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Boutin S, Lussier E, Laforest-Lapointe I. Investigating the spatiotemporal dynamics of apple tree phyllosphere bacterial and fungal communities across cultivars in orchards. Can J Microbiol 2024; 70:238-251. [PMID: 38452350 DOI: 10.1139/cjm-2023-0215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The phyllosphere, a reservoir of diverse microbial life associated with plant health, harbors microbial communities that are subject to various complex ecological processes acting at multiple scales. In this study, we investigated the determinants of the spatiotemporal variation in bacterial and fungal communities within the apple tree phyllosphere, employing 16S and ITS amplicon sequencing. Our research assessed the impact of key factors-plant compartment, site, time, and cultivar-on the composition and diversity of leaf and flower microbial communities. Our analyses, based on samples collected from three cultivars in three orchards in 2022, revealed that site and time are the strongest drivers of apple tree phyllosphere microbial communities. Conversely, plant compartment and cultivar exhibited minor roles in explaining community composition and diversity. Predominantly, bacterial communities comprised Hymenobacter (25%) and Sphingomonas (10%), while the most relatively abundant fungal genera included Aureobasidium (27%) and Sporobolomyces (10%). Additionally, our results show a gradual decrease in alpha-diversity throughout the growth season. These findings emphasize the necessity to consider local microbial ecology dynamics in orchards, especially as many groups worldwide aim for the development of biocontrol strategies (e.g., by manipulating plant-microbe interactions). More research is needed to improve our understanding of the determinants of time and site-specific disparities within apple tree phyllosphere microbial communities across multiple years, locations, and cultivars.
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Affiliation(s)
- Sophie Boutin
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Ema Lussier
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Isabelle Laforest-Lapointe
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
- Centre SÈVE, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
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Batantou Mabandza D, Colletin E, Dagot C, Quétel I, Breurec S, Guyomard-Rabenirina S. Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes? Antibiotics (Basel) 2024; 13:87. [PMID: 38247646 PMCID: PMC10812525 DOI: 10.3390/antibiotics13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.
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Affiliation(s)
- Degrâce Batantou Mabandza
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Edlyne Colletin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Christophe Dagot
- University of Limoges, INSERM, CHU Limoges, RESINFIT, U1092, 87000 Limoges, France
| | - Isaure Quétel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97110 Pointe-à-Pitre, France
- INSERM, Centre for Clinical Investigation 1424, 97110 Pointe-à-Pitre, France
- Department of Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, 34394 Montpellier, France
- Laboratory of Clinical Microbiology, University Hospital Centre of Guadeloupe, 971110 Pointe-à-Pitre, France
| | - Stéphanie Guyomard-Rabenirina
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97110 Pointe-à-Pitre, France
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Verhaegen M, Bergot T, Liebana E, Stancanelli G, Streissl F, Mingeot-Leclercq MP, Mahillon J, Bragard C. On the use of antibiotics to control plant pathogenic bacteria: a genetic and genomic perspective. Front Microbiol 2023; 14:1221478. [PMID: 37440885 PMCID: PMC10333595 DOI: 10.3389/fmicb.2023.1221478] [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: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
Despite growing attention, antibiotics (such as streptomycin, oxytetracycline or kasugamycin) are still used worldwide for the control of major bacterial plant diseases. This raises concerns on their potential, yet unknown impact on antibiotic and multidrug resistances and the spread of their genetic determinants among bacterial pathogens. Antibiotic resistance genes (ARGs) have been identified in plant pathogenic bacteria (PPB), with streptomycin resistance genes being the most commonly reported. Therefore, the contribution of mobile genetic elements (MGEs) to their spread among PPB, as well as their ability to transfer to other bacteria, need to be further explored. The only well-documented example of ARGs vector in PPB, Tn5393 and its highly similar variants (carrying streptomycin resistance genes), is concerning because of its presence outside PPB, in Salmonella enterica and Klebsiella pneumoniae, two major human pathogens. Although its structure among PPB is still relatively simple, in human- and animal-associated bacteria, Tn5393 has evolved into complex associations with other MGEs and ARGs. This review sheds light on ARGs and MGEs associated with PPB, but also investigates the potential role of antibiotic use in resistance selection in plant-associated bacteria.
