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Bartuv R, Berihu M, Medina S, Salim S, Feygenberg O, Faigenboim-Doron A, Zhimo VY, Abdelfattah A, Piombo E, Wisniewski M, Freilich S, Droby S. Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples. Environ Microbiol 2023; 25:1728-1746. [PMID: 36807446 DOI: 10.1111/1462-2920.16353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 02/16/2023] [Indexed: 02/23/2023]
Abstract
Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of 'Golden Delicious' apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.
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Affiliation(s)
- Rotem Bartuv
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Maria Berihu
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Shlomit Medina
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Shoshana Salim
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Adi Faigenboim-Doron
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - V Yeka Zhimo
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
| | - Ahmed Abdelfattah
- Department of Microbiome Biotechnology, Leibniz Institute for Agricultural Engineering and Bioeconomy, Potsdam, Germany
| | - Edoardo Piombo
- Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, Grugliasco, Italy
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute, and State University, Blacksburg, Virginia, USA
| | - Shiri Freilich
- Agricultural Research Organization (A.R.O.), Institute of Plant Sciences, Rishon LeZion/Ramat Yishay, Israel
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Institute, Rishon LeZion, Israel
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2
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Cheng JE, Su P, Zhang ZH, Zheng LM, Wang ZY, Hamid MR, Dai JP, Du XH, Chen LJ, Zhai ZY, Kong XT, Liu Y, Zhang DY. Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods. PLoS One 2022; 17:e0262517. [PMID: 35834536 PMCID: PMC9282544 DOI: 10.1371/journal.pone.0262517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 12/28/2021] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.
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Affiliation(s)
- Ju-E Cheng
- College of Plant Protection, Hunan Agricultural University, Changsha, China
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Pin Su
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Zhan-Hong Zhang
- Hunan Vegetable Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Li-Min Zheng
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Yong Wang
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Muhammad Rizwan Hamid
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Jian-Ping Dai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Hua Du
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Li-Jie Chen
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Zhong-Ying Zhai
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - Xiao-Ting Kong
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, China
| | - Yong Liu
- Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, China
| | - De-Yong Zhang
- Hunan Hybrid Rice Research Center, Changsha, China
- * E-mail:
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3
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Vermote L, Verce M, Mozzi F, De Vuyst L, Weckx S. Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity. Front Microbiol 2022; 13:872281. [PMID: 35898900 PMCID: PMC9309516 DOI: 10.3389/fmicb.2022.872281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits’ surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits’ surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.
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Affiliation(s)
- Louise Vermote
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Marko Verce
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernanda Mozzi
- Technology and Development Laboratory, Centro de Referencia para Lactobacilos (CERELA)-CONICET, San Miguel de Tucumán, Argentina
| | - Luc De Vuyst
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
| | - Stefan Weckx
- Faculty of Sciences and Bioengineering Sciences, Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit Brussel, Brussels, Belgium
- *Correspondence: Stefan Weckx,
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Gatzert X, Chun KP, Boner M, Hermanowski R, Mäder R, Breuer L, Gattinger A, Orlowski N. Assessment of multiple stable isotopes for tracking regional and organic authenticity of plant products in Hesse, Germany. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2021; 57:281-300. [PMID: 33855926 DOI: 10.1080/10256016.2021.1905635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/19/2021] [Indexed: 06/12/2023]
Abstract
As demand for regional and organically produced foodstuff has increased in Europe, the need has arisen to verify the products' origin and production method. For food authenticity tracking (production method and origin), we examined 286 samples of wheat (Triticum aestivum), potatoes (Solanum tuberosum), and apples (Malus domestica) from different regions in Germany for their stable isotope compositions of oxygen, hydrogen, carbon, nitrogen and sulphur. Single-variate authentication methods were used. Suitable isotope tracers to determine wheat's regional origin were δ18O and δ34S. δ13C helped to distinguish between organic and conventional wheat samples. For the separation of the production regions of potatoes, several isotope tracers were suitable (e.g. δ18O, δ2H, δ15N, δ13C and δ34S isotopes in potato protein), but only protein δ15N was suitable to differentiate between organic and conventional potato samples. For the apple samples, 2H and 18O isotopes helped to identify production regions, but no significant statistical differences could be found between organically and conventionally farmed apples. For food authenticity tracking, our study showed the need to take the various isotopes into account. There is an urgent need for a broad reference database if isotope measurements are to become a main tool for determining product's origin.
