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Garcia-Lemos AM, Gobbi A, Nicolaisen MH, Hansen LH, Roitsch T, Veierskov B, Nybroe O. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Front Microbiol 2020; 11:198. [PMID: 32194515 PMCID: PMC7064441 DOI: 10.3389/fmicb.2020.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/28/2020] [Indexed: 01/01/2023] Open
Abstract
Abies nordmanniana is an economically important tree crop widely used for Christmas tree production. After initial growth in nurseries, seedlings are transplanted to the field. Rhizosphere bacterial communities generally impact the growth and health of the host plant. However, the dynamics of these communities during A. nordmanniana growth in nurseries, and during transplanting, has not previously been addressed. By a 16S rRNA gene amplicon sequencing approach, we characterized the composition and dynamics of bacterial communities in the rhizosphere during early plant growth in field and greenhouse nurseries and for plants transplanted from the greenhouse to the field. Moreover, the N-cycling potential of rhizosphere bacteria across plant age was addressed in both nurseries. Overall, a rhizosphere core microbiome of A. nordmanniana, comprising 19.9% of the taxa at genus level, was maintained across plant age, nursery production systems, and even during the transplantation of plants from the greenhouse to the field. The core microbiome included the bacterial genera Bradyrhizobium, Burkholderia, Flavobacterium, Pseudomonas, Rhizobium, Rhodanobacter, and Sphingomonas, which harbor several N-fixing and plant growth–promoting taxa. Nevertheless, both plant age and production system caused significant changes in the rhizosphere bacterial communities. Concerning community composition, the relative abundance of Rhizobiales (genera Rhizobium, Bradyrhizobium, and Devosia) was higher in the rhizosphere of field-grown A. nordmanniana, whereas the relative abundance of Enterobacteriales and Pseudomonadales (genus Pseudomonas) was higher in the greenhouse. Analysis of community dynamics across plant age showed that in the field nursery, the most abundant bacterial orders showed more dynamic changes in their relative abundance in the rhizosphere than in the bulk soil. In the greenhouse, age-dependent dynamics even occurred but affected different taxa than for the field-grown plants. The N-cycling potential of rhizosphere bacterial communities showed an increase of the relative abundance of genes involved in nitrogen fixation and denitrification by plant age. Similarly, the relative abundance of reported nitrogen-fixing or denitrifying bacteria increased by plant age. However, different community structures seemed to lead to an increased potential for nitrogen fixation and denitrification in the field versus greenhouse nurseries.
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Affiliation(s)
- Adriana M Garcia-Lemos
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Alex Gobbi
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Mette Haubjerg Nicolaisen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark.,Department of Adaptive Biotechnologies, Global Change Research Institute, CAS, Brno, Czechia
| | - Bjarke Veierskov
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Nybroe
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Denmark
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Liu TH, Zhang XM, Tian SZ, Chen LG, Yuan JL. Bioinformatics analysis of endophytic bacteria related to berberine in the Chinese medicinal plant Coptis teeta Wall. 3 Biotech 2020; 10:96. [PMID: 32099737 DOI: 10.1007/s13205-020-2084-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 01/20/2020] [Indexed: 02/03/2023] Open
Abstract
Endophytic microorganisms absorb nutrients and prevent pathogen damage, supporting healthy plant growth. However, the relationship between endophytic bacteria and berberine synthesis in the medicinal plant Coptis teeta Wall. remains unclear. Herein, we explored the community composition of endophytic bacteria related to berberine in roots, stems, and leaves of wild-type and cultivated C. teeta. Endophytic bacterial communities were analyzed by 16S rRNA sequencing, and berberine content in roots was analyzed by high-performance liquid chromatography. Proteobacteria, Actinobacteria, and Bacteroidetes were the major phyla, and Mycobacterium, Salmonella, Nocardioides, Burkholderia-Paraburkholderia, and Rhizobium were the dominant genera in root, stem, and leaf tissues. Root berberine content was positively correlated with total N, total P, total K, and available K in rhizosphere soil. In addition, root berberine content was positively correlated with Microbacterium and norank_f_7B-8, whereas soil total K was positively correlated with Microbacterium and Burkholderia-Paraburkholderia in roots. Our results demonstrated a clear correlation between dominant endophytic bacteria and berberine synthesis in C. teeta. The findings are useful for the promotion of berberine production in C. teeta via manipulation of endophytic bacteria.