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Affiliation(s)
- Marie Verhaegen
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Thomas Bergot
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | | | | | - Marie-Paule Mingeot-Leclercq
- Cellular and Molecular Pharmacology Unit, Louvain Drug Research Institute, UCLouvain, Woluwe-Saint-Lambert, Belgium
| | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Catholic University of Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Claude Bragard
- Plant Health Laboratory, Earth and Life Institute, UCLouvain, Louvain-la-Neuve, Belgium
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Xu N, Zhao Q, Zhang Z, Zhang Q, Wang Y, Qin G, Ke M, Qiu D, Peijnenburg WJGM, Lu T, Qian H. Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4860-4870. [PMID: 35435673 DOI: 10.1021/acs.jafc.2c01113] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, Xinjiang 830011, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Post Office Box 1, 3720 BA Bilthoven, Netherlands
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
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Longa CMO, Antonielli L, Bozza E, Sicher C, Pertot I, Perazzolli M. Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment. Microbiol Res 2022; 258:126991. [DOI: 10.1016/j.micres.2022.126991] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/07/2022] [Accepted: 02/14/2022] [Indexed: 01/04/2023]
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Zalewski ZD, Page R, Lankau RA, McManus PS. Role of Yeasts in the Cranberry Fruit Rot Disease Complex. PLANT DISEASE 2021; 105:2141-2148. [PMID: 33289412 DOI: 10.1094/pdis-11-19-2303-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cranberry fruit rot (CFR) is an economically important disease caused by at least 10 species of filamentous fungi. Despite the application of fungicides, incidence of CFR is sometimes high, raising the possibility of a role for microbes other than fungi in the CFR complex. Isolation of microbes from rotten berries on culture media that favor either bacteria or yeasts resulted in mucoid colonies from <15% of dry-harvested rotten berries but up to 60% of wet-harvested berries. The mucoid colonies were identified as yeasts, primarily in the family Saccharomycetaceae. Inoculation of sound berries with three yeasts, Hanseniaspora uvarum, Pichia fermentans, and Pichia terricola, resulted in significantly higher incidence and severity of rot symptoms compared with mock-inoculated controls; these yeasts were recovered from inoculated berries, providing evidence of their pathogenicity. The minimum concentrations of azoxystrobin, chlorothalonil, and prothioconazole that resulted in 80% inhibition of growth compared with untreated controls (MIC80) were determined for a subset of yeasts. In general, MIC80s were higher for azoxystrobin and prothioconazole (usually >64 µg/ml) than for chlorothalonil (usually ≤1 µg/ml). To complement culture-dependent studies, DNA was isolated from wet- and dry-harvested rotten berries, and fungi were identified to the level of family by high-throughput sequencing of the fungal internal transcribed spacer region. There were no fungal families consistently detected among samples by one method (culturing or high-throughput sequencing) and missed by the other that have not previously been reported in cranberry; however, some fungal families were found to be more abundant by one method versus the other. Harvest method (wet or dry) had a significant effect on the composition of fungal communities of rotten berries (P < 0.001), and operational taxonomic units representing the Saccharomycetaceae were more abundant in wet- than dry-harvested berries. Taken together, the results suggest that some yeasts are pathogenic to cranberry and may be especially relevant in wet-harvested berries.
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Affiliation(s)
- Zachary D Zalewski
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Rae Page
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Richard A Lankau
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Patricia S McManus
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
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Chen X, Wicaksono WA, Berg G, Cernava T. Bacterial communities in the plant phyllosphere harbour distinct responders to a broad-spectrum pesticide. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 751:141799. [PMID: 32889475 DOI: 10.1016/j.scitotenv.2020.141799] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/29/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Pesticide application can be accompanied by harmful non-target effects that affect humans, animals, as well as whole ecosystems. However, such effects remain mainly unaddressed in connection with microorganisms, and especially bacteria therein, which are essential for ecosystem functioning and host health. We analysed bacterial communities by sequencing 16S rRNA gene fragment amplicons following spray application of a broad-spectrum fungicide based on the active ingredient N-(3,5-dichlorophenyl) succinimide on Nicotiana tabacum L. leaves. The plant's phyllosphere was predominantly colonized by Proteobacteria, with Alphaproteobacteria accounting for up to 33.8% of the indigenous bacterial community. Bioinformatic analyses indicated that pesticide applications had an effect on the core microbiome as well as the rare microbiome. Moreover, the interference of the pesticide with phyllosphere bacteria was found to be selective. We have identified four positive responders including an ASV assigned to the genus Acinetobacter and 12 negative responders mainly assigned to bacterial genera known for beneficial plant-microbe interactions, including Stenotrophomonas, Sphingomonas, Flavobacterium and Serratia. Complementary inference of bacterial functioning on community level indicated that microbes with distinct stress response systems were likely enriched in the conducted treatments. The overall findings confirmed that pesticide treatments can induce measureable shifts in non-target bacterial communities colonizing the plant phyllosphere. They also indicate that potentially beneficial bacteria, which are known for their intrinsic association with plants, are among the most sensitive responders to the employed fungicide and thus highlight the importance of off-target studies in the context of the plant microbiome.
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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, 550025 Guiyang, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 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, 550025 Guiyang, China; Institute of Environmental Biotechnology, Graz University of Technology, 8010 Graz, Austria.