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Affiliation(s)
- Xenia Gatzert
- Research Institute of Organic Agriculture (FiBL), Frankfurt am Main, Germany
- Institute for Plant Production and Plant Breeding II - Organic Farming with Focus on Sustainable Soil Use, Justus Liebig University Giessen, Giessen, Germany
| | - Kwok P Chun
- Department of Geography, Hong Kong Baptist University, Kowloon, Hong Kong
| | | | - Robert Hermanowski
- Research Institute of Organic Agriculture (FiBL), Frankfurt am Main, Germany
| | - Rolf Mäder
- Research Institute of Organic Agriculture (FiBL), Frankfurt am Main, Germany
| | - Lutz Breuer
- Institute for Landscape Ecology and Resources Management (ILR), Research Centre for BioSystems, Land Use and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
| | - Andreas Gattinger
- Institute for Plant Production and Plant Breeding II - Organic Farming with Focus on Sustainable Soil Use, Justus Liebig University Giessen, Giessen, Germany
| | - Natalie Orlowski
- Institute for Landscape Ecology and Resources Management (ILR), Research Centre for BioSystems, Land Use and Nutrition (IFZ), Justus-Liebig-University Giessen, Giessen, Germany
- Albert-Ludwigs-University of Freiburg, Freiburg, Germany
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5
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Carvalho CR, Dias AC, Homma SK, Cardoso EJ. Phyllosphere bacterial assembly in citrus crop under conventional and ecological management. PeerJ 2020; 8:e9152. [PMID: 32547860 PMCID: PMC7274167 DOI: 10.7717/peerj.9152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/17/2020] [Indexed: 11/20/2022] Open
Abstract
Divergences between agricultural management can result in different types of biological interactions between plants and microorganisms, which may affect food quality and productivity. Conventional practices are well-established in the agroindustry as very efficient and lucrative; however, the increasing demand for sustainable alternatives has turned attention towards agroecological approaches. Here we intend to explore microbial dynamics according to the agricultural management used, based on the composition and structure of these bacterial communities on the most environmentally exposed habitat, the phyllosphere. Leaf samples were collected from a Citrus crop (cultivated Orange) in Mogi-Guaçu (SP, Brazil), where either conventional or ecological management systems were properly applied in two different areas. NGS sequencing analysis and quantitative PCR allowed us to comprehend the phyllosphere behavior and µ-XRF (micro X-ray fluorescence) could provide an insight on agrochemical persistence on foliar tissues. Our results demonstrate that there is considerable variation in the phyllosphere community due to the management practices used in the citrus orchard, and it was possible to quantify most of this variation. Equally, high copper concentrations may have influenced bacterial abundance, having a relevant impact on the differences observed. Moreover, we highlight the intricate relationship microorganisms have with crop production, and presumably with crop yield as well.
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Affiliation(s)
- Carolinne R Carvalho
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Armando Cf Dias
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Elke Jbn Cardoso
- Department of Soil Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, São Paulo, Brazil
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6
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Longley R, Noel ZA, Benucci GMN, Chilvers MI, Trail F, Bonito G. Crop Management Impacts the Soybean ( Glycine max) Microbiome. Front Microbiol 2020; 11:1116. [PMID: 32582080 PMCID: PMC7283522 DOI: 10.3389/fmicb.2020.01116] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Soybean (Glycine max) is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by Sphingomonas and Methylobacterium while belowground samples were dominated by Bradyrhizobium and Sphingomonas. Aboveground fungal communities were dominated by Davidiella across all management systems, while belowground samples were dominated by Fusarium and Mortierella. Specific taxa including potential plant beneficials such as Mortierella were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as Bradyrhizobium and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.
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Affiliation(s)
- Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Zachary A Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Gian Maria Niccolò Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Genetics and Genomic Sciences Program, Michigan State University, East Lansing, MI, United States
| | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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7
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Bacterial communities associated with the surface of fresh sweet pepper (Capsicum annuum) and their potential as biocontrol. Sci Rep 2020; 10:8560. [PMID: 32444860 PMCID: PMC7244708 DOI: 10.1038/s41598-020-65587-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
Fresh produce vegetables are colonized by different bacterial species, some of which are antagonistic to microbes that cause postharvest losses. However, no comprehensive assessment of the diversity and composition of bacteria inhabiting surfaces of fresh pepper plants grown under different conditions has been conducted. In this study, 16S RNA amplicon sequencing was used to reveal bacterial communities inhabiting the surfaces of red and green pepper (fungicides-treated and non-fungicides-treated) grown under hydroponic and open field conditions. Results revealed that pepper fruit surfaces were dominated by bacterial phylum Proteobacteria, Firmicutes, Actinobacteria, and, Bacteroidetes. The majority of the bacterial operation taxonomic units (97% similarity cut-off) were shared between the two habitats, two treatments, and the two pepper types. Phenotypic predictions (at phylum level) detected a high abundance of potentially pathogenic, biofilm-forming, and stress-tolerant bacteria on samples grown on open soils than those from hydroponic systems. Furthermore, bacterial species of genera mostly classified as fungal antagonists including; Acinetobacter, Agrobacterium, and Burkholderia were the most abundant on the surfaces. These results suggest that peppers accommodate substantially different bacterial communities with antagonistic activities on their surfaces, independent of employed agronomic strategies and that the beneficial bacterial strains maybe more important for peppers established on open fields, which seems to be more vulnerable to abiotic and biotic stresses.
