protection, ICAR - Central Plantation Crops Research Institute, Kasaragod, India
| | - Suseelabhai Rajamma
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Kozhikode, India
| | - Santhosh J Eapen
- Division of Crop Protection, ICAR - Indian Institute of Spices Research, Kozhikode, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi, India.
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Abundance and ribotypes of phosphate-solubilizing bacteria in Argentinean agricultural soils under no-till management. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-014-1006-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Berg G, Erlacher A, Smalla K, Krause R. Vegetable microbiomes: is there a connection among opportunistic infections, human health and our 'gut feeling'? Microb Biotechnol 2014; 7:487-95. [PMID: 25186140 PMCID: PMC4265069 DOI: 10.1111/1751-7915.12159] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 12/17/2022] Open
Abstract
The highly diverse microbiomes of vegetables are reservoirs for opportunistic and emerging pathogens. In recent years, an increased consumption, larger scale production and more efficient distribution of vegetables together with an increased number of immunocompromised individuals resulted in an enhanced number of documented outbreaks of human infections associated with the consumption of vegetables. Here we discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues. Based on these results, we discuss the question if vegetables can serve as a source of infection for immunocompromised individuals as well as possible solutions to avoid outbreaks. Moreover, the potentially positive aspects of the vegetables microbiome for the gut microbiota and human health are presented.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, 8010, Austria
| | - Armin Erlacher
- Institute of Environmental Biotechnology, Graz University of TechnologyGraz, 8010, Austria
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI)Braunschweig, 38104, Germany
| | - Robert Krause
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut – Federal Research Centre for Cultivated Plants (JKI)Braunschweig, 38104, Germany
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Nallanchakravarthula S, Mahmood S, Alström S, Finlay RD. Influence of soil type, cultivar and Verticillium dahliae on the structure of the root and rhizosphere soil fungal microbiome of strawberry. PLoS One 2014; 9:e111455. [PMID: 25347069 PMCID: PMC4210224 DOI: 10.1371/journal.pone.0111455] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/02/2014] [Indexed: 12/31/2022] Open
Abstract
Sustainable management of crop productivity and health necessitates improved understanding of the ways in which rhizosphere microbial populations interact with each other, with plant roots and their abiotic environment. In this study we examined the effects of different soils and cultivars, and the presence of a soil-borne fungal pathogen, Verticillium dahliae, on the fungal microbiome of the rhizosphere soil and roots of strawberry plants, using high-throughput pyrosequencing. Fungal communities of the roots of two cultivars, Honeoye and Florence, were statistically distinct from those in the rhizosphere soil of the same plants, with little overlap. Roots of plants growing in two contrasting field soils had high relative abundance of Leptodontidium sp. C2 BESC 319 g whereas rhizosphere soil was characterised by high relative abundance of Trichosporon dulcitum or Cryptococcus terreus, depending upon the soil type. Differences between different cultivars were not as clear. Inoculation with the pathogen V. dahliae had a significant influence on community structure, generally decreasing the number of rhizosphere soil- and root-inhabiting fungi. Leptodontidium sp. C2 BESC 319 g was the dominant fungus responding positively to inoculation with V. dahliae. The results suggest that 1) plant roots select microorganisms from the wider rhizosphere pool, 2) that both rhizosphere soil and root inhabiting fungal communities are influenced by V. dahliae and 3) that soil type has a stronger influence on both of these communities than cultivar.
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Affiliation(s)
- Srivathsa Nallanchakravarthula
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Shahid Mahmood
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sadhna Alström
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger D. Finlay
- Uppsala BioCenter, Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Pindi PK, Sultana T, Vootla PK. Plant growth regulation of Bt-cotton through Bacillus species. 3 Biotech 2014; 4:305-315. [PMID: 28324434 PMCID: PMC4026452 DOI: 10.1007/s13205-013-0154-0] [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: 05/18/2013] [Accepted: 07/08/2013] [Indexed: 11/23/2022] Open
Abstract
Deccan plateau in India periodically experiences droughts due to irregular rain fall and the soil in many parts of the region is considered to be poor for farming. Plant growth promoting rhizobacteria are originally defined as root-colonizing bacteria, i.e., Bacillus that cause either plant growth promotion or biological control of plant diseases. The study aims at the isolation of novel Bacillus species and to assess the biotechnological potential of the novel species as a biofertilizer, with respect to their plant growth promoting properties as efficient phosphate-solubilizing bacteria. Seven different strains of Bacillus were isolated from cotton rhizosphere soil near boys’ hostel of Palamuru University which belongs to Deccan plateau. Among seven isolated strains, Bacillus strain-7 has shown maximum support for good growth of eight cotton cultivars. This bacterial species is named Bacillus sp. PU-7 based on the phenotypic and phylogenetic analysis. Among eight cotton cultivars, Mahyco has shown high levels of IAA, proteins, chlorophyll, sugars and low level of proline. Efficacy of novel Bacillus sp. PU-7 with Mahyco cultivar has been checked experimentally at field level in four different cotton grown agricultural soils. The strains supported plant growth in almost all the cases, especially in the deep black soil, with a clear evidence of maximum plant growth by increased levels of phytohormone production and biochemical analysis, followed by shallow black soil. Hence, it is inferred that the novel isolate can be used as bioinoculant in the cotton fields.
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Prashar P, Kapoor N, Sachdeva S. Rhizosphere: its structure, bacterial diversity and significance. REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2014; 13:63-77. [PMID: 0 DOI: 10.1007/s11157-013-9317-z] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Yergeau E, Sanschagrin S, Maynard C, St-Arnaud M, Greer CW. Microbial expression profiles in the rhizosphere of willows depend on soil contamination. THE ISME JOURNAL 2014; 8:344-58. [PMID: 24067257 PMCID: PMC3906822 DOI: 10.1038/ismej.2013.163] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 11/09/2022]
Abstract
The goal of phytoremediation is to use plants to immobilize, extract or degrade organic and inorganic pollutants. In the case of organic contaminants, plants essentially act indirectly through the stimulation of rhizosphere microorganisms. A detailed understanding of the effect plants have on the activities of rhizosphere microorganisms could help optimize phytoremediation systems and enhance their use. In this study, willows were planted in contaminated and non-contaminated soils in a greenhouse, and the active microbial communities and the expression of functional genes in the rhizosphere and bulk soil were compared. Ion Torrent sequencing of 16S rRNA and Illumina sequencing of mRNA were performed. Genes related to carbon and amino-acid uptake and utilization were upregulated in the willow rhizosphere, providing indirect evidence of the compositional content of the root exudates. Related to this increased nutrient input, several microbial taxa showed a significant increase in activity in the rhizosphere. The extent of the rhizosphere stimulation varied markedly with soil contamination levels. The combined selective pressure of contaminants and rhizosphere resulted in higher expression of genes related to competition (antibiotic resistance and biofilm formation) in the contaminated rhizosphere. Genes related to hydrocarbon degradation were generally more expressed in contaminated soils, but the exact complement of genes induced was different for bulk and rhizosphere soils. Together, these results provide an unprecedented view of microbial gene expression in the plant rhizosphere during phytoremediation.
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Affiliation(s)
- Etienne Yergeau
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Sylvie Sanschagrin
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Christine Maynard
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
| | - Marc St-Arnaud
- Biodiversity Center, Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, Montreal, Quebec, Canada
| | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment, Montreal, Quebec, Canada
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