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Antibiotic Resistance in Recreational Waters: State of the Science. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17218034. [PMID: 33142796 PMCID: PMC7663426 DOI: 10.3390/ijerph17218034] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]
Abstract
Ambient recreational waters can act as both recipients and natural reservoirs for antimicrobial resistant (AMR) bacteria and antimicrobial resistant genes (ARGs), where they may persist and replicate. Contact with AMR bacteria and ARGs potentially puts recreators at risk, which can thus decrease their ability to fight infections. A variety of point and nonpoint sources, including contaminated wastewater effluents, runoff from animal feeding operations, and sewer overflow events, can contribute to environmental loading of AMR bacteria and ARGs. The overall goal of this article is to provide the state of the science related to recreational exposure and AMR, which has been an area of increasing interest. Specific objectives of the review include (1) a description of potential sources of antibiotics, AMR bacteria, and ARGs in recreational waters, as documented in the available literature; (2) a discussion of what is known about human recreational exposures to AMR bacteria and ARGs, using findings from health studies and exposure assessments; and (3) identification of knowledge gaps and future research needs. To better understand the dynamics related to AMR and associated recreational water risks, future research should focus on source contribution, fate and transport-across treatment and in the environment; human health risk assessment; and standardized methods.
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Dagher F, Olishevska S, Philion V, Zheng J, Déziel E. Development of a novel biological control agent targeting the phytopathogen Erwinia amylovora. Heliyon 2020; 6:e05222. [PMID: 33102848 PMCID: PMC7578203 DOI: 10.1016/j.heliyon.2020.e05222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/18/2020] [Accepted: 10/08/2020] [Indexed: 10/27/2022] Open
Abstract
Antibiotics are used extensively to control animal, plant, and human pathogens. They are sprayed on apple and pear orchards to control the bacterium Erwinia amylovora, the causative agent of fire blight. This phytopathogen is developing antibiotic resistance and alternatives either have less efficacy, are phytotoxic, or more management intensive. The objective of our study was to develop an effective biological control agent colonizing the host plant and competing with Erwinia amylovora. It must not be phytotoxic, have a wide spectrum of activity, and be unlikely to induce resistance in the pathogen. To this end, several bacterial isolates from various environmental samples were screened to identify suitable candidates that are antagonistic to E. amylovora. We sampled bacteria from the flowers, leaves, and soil from apple and pear orchards from the springtime bloom period until the summer. The most effective bacteria, including isolates of Pseudomonas poae, Paenibacillus polymyxa, Bacillus amyloliquefaciens and Pantoea agglomerans, were tested in vitro and in vivo and formulated into products containing both the live strains and their metabolites that were stable for at least 9 months. Trees treated with the product based on P. agglomerans NY60 had significantly less fire blight than the untreated control and were statistically not different from streptomycin-treated control trees. With P. agglomerans NY60, fire blight never extended beyond the central vein of the inoculated leaf. The fire blight median disease severity score, 10 days after inoculation, was up to 70% less severe on trees treated with P. agglomerans NY60 as compared to untreated controls.
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Affiliation(s)
- Fadi Dagher
- INRS-Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
| | | | | | - Jie Zheng
- US Food and Drug Administration Regulatory Science Center for Food Safety and Applied Nutrition, 5100, Paint Branch Parkway, College Park, MD, USA
| | - Eric Déziel
- INRS-Armand-Frappier Santé Biotechnologie, Laval, Québec, Canada
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Aydogan EL, Budich O, Hardt M, Choi YH, Jansen-Willems AB, Moser G, Müller C, Kämpfer P, Glaeser SP. Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. FEMS Microbiol Ecol 2020; 96:5835220. [DOI: 10.1093/femsec/fiaa087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/08/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaFtype was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota.
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Affiliation(s)
- Ebru L Aydogan
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Olga Budich
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Martin Hardt
- Biomedical Research Center Seltersberg – Imaging Unit, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Anne B Jansen-Willems
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, D04V1W8 Dublin, Ireland
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
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Arrigoni E, Albanese D, Longa CMO, Angeli D, Donati C, Ioriatti C, Pertot I, Perazzolli M. Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees. Environ Microbiol 2020; 22:2080-2093. [PMID: 32114708 DOI: 10.1111/1462-2920.14963] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 01/09/2023]
Abstract
Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.