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8
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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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9
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Bigot C, Bugaud C, Camilo J, Kapitan A, Montet D, Meile JC. Impact of farming type, variety and geographical origin on bananas bacterial community. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Sare AR, Stouvenakers G, Eck M, Lampens A, Goormachtig S, Jijakli MH, Massart S. Standardization of Plant Microbiome Studies: Which Proportion of the Microbiota is Really Harvested? Microorganisms 2020; 8:microorganisms8030342. [PMID: 32121205 PMCID: PMC7142977 DOI: 10.3390/microorganisms8030342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/14/2020] [Accepted: 02/25/2020] [Indexed: 12/13/2022] Open
Abstract
Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.
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Affiliation(s)
- Abdoul Razack Sare
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
- Correspondence:
| | - Gilles Stouvenakers
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Mathilde Eck
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Amber Lampens
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- VIB-UGent Center of Plant Systems Biology, 9052 Ghent, Belgium; (A.L.); (S.G.)
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - M. Haïssam Jijakli
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
| | - Sebastien Massart
- Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium; (G.S.); (M.E.); (M.H.J.); (S.M.)
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11
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Janakiev T, Dimkić I, Bojić S, Fira D, Stanković S, Berić T. Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate. J Appl Microbiol 2019; 128:528-543. [PMID: 31606926 DOI: 10.1111/jam.14488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
AIMS The characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens. METHODS AND RESULTS The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with Pseudomonas syringae and Pseudomonas graminis, the most likely resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity. CONCLUSIONS Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens. SIGNIFICANCE AND IMPACT OF STUDY Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. The indigenous antagonistic isolate, B. thuringiensis R3/3, from plum could be further investigated for its potential use in biological control of plum diseases.
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Affiliation(s)
- T Janakiev
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - I Dimkić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Bojić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - D Fira
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Stanković
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - T Berić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
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Kim MS, Bae JW, Park EJ. Postharvest processing decreases the richness of bacterial taxa in the phyllosphere of broccoli. J Appl Microbiol 2018; 125:295-305. [PMID: 29573325 DOI: 10.1111/jam.13759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/06/2018] [Accepted: 03/12/2018] [Indexed: 02/06/2023]
Abstract
AIMS Diverse bacterial communities residing on the surfaces of fresh vegetables are important for food quality and safety; however, knowledge of the phyllosphere microbiota on fresh vegetables and of how it changes during postharvest stage is poorly understood. METHODS AND RESULTS We used culturing to quantify bacterial abundance and 16S rRNA 454 pyrosequencing to analyse the bacterial community composition on broccoli florets collected from farms (preharvest) and retail stores (postharvest). The bacterial community compositions of the preharvest and postharvest broccoli were significantly different. The number of non-Escherichia coli coliform bacteria (Hafnia sp. and Rahnella sp.) was higher in the postharvest broccoli than in the preharvest broccoli. Minor bacterial taxa at the phylum and genus levels had markedly disappeared in the postharvest broccoli, resulting in low bacterial species richness in the postharvest broccoli. CONCLUSIONS The dominant bacterial taxa persist and prevail in the phyllosphere of broccoli during the postharvest stage. SIGNIFICANCE AND IMPACT OF THE STUDY A popular crop of leafy vegetables, broccoli, is of great agricultural and nutritional importance. This study provides a detailed description of changes in the bacterial community of broccoli in harvest and storage. This study presents novel data on the impact of postharvest conditions on the bacterial populations on broccoli florets.
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Affiliation(s)
- M-S Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - J-W Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - E-J Park
- Department of Food Bioengineering, Jeju National University, Jeju, Korea
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Aydogan EL, Moser G, Müller C, Kämpfer P, Glaeser SP. Long-Term Warming Shifts the Composition of Bacterial Communities in the Phyllosphere of Galium album in a Permanent Grassland Field-Experiment. Front Microbiol 2018; 9:144. [PMID: 29487575 PMCID: PMC5816784 DOI: 10.3389/fmicb.2018.00144] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 01/23/2018] [Indexed: 11/13/2022] Open
Abstract
Global warming is currently a much discussed topic with as yet largely unexplored consequences for agro-ecosystems. Little is known about the warming effect on the bacterial microbiota inhabiting the plant surface (phyllosphere), which can have a strong impact on plant growth and health, as well as on plant diseases and colonization by human pathogens. The aim of this study was to investigate the effect of moderate surface warming on the diversity and composition of the bacterial leaf microbiota of the herbaceous plant Galium album. Leaves were collected from four control and four surface warmed (+2°C) plots located at the field site of the Environmental Monitoring and Climate Impact Research Station Linden in Germany over a 6-year period. Warming had no effect on the concentration of total number of cells attached to the leaf surface as counted by Sybr Green I staining after detachment, but changes in the diversity and phylogenetic composition of the bacterial leaf microbiota analyzed by bacterial 16S rRNA gene Illumina amplicon sequencing were observed. The bacterial phyllosphere microbiota were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Warming caused a significant higher relative abundance of members of the Gammaproteobacteria, Actinobacteria, and Firmicutes, and a lower relative abundance of members of the Alphaproteobacteria and Bacteroidetes. Plant beneficial bacteria like Sphingomonas spp. and Rhizobium spp. occurred in significantly lower relative abundance in leaf samples of warmed plots. In contrast, several members of the Enterobacteriaceae, especially Enterobacter and Erwinia, and other potential plant or human pathogenic genera such as Acinetobacter and insect-associated Buchnera and Wolbachia spp. occurred in higher relative abundances in the phyllosphere samples from warmed plots. This study showed for the first time the long-term impact of moderate (+2°C) surface warming on the phyllosphere microbiota on plants. A reduction of beneficial bacteria and an enhancement of potential pathogenic bacteria in the phyllosphere of plants may indicate that this aspect of the ecosystem which has been largely neglected up till now, can be a potential risk for pathogen transmission in agro-ecosystems in the near future.