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Affiliation(s)
- Tian-Hao Liu
- 1Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine, Chenggong District, No. 1076 Yuhua Road, Kunming, 650500 Yunnan China
- 2College of Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Xiao-Mei Zhang
- 1Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine, Chenggong District, No. 1076 Yuhua Road, Kunming, 650500 Yunnan China
| | - Shou-Zheng Tian
- 1Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine, Chenggong District, No. 1076 Yuhua Road, Kunming, 650500 Yunnan China
| | - Li-Guo Chen
- 2College of Chinese Medicine, Jinan University, Guangzhou, Guangdong China
| | - Jia-Li Yuan
- 1Yunnan Key Laboratory of Molecular Biology of Chinese Medicine, Faculty of Basic Medical Science, Yunnan University of Chinese Medicine, Chenggong District, No. 1076 Yuhua Road, Kunming, 650500 Yunnan China
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Firrincieli A, Khorasani M, Frank AC, Doty SL. Influences of Climate on Phyllosphere Endophytic Bacterial Communities of Wild Poplar. FRONTIERS IN PLANT SCIENCE 2020; 11:203. [PMID: 32184800 PMCID: PMC7058686 DOI: 10.3389/fpls.2020.00203] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/11/2020] [Indexed: 05/02/2023]
Abstract
Plant-associated microbial communities play a central role in the plant response to biotic and abiotic stimuli, improving plant fitness under challenging growing conditions. Many studies have focused on the characterization of changes in abundance and composition of root-associated microbial communities as a consequence of the plant response to abiotic factors such as altered soil nutrients and drought. However, changes in composition in response to abiotic factors are still poorly understood concerning the endophytic community associated to the phyllosphere, the above-ground plant tissues. In the present study, we applied high-throughput 16S rDNA gene sequencing of the phyllosphere endophytic bacterial communities colonizing wild Populus trichocarpa (black cottonwood) plants growing in native, nutrient-limited environments characterized by hot-dry (xeric) riparian zones (Yakima River, WA), riparian zones with mid hot-dry (Tieton and Teanaway Rivers, WA) and moist (mesic) climates (Snoqualmie, Skykomish and Skagit Rivers, WA). From sequencing data, 587 Amplicon Sequence Variants (ASV) were identified. Surprisingly, our data show that a core microbiome could be found in phyllosphere-associated endophytic communities in trees growing on opposite sides of the Cascades Mountain Range. Considering only taxa appearing in at least 90% of all samples within each climatic zone, the core microbiome was dominated only by two ASVs affiliated Pseudomonadaceae and two ASVs of the Enterobacteriaceae family. Alpha-diversity measures indicated that plants colonizing hot-dry environments showed a lower diversity than those from mid hot-dry and moist climates. Beta-diversity measures showed that bacterial composition was significantly different across sampling sites. Accordingly, we found that specific ASV affiliated to Pseudomonadaceae and Enterobacteriaceae were significantly more abundant in the phyllosphere endophytic community colonizing plants adapted to the xeric environment. In summary, this study highlights that sampling site is the major driver of variation and that only a few ASV showed a distribution that significantly correlated to climate variables.