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Affiliation(s)
- Elena Arrigoni
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Department of Agricultural and Environmental Sciences, University of Udine, 33100, Udine, Italy
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | | | - Dario Angeli
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Donati
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Claudio Ioriatti
- Technology Transfer Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Ilaria Pertot
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
| | - Michele Perazzolli
- Research and Innovation Centre, Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, 38010, San Michele all'Adige, Italy
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13
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Chanvatik S, Donnua S, Lekagul A, Kaewkhankhaeng W, Vongmongkol V, Athipunyakom P, Khamlar S, Prommintara M, Tangcharoensathien V. Antibiotic use in mandarin production (Citrus reticulata Blanco) in major mandarin-producing areas in Thailand: A survey assessment. PLoS One 2019; 14:e0225172. [PMID: 31721802 PMCID: PMC6853317 DOI: 10.1371/journal.pone.0225172] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/30/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR), one of the major global threats to human security, has serious negative consequences for both health and economies. Excessive and inappropriate uses of antibiotics are the main drivers of the emergence of resistant bacterial strains. In Thailand, antibiotics have been used in citrus production since 2012 to treat citrus greening disease or Huanglongbing disease, despite no antibiotics being registered for use in mandarin. This raises concerns about irrational use of antibiotics, which can cause AMR. OBJECTIVE To assess the status of greening disease and the use of antibiotics in mandarin production. METHOD A face-to-face interview survey in 2017 with 221 mandarin growers in two major mandarin-producing areas. FINDINGS Greening disease is one of the most serious diseases in mandarins and farmers in the two major mandarin-producing areas in Thailand used ampicillin, amoxicillin, tetracycline and penicillin to treat it. As no antibiotics are registered for use in plants, farmers used antibiotics (registered with the Thai Food and Drug Administration) for human use, either active pharmaceutical ingredients or finished products. They commonly purchased them from retail pharmacies or agrochemical suppliers. Farmers were influenced to use antibiotics by their orchard neighbours and advice from a few academics. The farmers injected antibiotics into the tree trunks approximately three to four times a year and stopped for more than two months before harvesting for in-season fruits. CONCLUSION Antibiotics registered for human use are being applied to control greening diseases. We recommend scaling up sustainable disease control measures and curtail the use of antibiotics through close and effective dialogue among 'One Health' partners.
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Affiliation(s)
- Sunicha Chanvatik
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | - Siriporn Donnua
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Bangkok, Thailand
| | - Angkana Lekagul
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Vuthiphan Vongmongkol
- International Health Policy Program, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Saenchai Khamlar
- Department of Agriculture, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
| | - Maitree Prommintara
- Department of Agriculture, Ministry of Agriculture and Cooperatives, Bangkok, Thailand
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Bacterial communities in the rhizosphere, phyllosphere and endosphere of tomato plants. PLoS One 2019; 14:e0223847. [PMID: 31703074 PMCID: PMC6839845 DOI: 10.1371/journal.pone.0223847] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/30/2019] [Indexed: 11/19/2022] Open
Abstract
Plants harbor diverse bacterial communities, which play crucial roles in plant health and growth, in their rhizosphere, phyllosphere and endosphere. Tomato is an important model for studying plant-microbe interactions, but comparison of its associated bacterial community is still lacking. In this study, using Illumina sequencing of 16S rRNA amplicons, we characterized and compared the bacterial size and community from rootzone soil as well as the rhizosphere, phyllosphere and endosphere of roots, stems, leaves, fruits and seeds of tomato plants that were grown in greenhouse conditions. Habitat (soil, phyllospheric, and endophytic) structured the community. The bacterial communities from the soil-type samples (rootzone soil and rhizosphere) showed the highest richness and diversity. The lowest bacterial diversity occurred in the phyllospheric samples, while the lowest richness occurred in the endosphere. Among the endophytic samples, both bacterial diversity and richness varied in different tissues, with the highest values in roots. The most abundant phyla in the tomato-associated community was Proteobacteria, with the exception of the seeds and jelly, where both Proteobacteria and Firmicutes were dominant. At the genus level, the sequences of Pseudomonas and Acinetobacter were prevalent in the rhizosphere, and in the phyllosphere, more than 97% of the sequences were assigned to Acinetobacter. For the endophytes, Acinetobacter, Enterobacter, and Pseudomonas were the abundant genera in the roots, stems and leaves. In the fruits, the bacterial endophytes varied in different compartments, with Enterobacter being enriched in the pericarp and seeds, Acinetobacter in the placenta, and Weissella in the jelly. The present data provide a comprehensive description of the tomato-associated bacterial community and will be useful for better understanding plant-microbe interactions and selecting suitable bacterial taxa for tomato production.