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Affiliation(s)
- Ebru L. Aydogan
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Gerald Moser
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
| | - Christoph Müller
- Institute for Plant Ecology, Justus Liebig University Giessen, Giessen, Germany
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Peter Kämpfer
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Stefanie P. Glaeser
- Institute for Applied Microbiology, Justus Liebig University Giessen, Giessen, Germany
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Hurtado-Barroso S, Tresserra-Rimbau A, Vallverdú-Queralt A, Lamuela-Raventós RM. Organic food and the impact on human health. Crit Rev Food Sci Nutr 2017; 59:704-714. [PMID: 29190113 DOI: 10.1080/10408398.2017.1394815] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In the last decade, the production and consumption of organic food have increased steadily worldwide, despite the lower productivity of organic crops. Indeed, the population attributes healthier properties to organic food. Although scientific evidence is still scarce, organic agriculture seems to contribute to maintaining an optimal health status and decreases the risk of developing chronic diseases. This may be due to the higher content of bioactive compounds and lower content of unhealthy substances such as cadmium and synthetic fertilizers and pesticides in organic foods of plant origin compared to conventional agricultural products. Thus, large long-term intervention studies are needed to determine whether an organic diet is healthier than a diet including conventionally grown food products. This review provides an update of the present knowledge of the impact of an organic versus a conventional food diet on health.
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Affiliation(s)
- Sara Hurtado-Barroso
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
| | - Anna Tresserra-Rimbau
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
| | - Anna Vallverdú-Queralt
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain
| | - Rosa María Lamuela-Raventós
- a Department of Nutrition, Food Sciences and Gastronomy, School of Pharmacy and Food Sciences , University of Barcelona , Barcelona , Spain.,b CIBER Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III , Spain.,c INSA-UB, Nutrition and Food Safety Research Institute, University of Barcelona , Barcelona , Spain
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Cousin FJ, Le Guellec R, Schlusselhuber M, Dalmasso M, Laplace JM, Cretenet M. Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions. Microorganisms 2017; 5:E39. [PMID: 28757560 PMCID: PMC5620630 DOI: 10.3390/microorganisms5030039] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 12/18/2022] Open
Abstract
Production of fermented apple beverages is spread all around the world with specificities in each country. 'French ciders' refer to fermented apple juice mainly produced in the northwest of France and often associated with short periods of consumption. Research articles on this kind of product are scarce compared to wine, especially on phenomena associated with microbial activities. The wine fermentation microbiome and its dynamics, organoleptic improvement for healthy and pleasant products and development of starters are now widely studied. Even if both beverages seem close in terms of microbiome and process (with both alcoholic and malolactic fermentations), the inherent properties of the raw materials and different production and environmental parameters make research on the specificities of apple fermentation beverages worthwhile. This review summarizes current knowledge on the cider microbial ecosystem, associated activities and the influence of process parameters. In addition, available data on cider quality and safety is reviewed. Finally, we focus on the future role of lactic acid bacteria and yeasts in the development of even better or new beverages made from apples.
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Affiliation(s)
- Fabien J Cousin
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Rozenn Le Guellec
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Margot Schlusselhuber
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Marion Dalmasso
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Jean-Marie Laplace
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
| | - Marina Cretenet
- Aliments Bioprocédés Toxicologie Environnements, Normandie Univ., UNICAEN, UNIROUEN, 14000 Caen, France.