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Affiliation(s)
- Andrea Firrincieli
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - Mahsa Khorasani
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
| | - A. Carolin Frank
- Life & Environmental Sciences School of Natural Sciences, University of California, Merced, Merced, CA, United States
- Sierra Nevada Research Institute, School of Natural Sciences, University of California, Merced, Merced, CA, United States
| | - Sharon Lafferty Doty
- School of Environmental and Forest Sciences, College of the Environment, University of Washington, Seattle, WA, United States
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Tkacz A, Bestion E, Bo Z, Hortala M, Poole PS. Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison. mBio 2020; 11:e02785-19. [PMID: 32019791 PMCID: PMC7002342 DOI: 10.1128/mbio.02785-19] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/11/2019] [Indexed: 11/20/2022] Open
Abstract
Plant roots influence the soil microbiota via physical interaction, secretion, and plant immunity. However, it is unclear whether the root fraction or soil is more important in determining the structure of the prokaryotic or eukaryotic community and whether this varies between plant species. Furthermore, the leaf (phyllosphere) and root microbiotas have a large overlap; however, it is unclear whether this results from colonization of the phyllosphere by the root microbiota. Soil, rhizosphere, rhizoplane, and root endosphere prokaryote-, eukaryote-, and fungus-specific microbiotas of four plant species were analyzed with high-throughput sequencing. The strengths of factors controlling microbiota structure were determined using permutational multivariate analysis of variance (PERMANOVA) statistics. The origin of the phyllosphere microbiota was investigated using a soil swap experiment. Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root itself more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. A reciprocal soil swap experiment shows that the phyllosphere is colonized from the soil in which the plant is grown.IMPORTANCE Global microbial kingdom analysis conducted simultaneously on multiple plants shows that cereals, legumes, and Brassicaceae establish similar prokaryotic and similar eukaryotic communities inside and on the root surface. While the bacterial microbiota is recruited from the surrounding soil, its profile is influenced by the root fraction more so than by soil or plant species. However, in contrast, the fungal microbiota is most strongly influenced by soil. This was observed in two different soils and for all plant species examined, indicating conserved adaptation of microbial communities to plants. Microbiota structure is established within 2 weeks of plant growth in soil and remains stable thereafter. We observed a remarkable similarity in the structure of a plant's phyllosphere and root microbiotas and show by reciprocal soil swap experiments that both fractions are colonized from the soil in which the plant is grown. Thus, the phyllosphere is continuously colonized by the soil microbiota.
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Affiliation(s)
- Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Eloïne Bestion
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Zhiyan Bo
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marion Hortala
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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Chen X, Krug L, Yang H, Li H, Yang M, Berg G, Cernava T. Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars. Comput Struct Biotechnol J 2020; 18:287-295. [PMID: 32071705 PMCID: PMC7013131 DOI: 10.1016/j.csbj.2020.01.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 02/01/2023] Open
Abstract
A common core microbiome was found in seeds of diverging N. tabacum cultivars. Enterobacteriaceae accounted for the predominant fraction of this core microbiome. Cultivars from the same breeding line shared the highest number of bacterial taxa. Seed-endophytic communities were extended by distinct taxa in each cultivar.
Seed endophytes of crop plants have recently received increased attention due to their implications in plant health and the potential to be included in agro-biotechnological applications. While previous studies indicated that plants from the Solanaceae family harbor a highly diverse seed microbiome, genotype-specific effects on the community composition and structure remained largely unexplored. The present study revealed Enterobacteriaceae-dominated seed-endophytic communities in four Nicotiana tabacum L. cultivars originating from Brazil, China, and the USA. When the dissimilarity of bacterial communities was assessed, none of the cultivars showed significant differences in microbial community composition. Various unusual endophyte signatures were represented by Spirochaetaceae family members and the genera Mycobacterium, Clostridium, and Staphylococcus. The bacterial fraction shared by all cultivars was dominated by members of the phyla Proteobacteria and Firmicutes. In total, 29 OTUs were present in all investigated cultivars and accounted for 65.5% of the combined core microbiome reads. Cultivars from the same breeding line were shown to share a higher number of common OTUs than more distant lines. Moreover, the Chinese cultivar Yunyan 87 contained the highest number (33 taxa) of unique signatures. Our results indicate that a distinct proportion of the seed microbiome of N. tabacum remained unaffected by breeding approaches of the last century, while a substantial proportion co-diverged with the plant genotype. Moreover, they provide the basis to identify plant-specific endophytes that could be addressed for upcoming biotechnological approaches in agriculture.