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15
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Effect of high hydrostatic pressure and activated film packaging on bacterial diversity of fruit puree. Lebensm Wiss Technol 2019. [DOI: 10.1016/j.lwt.2018.10.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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16
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Purahong W, Orrù L, Donati I, Perpetuini G, Cellini A, Lamontanara A, Michelotti V, Tacconi G, Spinelli F. Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1563. [PMID: 30464766 PMCID: PMC6234494 DOI: 10.3389/fpls.2018.01563] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/05/2018] [Indexed: 05/20/2023]
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, Helmholtz Center for Environmental Research - UFZ, Halle, Germany
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Irene Donati
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Giorgia Perpetuini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | | | - Vania Michelotti
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Gianni Tacconi
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
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17
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Phani V, Rao U. Revisiting the Life-Cycle of Pasteuria penetrans Infecting Meloidogyne incognita under Soil-Less Medium, and Effect of Streptomycin Sulfate on its Development. J Nematol 2018; 50:91-98. [PMID: 30451430 DOI: 10.21307/jofnem-2018-022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Pasteuria penetrans is a Gram-positive, endospore forming soil bacterium, infecting root-knot nematodes, Meloidogyne spp. Being obligate in nature, the bacterium is not easily grown in vitro, and the in vivo culturing technique is relied on the soil-based microcosm since long. Hence, culturing of P. penetrans using CYG germination pouches as a soil-less medium for plant growth, promises to provide a contamination free environment along with ease in isolation of infected females from the plant roots. Additionally, this method increases the percentage of P. penetrans infected nematode females as compared with the soil-based system. Schematic observation of all the life stages of P. penetrans was documented, which revealed chronological fragmentation of vegetative microcolony inside the nematode body demonstrating the formation of some stages not reported earlier. Further, germination of endospores attached to infective juveniles was found to be most likely asynchronous as single female nematode contained most of the developing stages of P. penetrans concurrently. Additionally, the effect of an antibiotic, streptomycin sulfate was evaluated for effects on the growth and development of the bacterium at different concentrations. Higher doses of antibiotic were found to exert a negative impact on the development of P. penetrans , which shows the incompatibility of Pasteuria and streptomycin sulfate.
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Affiliation(s)
- Victor Phani
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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18
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Abstract
Antibiotics have been used for the management of relatively few bacterial plant diseases and are largely restricted to high-value fruit crops because of the expense involved. Antibiotic resistance in plant-pathogenic bacteria has become a problem in pathosystems where these antibiotics have been used for many years. Where the genetic basis for resistance has been examined, antibiotic resistance in plant pathogens has most often evolved through the acquisition of a resistance determinant via horizontal gene transfer. For example, the strAB streptomycin-resistance genes occur in Erwinia amylovora, Pseudomonas syringae, and Xanthomonas campestris, and these genes have presumably been acquired from nonpathogenic epiphytic bacteria colocated on plant hosts under antibiotic selection. We currently lack knowledge of the effect of the microbiome of commensal organisms on the potential of plant pathogens to evolve antibiotic resistance. Such knowledge is critical to the development of robust resistance management strategies to ensure the safe and effective continued use of antibiotics in the management of critically important diseases.
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Affiliation(s)
- George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, Michigan 48824, USA;
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, Florida 33850, USA
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19
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Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain-Specific Viability Quantitative PCR Method. Appl Environ Microbiol 2018. [PMID: 29523544 PMCID: PMC5930365 DOI: 10.1128/aem.00107-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity. The nucleic acid-binding dye PEMAX was used to selectively detect and enumerate viable bacteria by v-qPCR. The primer set amplifying a 188-bp DNA fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed on apple blossoms, pear, strawberry, and kiwifruit leaves in potted plants under controlled environmental conditions, as well as pear and apple blossoms under field conditions, by comparing v-qPCR population estimations to those obtained by qPCR and specific plate counting on de Man-Rogosa-Sharpe (MRS)-rifampin. The population estimation did not differ significantly between methods when conditions were conducive to bacterial survival. However, under stressful conditions, differences between methods were observed due to cell death or viable-but-nonculturable state induction. While qPCR overestimated the population level, plate counting underestimated this value in comparison to v-qPCR. PM411 attained stable population levels of viable cells on the flower environment under high relative humidity. However, the unfavorable conditions on the leaf surface and the relatively dryness in the field caused an important decrease in the viable population. IMPORTANCE The v-qPCR method in combination with plate counting and qPCR is a powerful tool for studies of colonization and survival under field conditions, to improve formulations and delivery strategies of PM411, and to optimize the dose and timing of spray schedules. It is expected that PEMAX v-qPCR could also be developed for monitoring other strains on plant surfaces not only as biological control agents but also beneficial bacteria useful in the sustainable management of crop production.
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20
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Tancos KA, Cox KD. Effects of Consecutive Streptomycin and Kasugamycin Applications on Epiphytic Bacteria in the Apple Phyllosphere. PLANT DISEASE 2017; 101:158-164. [PMID: 30682301 DOI: 10.1094/pdis-06-16-0794-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Antibiotic applications are essential for fire blight management in the eastern United States. Recently, streptomycin-resistant Erwinia amylovora strains were found in New York. There are growing concerns that streptomycin resistance may develop from postbloom streptomycin applications in local orchards. Our goal was to investigate the impacts of increasing streptomycin and kasugamycin applications on bacterial epiphyte community composition and antibiotic resistance in the phyllosphere of 'Idared' apple plantings in 2014 and 2015. Rinsate samples from leaves treated with 0, 3, 5, and 10 applications of streptomycin and kasugamycin were collected to isolate, enumerate, and identify epiphytic bacterial species. The majority of isolated epiphytic bacteria were identified as Pantoea agglomerans and fluorescent Pseudomonas spp., whereas E. amylovora was rarely found. Overall, postbloom streptomycin use did not result in an increased recovery of streptomycin-resistant E. amylovora. However, other streptomycin-resistant epiphytes (P. agglomerans and Pseudomonas spp.) did increase with increasing streptomycin applications. Increasing kasugamycin applications reduced the overall number and percentage of streptomycin-resistant epiphytes in the phyllosphere, which has important implications regarding the use of kasugamycin in orchards where streptomycin resistance is a concern.