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Karlsson I, Friberg H, Kolseth AK, Steinberg C, Persson P. Organic farming increases richness of fungal taxa in the wheat phyllosphere. Mol Ecol 2017; 26:3424-3436. [DOI: 10.1111/mec.14132] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/06/2017] [Accepted: 03/21/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ida Karlsson
- Department of Crop Production Ecology; Swedish University of Agricultural Sciences; Uppsala Sweden
- Department of Forest Mycology and Plant Pathology; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Hanna Friberg
- Department of Forest Mycology and Plant Pathology; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Anna-Karin Kolseth
- Department of Crop Production Ecology; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - Christian Steinberg
- Agroécologie; AgroSup Dijon; CNRS; INRA; Université Bourgogne Franche-Comté; Dijon France
| | - Paula Persson
- Department of Crop Production Ecology; Swedish University of Agricultural Sciences; Uppsala Sweden
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Duvenage FJ, Duvenage S, Du Plessis EM, Volschenk Q, Korsten L. Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:1185-1192. [PMID: 27300139 DOI: 10.1002/jsfa.7847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 05/20/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Knowledge on the culturable bacteria and foodborne pathogen presence on pears is important for understanding the impact of postharvest practices on food safety assurance. Pear fruit bacteria were investigated from the point of harvest, following chlorine drenching and after controlled atmosphere (CA) storage to assess the impact on natural bacterial populations and potential foodborne pathogens. RESULTS Salmonella spp. and Listeria monocytogenes were detected on freshly harvested fruit in season one. During season one, chemical drenching and CA storage did not have a significant effect on the bacterial load of orchard pears, except for two farms where the populations were lower 'after CA storage'. During season two, bacterial populations of orchard pears from three of the four farms increased significantly following drenching; however, the bacterial load decreased 'after CA storage'. Bacteria isolated following enumeration included Enterobacteriaceae, Microbacteriaceae, Pseudomonadaceae and Bacillaceae, with richness decreasing 'after drench' and 'after CA storage'. CONCLUSION Salmonella spp. and L. monocytogenes were not detected after postharvest practices. Postharvest practices resulted in decreased bacterial species richness. Understanding how postharvest practices have an impact on the viable bacterial populations of pear fruit will contribute to the development of crop-specific management systems for food safety assurance. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Francois J Duvenage
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Stacey Duvenage
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Erika M Du Plessis
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Quinton Volschenk
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
| | - Lise Korsten
- Department of Plant Science, University of Pretoria, Lynnwood Road, Pretoria, 0001, South Africa
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18
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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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Knight AL, Basoalto E, Yee W, Hilton R, Kurtzman CP. Adding yeasts with sugar to increase the number of effective insecticide classes to manage Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) in cherry. PEST MANAGEMENT SCIENCE 2016; 72:1482-90. [PMID: 26454150 DOI: 10.1002/ps.4171] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 10/06/2015] [Accepted: 10/07/2015] [Indexed: 05/25/2023]
Abstract
BACKGROUND Drosophila suzukii is a major pest of cherry in the western United States. We evaluated whether the addition of sugary baits could improve the efficacy of two classes of insecticides not considered to be sufficiently effective for this pest, diamides and spinosyns, in laboratory and field trials in cherry. RESULTS Adding cane sugar alone or in combination with the yeasts Saccharomyces cerevisiae or Aureobasidium pullulans significantly improved insecticide efficacy. However, the significance of adding yeasts to the sugar plus insecticide on fly mortality varied with respect to both the insecticide and yeast species. The addition of S. cerevisiae to sugar also did not significantly reduce egg densities in fruit compared with sugar alone. The addition of a yeast plus sugar significantly reduced egg densities in three field trials with cyantraniliprole and in two out of three trials with spinosad. CONCLUSION The addition of cane sugar with or without yeast can improve the effectiveness of diamide and spinosyn insecticides for D. suzukii in cherry. Inclusion of these two insecticides in D. suzukii management programs may alleviate the strong selection pressure currently being imposed on a few mode-of-action insecticide classes used by growers to maintain fly suppression over long continuous harvest periods of mixed cultivars. Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Alan L Knight
- Yakima Agricultural Research Laboratory, Agricultural Research Service, USDA, Wapato, WA, USA
| | - Esteban Basoalto
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias, Universidad Austral de Chile, Valdivia, Chile
| | - Wee Yee
- Yakima Agricultural Research Laboratory, Agricultural Research Service, USDA, Wapato, WA, USA
| | - Rick Hilton
- Southern Oregon Research and Extension Center, Oregon State University, Medford, OR, USA
| | - Cletus P Kurtzman
- Bacterial Foodborne Pathogens and Mycology Research Unit, Agricultural Research Service, USDA, Peoria, IL, USA
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20
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McGarvey J, Han R, Connell J, Stanker L, Hnasko R. Bacterial populations on the surfaces of organic and conventionally grown almond drupes. J Appl Microbiol 2015; 119:529-38. [DOI: 10.1111/jam.12850] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 04/17/2015] [Accepted: 05/11/2015] [Indexed: 11/27/2022]
Affiliation(s)
- J.A. McGarvey
- Foodborne Toxin Detection and Protection Research Unit; Agricultural Research Service; United States Department of Agriculture; Albany CA USA
| | - R. Han
- Department of Plant Sciences; University of California; Davis CA USA
| | - J.H. Connell
- University of California Cooperative Extension; Oroville CA USA
| | - L.H. Stanker
- Foodborne Toxin Detection and Protection Research Unit; Agricultural Research Service; United States Department of Agriculture; Albany CA USA
| | - R. Hnasko
- Foodborne Toxin Detection and Protection Research Unit; Agricultural Research Service; United States Department of Agriculture; Albany CA USA
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21