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Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, 550025 Guiyang, China.,College of Tobacco Science, Guizhou University, 550025 Guiyang, China.,Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, 550025 Guiyang, China
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Hong Yang
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China.,Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, 550025 Guiyang, China
| | - Haoxi Li
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China.,Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, 550025 Guiyang, China
| | - Maofa Yang
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China.,Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, 550025 Guiyang, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China.,Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guizhou University, 550025 Guiyang, China.,Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
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56
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Mao X, Kusstatscher P, Li H, Chen X, Berg G, Yang M, Cernava T. Microbiome-Guided Exploration of the Microbial Assemblage of the Exotic Beverage "Insect Tea" Native to Southwestern China. Front Microbiol 2020; 10:3087. [PMID: 32063890 PMCID: PMC7000658 DOI: 10.3389/fmicb.2019.03087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/20/2019] [Indexed: 01/06/2023] Open
Abstract
Insect tea is a unique beverage that is native to Southwestern China and traditionally produced by local farmers in an elaborate process. It consists of insect larvae excrements that are commonly obtained from meal moths (Pyralis farinalis Linnaeus 1758) reared on a specific plant-based diet. We have reconstructed the whole production process under laboratory conditions in order to obtain microbiome-level insights into this uncommon beverage and to trace back the origin of the prevalent bacteria in the final product. The bacterial community composition was specific for each production stage, with a high proportion of Streptomycetacea, Pseudonocaridaceae, Enterococcaceae, and Enterobacteriaceae in the insect tea. A large proportion of the constituents was traced back to the producing insect (13.2%) and its excrements (43.8%), while the initial plant-based substrate for tea production was found to contribute only 0.6% of the traceable bacteria in the final product. Moreover, an enrichment of Enterobactericeae was observed during the analyzed process steps and verified with complementary analyses. The cultivation experiments indicated a high occurrence of viable bacteria in the tea at 2.7 × 105 ± 1.2 × 105 cfu g-1. The isolated bacteria included Bordetella petrii and Enterococcus spp. that were recovered from a commercial product. By implementing an integrative approach, the insect tea was shown to harbor a species-rich bacterial community that can be traced back to certain plant and insect microbiome constituents from distinct production steps. Moreover, the microbial profile of the insect tea was found to be unique for a food product so far and contained several bacterial groups that are considered from the current perspective as food contaminants or yet unreported in other beverages. Due to the high number of viable bacteria, the tea harbors a so far undescribed dynamic component that might have implications for human health.
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Affiliation(s)
- Xin Mao
- College of Forestry, Guizhou University, Guiyang, China
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Haoxi Li
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Xiaoyulong Chen
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Maofa Yang
- Institute of Entomology, Guizhou University, Guiyang, China
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- College of Tobacco Science, Guizhou University, Guiyang, China
| | - Tomislav Cernava
- Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Guiyang, China
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- College of Tobacco Science, Guizhou University, Guiyang, China
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57
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Xie WY, Zou X, Liu DY, Li Q, Shen Q, Zhao FJ. Dynamics of metal(loid) resistance genes driven by succession of bacterial community during manure composting. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113276. [PMID: 31563779 DOI: 10.1016/j.envpol.2019.113276] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
Metal(loid) resistance genes (MRGs) play important roles in conferring resistance to metal(loid)s in bacterial communities. How MRGs respond to bacterial succession during manure composting remains largely unknown. Metagenomics was used in the present study to investigate the compositional changes of MRGs, their candidate hosts and association with integrons during thermophilic composting of chicken manures. MRGs conferring resistance to 20 metal(loid)s were detected, and their diversity and abundance (normalized to the abundance of 16S rRNA genes) were significantly reduced during composting. MRGs associated with integron were exclusively observed in proteobacterial species. Class 1 integron likely played an important role in maintaining mercury-resistance mer operon genes in composts. Escherichia coli harbored the most abundant MRGs in the original composting material, whereas species of Actinobacteria and Bacilli became more important in carrying MRGs during the late phases. There were significant linear relationships between the relative abundance of some specific bacterial species (E. coli, Actinobacteria species and Enterococcus faecium) and the abundance of MRGs they potentially harbored. The succession of these bacteria contributed to an overall linear regression between the relative abundance of all predicted candidate hosts and the abundance of total MRGs. Our results suggest that the succession of bacterial community was the main driver of MRG dynamics during thermophilic composting.
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Affiliation(s)
- Wan-Ying Xie
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Zou
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong-Yang Liu
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Li
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qirong Shen
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Fang-Jie Zhao
- Jiangsu Key Laboratory for Organic Solid Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
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Padhi EMT, Maharaj N, Lin SY, Mishchuk DO, Chin E, Godfrey K, Foster E, Polek M, Leveau JHJ, Slupsky CM. Metabolome and Microbiome Signatures in the Roots of Citrus Affected by Huanglongbing. PHYTOPATHOLOGY 2019; 109:2022-2032. [PMID: 31433274 DOI: 10.1094/phyto-03-19-0103-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Huanglongbing (HLB) is a severe, incurable citrus disease caused by the bacterium 'Candidatus Liberibacter asiaticus' (CLas). Although citrus leaves serve as the site of initial infection, CLas is known to migrate to and colonize the root system; however, little is known about the impact of CLas infection on root metabolism and resident microbial communities. Scions of 'Lisbon' lemon and 'Washington Navel' orange grafted onto 'Carrizo' rootstock were grafted with either CLas-infected citrus budwood or uninfected budwood. Roots were obtained from trees 46 weeks after grafting and analyzed via 1H nuclear magnetic resonance spectroscopy to identify water-soluble root metabolites and high-throughput sequencing of 16S rRNA and ITS gene amplicons to determine the relative abundance of bacterial and fungal taxa in the root rhizosphere and endosphere. In both citrus varieties, 27 metabolites were identified, of which several were significantly different between CLas(+) and control plants. CLas infection also appeared to alter the microbial community structure near and inside the roots of citrus plants. Nonmetric multidimensional scaling (NMDS) and a principal coordinate analysis (PCoA) revealed distinct metabolite and microbial profiles, demonstrating that CLas impacts the root metabolome and microbiome in a manner that is variety-specific.