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Affiliation(s)
- K A Tancos
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experiment Station, Cornell University, Geneva NY 14456
| | - K D Cox
- Department of Plant Pathology and Plant-Microbe Biology, New York State Agricultural Experiment Station, Cornell University, Geneva NY 14456
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21
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Vacher C, Hampe A, Porté AJ, Sauer U, Compant S, Morris CE. The Phyllosphere: Microbial Jungle at the Plant–Climate Interface. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032238] [Citation(s) in RCA: 229] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Arndt Hampe
- BIOGECO, INRA, Univ. Bordeaux, 33610 Cestas, France
| | | | - Ursula Sauer
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Stéphane Compant
- Bioresources Unit, Department of Health and Environment, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria
| | - Cindy E. Morris
- INRA, Unité de Recherche de Pathologie Végétale, 84143 Montfavet, France
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22
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Using a Control to Better Understand Phyllosphere Microbiota. PLoS One 2016; 11:e0163482. [PMID: 27669159 PMCID: PMC5036865 DOI: 10.1371/journal.pone.0163482] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/10/2016] [Indexed: 11/26/2022] Open
Abstract
An important data gap in our understanding of the phyllosphere surrounds the origin of the many microbes described as phyllosphere communities. Most sampling in phyllosphere research has focused on the collection of microbiota without the use of a control, so the opportunity to determine which taxa are actually driven by the biology and physiology of plants as opposed to introduced by environmental forces has yet to be fully realized. To address this data gap, we used plastic plants as inanimate controls adjacent to live tomato plants (phyllosphere) in the field with the hope of distinguishing between bacterial microbiota that may be endemic to plants as opposed to introduced by environmental forces. Using 16S rRNA gene amplicons to study bacterial membership at four time points, we found that the vast majority of all species-level operational taxonomic units were shared at all time-points. Very few taxa were unique to phyllosphere samples. A higher taxonomic diversity was consistently observed in the control samples. The high level of shared taxonomy suggests that environmental forces likely play a very important role in the introduction of microbes to plant surfaces. The observation that very few taxa were unique to the plants compared to the number that were unique to controls was surprising and further suggests that a subset of environmentally introduced taxa thrive on plants. This finding has important implications for improving our approach to the description of core phytobiomes as well as potentially helping us better understand how foodborne pathogens may become associated with plant surfaces.
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Friedman M. Antibiotic-resistant bacteria: prevalence in food and inactivation by food-compatible compounds and plant extracts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:3805-3822. [PMID: 25856120 DOI: 10.1021/acs.jafc.5b00778] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Foodborne antibiotic-resistant pathogenic bacteria such as Campylobacter jejuni, Bacillus cereus, Clostridium perfringens, Escherichia coli, Salmonella enterica, Staphylococcus aureus, Vibrio cholerae, and Vibrio parahemolyticus can adversely affect animal and human health, but a better understanding of the factors involved in their pathogenesis is needed. To help meet this need, this overview surveys and interprets much of our current knowledge of antibiotic (multidrug)-resistant bacteria in the food chain and the implications for microbial food safety and animal and human health. Topics covered include the origin and prevalence of resistant bacteria in the food chain (dairy, meat, poultry, seafood, and herbal products, produce, and eggs), their inactivation by different classes of compounds and plant extracts and by the use of chlorine and physicochemical methods (heat, UV light, pulsed electric fields, and high pressure), the synergistic antimicrobial effects of combinations of natural antimicrobials with medicinal antibiotics, and mechanisms of antimicrobial activities and resistant effects. Possible areas for future research are suggested. Plant-derived and other safe natural antimicrobial compounds have the potential to control the prevalence of both susceptible and resistant pathogens in various environments. The collated information and suggested research will hopefully contribute to a better understanding of approaches that could be used to minimize the presence of resistant pathogens in animal feed and human food, thus reducing adverse effects, improving microbial food safety, and helping to prevent or treat animal and human infections.