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Microbial genome-enabled insights into plant–microorganism interactions. Nat Rev Genet 2014; 15:797-813. [DOI: 10.1038/nrg3748] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Torjusen H, Brantsæter AL, Haugen M, Alexander J, Bakketeig LS, Lieblein G, Stigum H, Næs T, Swartz J, Holmboe-Ottesen G, Roos G, Meltzer HM. Reduced risk of pre-eclampsia with organic vegetable consumption: results from the prospective Norwegian Mother and Child Cohort Study. BMJ Open 2014; 4:e006143. [PMID: 25208850 PMCID: PMC4160835 DOI: 10.1136/bmjopen-2014-006143] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE Little is known about the potential health effects of eating organic food either in the general population or during pregnancy. The aim of this study was to examine associations between organic food consumption during pregnancy and the risk of pre-eclampsia among nulliparous Norwegian women. DESIGN Prospective cohort study. SETTING Norway, years 2002-2008. PARTICIPANTS 28 192 pregnant women (nulliparous, answered food frequency questionnaire and general health questionnaire in mid-pregnancy and no missing information on height, body weight or gestational weight gain). MAIN OUTCOME MEASURE Relative risk was estimated as ORs by performing binary logistic regression with pre-eclampsia as the outcome and organic food consumption as the exposure. RESULTS The prevalence of pre-eclampsia in the study sample was 5.3% (n=1491). Women who reported to have eaten organic vegetables 'often' or 'mostly' (n=2493, 8.8%) had lower risk of pre-eclampsia than those who reported 'never/rarely' or 'sometimes' (crude OR=0.76, 95% CI 0.61 to 0.96; adjusted OR=0.79, 95% CI 0.62 to 0.99). The lower risk associated with high organic vegetable consumption was evident also when adjusting for overall dietary quality, assessed as scores on a healthy food pattern derived by principal component analysis. No associations with pre-eclampsia were found for high intake of organic fruit, cereals, eggs or milk, or a combined index reflecting organic consumption. CONCLUSIONS These results show that choosing organically grown vegetables during pregnancy was associated with reduced risk of pre-eclampsia. Possible explanations for an association between pre-eclampsia and use of organic vegetables could be that organic vegetables may change the exposure to pesticides, secondary plant metabolites and/or influence the composition of the gut microbiota.
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Affiliation(s)
- Hanne Torjusen
- National Institute for Consumer Research (SIFO), Oslo, Norway
- Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo, Norway
| | - Anne Lise Brantsæter
- Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo, Norway
| | - Margaretha Haugen
- Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo, Norway
| | - Jan Alexander
- Office of the Director-General, Norwegian Institute of Public Health, Oslo, Norway
| | - Leiv S Bakketeig
- Division of Epidemiology, The Norwegian Institute of Public Health, Oslo, Norway
| | - Geir Lieblein
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Hein Stigum
- Division of Epidemiology, The Norwegian Institute of Public Health, Oslo, Norway
| | - Tormod Næs
- Nofima, Ås, Norway
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jackie Swartz
- Uppsala University Hospital, Uppsala, Sweden
- Vidarkliniken, Järna, Sweden
| | - Gerd Holmboe-Ottesen
- Department of General Practice and Community Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Gun Roos
- Division of Environmental Medicine, Norwegian Institute of Public Health, Oslo, Norway
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Williams TR, Marco ML. Phyllosphere microbiota composition and microbial community transplantation on lettuce plants grown indoors. mBio 2014; 5:e01564-14. [PMID: 25118240 PMCID: PMC4145687 DOI: 10.1128/mbio.01564-14] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of Escherichia coli O157:H7 was unchanged by microbial community transfer; however, the inoculation of E. coli O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety. IMPORTANCE The phyllosphere is a habitat for a variety of microorganisms, including bacteria with significant relevance to plant and human health. Some indigenous epiphytic bacteria might affect the persistence of human food-borne pathogens in the phyllosphere. However, studies on human pathogens are typically performed on plants grown indoors. This study compares the phyllosphere microbiota on Romaine lettuce plants grown in a Salinas Valley, CA, field to that on lettuce plants grown in environmental chambers. We show that phyllosphere microbiota from laboratory-grown plants is distinct from that colonizing plants grown in the field and that the field microbiota can be successfully transferred to plants grown indoors. The microbiota transplantation method was used to examine alterations to the phyllosphere microbiota after Escherichia coli O157:H7 inoculation on lettuce plants in a controlled environment. Our findings show the importance and validity of phyllosphere microbiota transplantation for future phyllosphere microbiology research.
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Affiliation(s)
- Thomas R Williams
- Department of Food Science & Technology, University of California, Davis, California, USA
| | - Maria L Marco
- Department of Food Science & Technology, University of California, Davis, California, USA
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Introduction of Aureobasidium pullulans to the Phyllosphere of Organically Grown Strawberries with Focus on Its Establishment and Interactions with the Resident Microbiome. AGRONOMY-BASEL 2013. [DOI: 10.3390/agronomy3040704] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Sylla J, Alsanius BW, Krüger E, Reineke A, Strohmeier S, Wohanka W. Leaf microbiota of strawberries as affected by biological control agents. PHYTOPATHOLOGY 2013; 103:1001-11. [PMID: 24020904 DOI: 10.1094/phyto-01-13-0014-r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The increasing use of biological control agents (BCAs) against Botrytis cinerea in strawberry raises the question of whether there are any undesirable impacts of foliar applications of BCAs on nontarget microorganisms in the phyllosphere. Therefore, our objective was to investigate this issue within a field study. Strawberry plants were repeatedly sprayed with three BCAs-namely, RhizoVital 42 fl. (Bacillus amyloliquefaciens FZB42), Trianum-P (Trichoderma harzianum T22), and Naturalis (Beauveria bassiana ATCC 74040)-to suppress Botrytis cinerea infections. Microbial communities of differentially treated leaves were analyzed using plate counts and pyrosequencing and compared with the microbial community of nontreated leaves. Plate count results indicate that the applied Bacillus and Trichoderma spp. survived in the strawberry phyllosphere throughout the strawberry season. However, no significant impacts on the leaf microbiota could be detected by this culture-dependent technique. Pyrosequencing of internal transcribed spacer ribosomal RNA and 16S RNA sequences revealed a change in fungal composition and diversity at class level after the introduction of T. harzianum T22 to the phyllosphere, whereas the bacterial composition and diversity was not affected by either this Trichoderma preparation or the other two BCAs. Our results suggest that pyrosequencing represents a useful method for studying microbial interactions in the phyllosphere.