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Affiliation(s)
- Emily M T Padhi
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Nilesh Maharaj
- Department of Plant Pathology, University of California at Davis, Davis, CA 95616
| | - Shin-Yi Lin
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Darya O Mishchuk
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Elizabeth Chin
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
| | - Kris Godfrey
- Contained Research Facility, University of California at Davis, Davis, CA 95616
| | - Elizabeth Foster
- Contained Research Facility, University of California at Davis, Davis, CA 95616
| | - Marylou Polek
- U.S. Department of Agriculture-Agricultural Research Service National Germplasm Repository, Riverside, CA 92507
| | - Johan H J Leveau
- Department of Plant Pathology, University of California at Davis, Davis, CA 95616
| | - Carolyn M Slupsky
- Department of Food Science and Technology, University of California at Davis, Davis, CA 95616
- Department of Nutrition, University of California at Davis, Davis, CA 95616
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Ben Mefteh F, Bouket AC, Daoud A, Luptakova L, Alenezi FN, Gharsallah N, Belbahri L. Metagenomic Insights and Genomic Analysis of Phosphogypsum and Its Associated Plant Endophytic Microbiomes Reveals Valuable Actors for Waste Bioremediation. Microorganisms 2019; 7:microorganisms7100382. [PMID: 31547633 PMCID: PMC6843645 DOI: 10.3390/microorganisms7100382] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/08/2019] [Accepted: 09/19/2019] [Indexed: 12/04/2022] Open
Abstract
The phosphogypsum (PG) endogenous bacterial community and endophytic bacterial communities of four plants growing in phosphogypsum-contaminated sites, Suaeda fruticosa (SF), Suaeda mollis (SM), Mesembryanthmum nodiflorum (MN) and Arthrocnemum indicum (AI) were investigated by amplicon sequencing. Results highlight a more diverse community of phosphogypsum than plants associated endophytic communities. Additionally, the bacterial culturable communities of phosphogypsum and associated plant endophytes were isolated and their plant-growth promotion capabilities, bioremediation potential and stress tolerance studied. Most of plant endophytes were endowed with plant growth-promoting (PGP) activities and phosphogypsum communities and associated plants endophytes proved highly resistant to salt, metal and antibiotic stress. They also proved very active in bioremediation of phosphogypsum and other organic and inorganic environmental pollutants. Genome sequencing of five members of the phosphogypsum endogenous community showed that they belong to the recently described species Bacillus albus (BA). Genome mining of BA allowed the description of pollutant degradation and stress tolerance mechanisms. Prevalence of this tool box in the core, accessory and unique genome allowed to conclude that accessory and unique genomes are critical for the dynamics of strain acquisition of bioremediation abilities. Additionally, secondary metabolites (SM) active in bioremediation such as petrobactin have been characterized. Taken together, our results reveal hidden untapped valuable bacterial actors for waste remediation.
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Affiliation(s)
- Fedia Ben Mefteh
- NextBiotech, 98 Rue Ali Belhouane, Agareb 3030, Tunisia.
- Faculty of Sciences, University of Sfax, Sfax 3029, Tunisia.
| | - Ali Chenari Bouket
- Plant Protection Research Department, East Azarbaijan Agricultural and Natural Resources Research and Education Center, AREEO, Tabriz 5355179854, Iran.
| | - Amal Daoud
- NextBiotech, 98 Rue Ali Belhouane, Agareb 3030, Tunisia.
| | - Lenka Luptakova
- NextBiotech, 98 Rue Ali Belhouane, Agareb 3030, Tunisia.