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Affiliation(s)
- Mendel Friedman
- Western Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Albany, California 94710, United States
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24
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Sun J, Li L, Liu B, Xia J, Liao X, Liu Y. Development of aminoglycoside and β-lactamase resistance among intestinal microbiota of swine treated with lincomycin, chlortetracycline, and amoxicillin. Front Microbiol 2014; 5:580. [PMID: 25408688 PMCID: PMC4219486 DOI: 10.3389/fmicb.2014.00580] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/14/2014] [Indexed: 01/28/2023] Open
Abstract
Lincomycin, chlortetracycline, and amoxicillin are commonly used antimicrobials for growth promotion and infectious disease prophylaxis in swine production. In this study, we investigated the shifts and resistance development among intestinal microbiota in pregnant sows before and after lincomycin, chlortetracycline, and amoxicillin treatment by using phylogenetic analysis, bacterial enumeration, and PCR. After the antimicrobial treatment, shifts in microbial community, an increased proportion of resistant bacteria, and genes related to antimicrobial resistance as compared to the day before antimicrobial administration (day 0) were observed. Importantly, a positive correlation between antimicrobial resistance gene expression in different categories, especially those encoding aminoglycoside and β-lactamase and antimicrobial resistance, was observed. These findings demonstrate an important role of antimicrobial usage in animals in the development of antimicrobial resistance, and support the notion that prudent use of antimicrobials in swine is needed to reduce the risk of the emergence of multi-drug resistant zoonotic pathogens.
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Affiliation(s)
| | | | | | | | | | - Yahong Liu
- Laboratory of Veterinary Pharmacology, College of Veterinary Medicine, South China Agricultural UniversityGuangzhou, China
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25
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Liang J, Sun S, Ji J, Wu H, Meng F, Zhang M, Zheng X, Wu C, Zhang Z. Comparison of the rhizosphere bacterial communities of Zigongdongdou soybean and a high-methionine transgenic line of this cultivar. PLoS One 2014; 9:e103343. [PMID: 25079947 PMCID: PMC4117502 DOI: 10.1371/journal.pone.0103343] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 07/01/2014] [Indexed: 11/19/2022] Open
Abstract
Previous studies have shown that methionine from root exudates affects the rhizosphere bacterial population involved in soil nitrogen fixation. A transgenic line of Zigongdongdou soybean cultivar (ZD91) that expresses Arabidopsis cystathionine γ-synthase resulting in an increased methionine production was examined for its influence to the rhizosphere bacterial population. Using 16S rRNA gene-based pyrosequencing analysis of the V4 region and DNA extracted from bacterial consortia collected from the rhizosphere of soybean plants grown in an agricultural field at the pod-setting stage, we characterized the populational structure of the bacterial community involved. In total, 87,267 sequences (approximately 10,908 per sample) were analyzed. We found that Acidobacteria, Proteobacteria, Bacteroidetes, Actinobacteria, Chloroflexi, Planctomycetes, Gemmatimonadetes, Firmicutes, and Verrucomicrobia constitute the dominant taxonomic groups in either the ZD91 transgenic line or parental cultivar ZD, and that there was no statistically significant difference in the rhizosphere bacterial community structure between the two cultivars.
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Affiliation(s)
- Jingang Liang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Shi Sun
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Ji
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Haiying Wu
- Nanchong Academy of Agricultural Science, Nanchong, China
| | - Fang Meng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Mingrong Zhang
- Nanchong Academy of Agricultural Science, Nanchong, China
| | - Xiaobo Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Cunxiang Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), MOA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Science, The Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
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26
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McManus PS. Does a drop in the bucket make a splash? Assessing the impact of antibiotic use on plants. Curr Opin Microbiol 2014; 19:76-82. [PMID: 25006016 DOI: 10.1016/j.mib.2014.05.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 04/29/2014] [Accepted: 05/21/2014] [Indexed: 11/27/2022]
Abstract
Antibiotics are applied to plants to prevent bacterial diseases, although the diversity of antibiotics and total amounts used are dwarfed by antibiotic use in animal agriculture. Nevertheless, the release of antibiotics into the open environment during crop treatment draws scrutiny for its potential impact on the global pool of resistance genes. The main use of antibiotics on plants is application of streptomycin to prevent fire blight, a serious disease of apple and pear trees. A series of recent studies identified and quantified antibiotic resistance genes and profiled bacterial communities in apple orchard plots that were or were not sprayed with streptomycin. While the specific objectives and methods varied, the results of these studies suggest that streptomycin application for fire blight control does not influence bacterial community structure or increase the abundance of resistance genes in orchards.
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Affiliation(s)
- Patricia S McManus
- Department of Plant Pathology, University of Wisconsin-Madison, United States.