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Rastogi G, Coaker GL, Leveau JH. New insights into the structure and function of phyllosphere microbiota through high-throughput molecular approaches. FEMS Microbiol Lett 2013; 348:1-10. [DOI: 10.1111/1574-6968.12225] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/21/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022] Open
Affiliation(s)
- Gurdeep Rastogi
- Department of Plant Pathology; University of California; Davis; CA; USA
| | - Gitta L. Coaker
- Department of Plant Pathology; University of California; Davis; CA; USA
| | - Johan H.J. Leveau
- Department of Plant Pathology; University of California; Davis; CA; USA
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Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiol 2013; 13:114. [PMID: 23705801 PMCID: PMC3680157 DOI: 10.1186/1471-2180-13-114] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 05/13/2013] [Indexed: 12/22/2022] Open
Abstract
Background Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop. Results DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe “native” bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes. Conclusions Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas. Dominant fungal taxa that could be identified to genus with 18S amplicons included Hypocrea, Aureobasidium and Cryptococcus. No definitive presence of Salmonella could be confirmed in any of the plant samples, although 16S sequences suggested that closely related genera were present on leaves, fruits and roots.
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Leff JW, Fierer N. Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 2013; 8:e59310. [PMID: 23544058 PMCID: PMC3609859 DOI: 10.1371/journal.pone.0059310] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/15/2013] [Indexed: 11/19/2022] Open
Abstract
Fresh fruits and vegetables can harbor large and diverse populations of bacteria. However, most of the work on produce-associated bacteria has focused on a relatively small number of pathogenic bacteria and, as a result, we know far less about the overall diversity and composition of those bacterial communities found on produce and how the structure of these communities varies across produce types. Moreover, we lack a comprehensive view of the potential effects of differing farming practices on the bacterial communities to which consumers are exposed. We addressed these knowledge gaps by assessing bacterial community structure on conventional and organic analogs of eleven store-bought produce types using a culture-independent approach, 16 S rRNA gene pyrosequencing. Our results demonstrated that the fruits and vegetables harbored diverse bacterial communities, and the communities on each produce type were significantly distinct from one another. However, certain produce types (i.e., sprouts, spinach, lettuce, tomatoes, peppers, and strawberries) tended to share more similar communities as they all had high relative abundances of taxa belonging to the family Enterobacteriaceae when compared to the other produce types (i.e., apples, peaches, grapes, and mushrooms) which were dominated by taxa belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla. Although potentially driven by factors other than farming practice, we also observed significant differences in community composition between conventional and organic analogs within produce types. These differences were often attributable to distinctions in the relative abundances of Enterobacteriaceae taxa, which were generally less abundant in organically-grown produce. Taken together, our results suggest that humans are exposed to substantially different bacteria depending on the types of fresh produce they consume with differences between conventionally and organically farmed varieties contributing to this variation.
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Affiliation(s)
- Jonathan W. Leff
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, United States of America
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, United States of America
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, United States of America
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Gosalbes MJ, Llop S, Vallès Y, Moya A, Ballester F, Francino MP. Meconium microbiota types dominated by lactic acid or enteric bacteria are differentially associated with maternal eczema and respiratory problems in infants. Clin Exp Allergy 2013; 43:198-211. [PMID: 23331561 DOI: 10.1111/cea.12063] [Citation(s) in RCA: 236] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 10/09/2012] [Accepted: 11/01/2012] [Indexed: 02/05/2023]
Abstract
BACKGROUND Culture-dependent methods have shown that meconium, the newborn's first intestinal discharge, is not sterile, but the diversity of bacteria present in this material needs to be further characterized by means of more sensitive molecular techniques. OBJECTIVE Our aims were to characterize molecularly the meconium microbiota in term infants, to assess whether it contributes to the future microbiota of the infants' gastrointestinal tract, and to evaluate how it relates to lifestyle variables and atopy-related conditions. METHODS We applied high-throughput pyrosequencing of the 16S rRNA gene to study the meconium microbiota in twenty term newborns from a Spanish birth cohort. For comparison, we characterized the microbiota in fecal samples from seven pregnant women days before delivery and in two series of infant samples spanning the first seven months of life. We also compared our data with vaginal and skin microbiota characterized in independent studies. Different types of meconium microbiota were defined based on taxonomic composition and abundance and their associations with different factors were statistically evaluated. RESULTS The meconium microbiota differs from those in adult feces, vagina and skin, but resembles that of fecal samples from young infants. Meconium samples clustered into two types with different bacterial diversity, richness and composition. One of the types was less diverse, dominated by enteric bacteria and associated with a history of atopic eczema in the mother (P = 0.038), whereas the second type was dominated by lactic acid bacteria and associated with respiratory problems in the infant (P = 0.040). CONCLUSIONS & CLINICAL RELEVANCE Our findings suggest that the meconium microbiota has an intrauterine origin and participates in gut colonization. Although based on a small population sample, our association analyses also suggest that the type of bacteria detected in meconium is influenced by maternal factors and may have consequences for childhood health.