- Department of Biology and Genetics, Institute of Biology, Zoology and Radiobiology, University of Veterinary Medicine and Pharmacy in Košice, 04181 Kosice, Slovakia.
| | | | - Neji Gharsallah
- Faculty of Sciences, University of Sfax, Sfax 3029, Tunisia.
| | - Lassaad Belbahri
- NextBiotech, 98 Rue Ali Belhouane, Agareb 3030, Tunisia.
- Laboratory of Soil Biodiversity, University of Neuchâtel, CH-2000 Neuchatel, Switzerland.
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Cernava T, Chen X, Krug L, Li H, Yang M, Berg G. The tea leaf microbiome shows specific responses to chemical pesticides and biocontrol applications. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 667:33-40. [PMID: 30825819 DOI: 10.1016/j.scitotenv.2019.02.319] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/01/2019] [Accepted: 02/20/2019] [Indexed: 05/16/2023]
Abstract
The plant microbiome is known to be influenced by certain biotic as well as abiotic factors. Nevertheless, the drivers for specific changes in microbial community composition and structure are largely unknown. In the present study, the effects of chemical and biological treatments for plant protection on the indigenous microbiome of Camellia sinensis (L.) Kuntze were contrasted. Assessment of bacteria-specific ribosomal RNA gene fragment amplicons from a representative set of samples showed an increased microbial diversity in treated plants when compared to untreated samples. Moreover, distinct microbial fingerprints were found for plants subjected to a conventional pesticide treatment with lime sulfur as well as for plants that were biologically treated with a Piriformospora indica spore solution. The bacterial community of pesticide-treated plants was augmented by 11 taxa assigned to Proteobacteria and Actinobacteria. In contrast, plants from biological control treatments were augmented by 10 taxa representing a more diversified community enrichment and included members of Actionobacteria, Proteobacteria, Bacteroidetes, Planctomycetes, and Verrucomicrobia. Complementary, molecular quantification of fungi in the samples showed a significantly lower number of internal transcribed spacer copies in plants subjected to biological control treatments, indicating the highest efficiency against fungal pathogens. The overall results show that leaves that are used for tea production show distinct microbiome shifts that are elicited by common pest and pathogen management practices. These shifts in the microbial population indicate non-target effects of the applied treatments.
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Affiliation(s)
- Tomislav Cernava
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China.
| | - Xiaoyulong Chen
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China.
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.
| | - Haoxi Li
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China
| | - Maofa Yang
- College of Tobacco Science, Guizhou University, 550025 Guiyang, China; Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, 550025 Guiyang, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria.
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Novel insights into plant-associated archaea and their functioning in arugula ( Eruca sativa Mill.). J Adv Res 2019; 19:39-48. [PMID: 31341668 PMCID: PMC6629838 DOI: 10.1016/j.jare.2019.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 01/21/2023] Open
Abstract
A plant's microbiota has various implications for the plant's health and performance; however, the roles of many microbial lineages, particularly Archaea, have not been explored in detail. In the present study, analysis of archaea-specific 16S rRNA gene fragments and shotgun-sequenced metagenomes was combined with visualization techniques to obtain the first insights into the archaeome of a common salad plant, arugula (Eruca sativa Mill.). The archaeal communities associated with the soil, rhizosphere and phyllosphere were distinct, but a high proportion of community members were shared among all analysed habitats. Soil habitats exhibited the highest diversity of Archaea, followed by the rhizosphere and the phyllosphere. The archaeal community was dominated by Thaumarchaeota and Euryarchaeota, with the most abundant taxa assigned to Candidatus Nitrosocosmicus, species of the 'Soil Crenarchaeotic Group' and, interestingly, Methanosarcina. Moreover, a large number of archaea-assigned sequences remained unassigned at lower taxonomic levels. Overall, analysis of shotgun-sequenced total-community DNA revealed a more diverse archaeome. Differences were evident at the class level and at higher taxonomic resolutions when compared to results from the 16S rRNA gene fragment amplicon library. Functional assessments primarily revealed archaeal genes related to response to stress (especially oxidative stress), CO2 fixation, and glycogen degradation. Microscopic visualizations of fluorescently labelled archaea in the phyllosphere revealed small scattered colonies, while archaea in the rhizosphere were found to be embedded within large bacterial biofilms. Altogether, Archaea were identified as a rather small but niche-specific component of the microbiomes of the widespread leafy green plant arugula.
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