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27
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Walsh F, Smith DP, Owens SM, Duffy B, Frey JE. Restricted streptomycin use in apple orchards did not adversely alter the soil bacteria communities. Front Microbiol 2014; 4:383. [PMID: 24550889 PMCID: PMC3908321 DOI: 10.3389/fmicb.2013.00383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 11/25/2013] [Indexed: 02/01/2023] Open
Abstract
Streptomycin has been authorized for restricted use in the prevention of the fire blight disease of pome fruit orchards in the EU and Switzerland. This study addresses the important topic of the influence of the use of streptomycin in agriculture on the total bacteria community within the soil ecosystem. Soil samples were taken from soils under apple trees, prior to streptomycin application and 2 weeks post streptomycin application or water application (untreated control). High throughput 16S rRNA gene amplicon sequencing was used to generate datasets from the soils under apple trees in apple orchards from three different locations in Switzerland. We hypothesized that the use of streptomycin would reduce the bacterial diversity within the soil samples and enhance a reduction in the variety of taxa present. Bacterial species such as Pseudomonas, Burkholderia, and Stenotrophomonas are intrinsically resistant to many antibiotics and as such it is of interest to investigate if the use of streptomycin provided a selective advantage for these bacteria in the soil ecosystem. The application of streptomycin did not influence the abundance and diversities of major bacteria taxa of the soils or the Pseudomonas, Burkholderia, and Stenotrophomonas species. We also discovered that apple orchards under the same management practices, did not harbor the same bacterial communities. The restricted application of streptomycin in the protection of apple orchards from the fire blight pathogen Erwinia amylovora under the guidelines in Switzerland did not alter either the bacterial diversity or abundance within these soil ecosystems.
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Affiliation(s)
- Fiona Walsh
- Federal Department of Economic Affairs, Education and Research EAER, Research Station Agroscope Changins-Wädenswil ACWWädenswil, Switzerland
| | - Daniel P. Smith
- Institute of Genomic and Systems Biology, Argonne National LaboratoryArgonne, IL, USA
| | - Sarah M. Owens
- Institute of Genomic and Systems Biology, Argonne National LaboratoryArgonne, IL, USA
- Computation Institute, University of ChicagoChicago, IL, USA
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, LSFM, Zurich University of Applied SciencesZurich, Switzerland
| | - Jürg E. Frey
- Federal Department of Economic Affairs, Education and Research EAER, Research Station Agroscope Changins-Wädenswil ACWWädenswil, Switzerland
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Duffy B, Holliger E, Walsh F. Streptomycin use in apple orchards did not increase abundance of mobile resistance genes. FEMS Microbiol Lett 2013; 350:180-9. [PMID: 24164283 DOI: 10.1111/1574-6968.12313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Revised: 09/26/2013] [Accepted: 10/22/2013] [Indexed: 11/26/2022] Open
Abstract
Streptomycin is used as a first-line defense and tetracycline as a second-line defense, in the fight against fire blight disease in apple and pear orchards. We have performed the first study to quantitatively analyze the influence of streptomycin use in agriculture on the abundance of streptomycin and tetracycline resistance genes in apple orchards. Flowers, leaves, and soil were collected from three orchard sites in 2010, 2011, and 2012. Gene abundance distribution was analyzed using two-way anova and principal component analysis to investigate relationships between gene abundance data over time and treatment. The mobile antibiotic resistance genes, strA, strB, tetB, tetM, tetW, and the insertion sequence IS1133, were detected prior to streptomycin treatment in almost all samples, indicating the natural presence of these resistance genes in nature. Statistically significant increases in the resistance gene abundances were occasional, inconsistent, and not reproducible from one year to the next. We conclude that the application of streptomycin in these orchards was not associated with sustained increases in streptomycin or tetracycline resistance gene abundances.
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Affiliation(s)
- Brion Duffy
- Federal Department of Economic Affairs, Education and Research EAER, Research Station Agroscope Changins-Wädenswil ACW, Wädenswil, Switzerland
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Shade A, Klimowicz AK, Spear RN, Linske M, Donato JJ, Hogan CS, McManus PS, Handelsman J. Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil. Appl Environ Microbiol 2013; 79:6617-25. [PMID: 23974143 PMCID: PMC3811482 DOI: 10.1128/aem.02017-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/15/2013] [Indexed: 11/20/2022] Open
Abstract
Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou's evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.
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Affiliation(s)
- Ashley Shade
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Amy K. Klimowicz
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Russell N. Spear
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Matthew Linske
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Justin J. Donato
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of St. Thomas, St. Paul, Minnesota, USA
| | - Clifford S. Hogan
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Patricia S. McManus
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
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Shade A, McManus PS, Handelsman J. Unexpected diversity during community succession in the apple flower microbiome. mBio 2013; 4:e00602-12. [PMID: 23443006 PMCID: PMC3585449 DOI: 10.1128/mbio.00602-12] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 01/09/2013] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. IMPORTANCE Flowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated with Deinococcus-Thermus and TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.
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Affiliation(s)
- Ashley Shade
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Patricia S. McManus
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
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Que X, Liu B, Fu L, Zhuang J, Chen G, Tang D. Molecular Imprint for Electrochemical Detection of Streptomycin Residues Using Enzyme Signal Amplification. ELECTROANAL 2013. [DOI: 10.1002/elan.201200468] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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