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Affiliation(s)
- M J Gosalbes
- Unidad Mixta de Investigación en Genómica y Salud-Centro Superior de Investigación en Salud Pública Generalitat Valenciana, Institut Cavanilles de Biodiversitat i Biologia Evolutiva Universitat de València, Valencia, Spain
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Berlec A. Novel techniques and findings in the study of plant microbiota: search for plant probiotics. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 193-194:96-102. [PMID: 22794922 DOI: 10.1016/j.plantsci.2012.05.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 04/11/2012] [Accepted: 05/20/2012] [Indexed: 05/12/2023]
Abstract
Plants live in intimate relationships with numerous microorganisms present inside or outside plant tissues. The plant exterior provides two distinct ecosystems, the rhizosphere (below ground) and the phyllosphere (above ground), both populated by microbial communities. Most studies on plant microbiota deal with pathogens or mutualists. This review focuses on plant commensal bacteria, which could represent a rich source of bacteria beneficial to plants, alternatively termed plant probiotics. Plant commensal bacteria have been addressed only recently with culture-independent studies. These use next-generation sequencing, DNA microarray technologies and proteomics to decipher microbial community composition and function. Diverse bacterial populations are described in both rhizosphere and phyllosphere of different plants. The microorganisms can emerge from neighboring environmental ecosystems at random; however their survival is regulated by the plant. Influences from the environment, such as pesticides, farming practice and atmosphere, also affect the composition of microbial communities. Apart from community composition studies, some functional studies have also been performed. These include identification of broad-substrate surface receptors and methanol utilization enzymes by the proteomic approach, as well as identification of bacterial species that are important mediators of disease-suppressive soil phenomenon. Experience from more advanced human microbial studies could provide useful information and is discussed in the context of methodology and common trends. Administration of microbial mixtures of whole communities, rather than individual species, is highlighted and should be considered in future agricultural applications.
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Affiliation(s)
- Aleš Berlec
- Department of Biotechnology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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Yashiro E, McManus PS. Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere. PLoS One 2012; 7:e37131. [PMID: 22629357 PMCID: PMC3357425 DOI: 10.1371/journal.pone.0037131] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/17/2012] [Indexed: 11/18/2022] Open
Abstract
We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65%) was greater than at sprayed orchards (mean of 50%) (P = 0.0271). For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity) and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM) indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R = -0.104, P = 0.655). Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.
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Affiliation(s)
- Erika Yashiro
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Patricia S. McManus
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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Telias A, White JR, Pahl DM, Ottesen AR, Walsh CS. Bacterial community diversity and variation in spray water sources and the tomato fruit surface. BMC Microbiol 2011; 11:81. [PMID: 21510867 PMCID: PMC3108269 DOI: 10.1186/1471-2180-11-81] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 04/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tomato (Solanum lycopersicum) consumption has been one of the most common causes of produce-associated salmonellosis in the United States. Contamination may originate from animal waste, insects, soil or water. Current guidelines for fresh tomato production recommend the use of potable water for applications coming in direct contact with the fruit, but due to high demand, water from other sources is frequently used. We sought to describe the overall bacterial diversity on the surface of tomato fruit and the effect of two different water sources (ground and surface water) when used for direct crop applications by generating a 454-pyrosequencing 16S rRNA dataset of these different environments. This study represents the first in depth characterization of bacterial communities in the tomato fruit surface and the water sources commonly used in commercial vegetable production. RESULTS The two water sources tested had a significantly different bacterial composition. Proteobacteria was predominant in groundwater samples, whereas in the significantly more diverse surface water, abundant phyla also included Firmicutes, Actinobacteria and Verrucomicrobia. The fruit surface bacterial communities on tomatoes sprayed with both water sources could not be differentiated using various statistical methods. Both fruit surface environments had a high representation of Gammaproteobacteria, and within this class the genera Pantoea and Enterobacter were the most abundant. CONCLUSIONS Despite the major differences observed in the bacterial composition of ground and surface water, the season long use of these very different water sources did not have a significant impact on the bacterial composition of the tomato fruit surface. This study has provided the first next-generation sequencing database describing the bacterial communities living in the fruit surface of a tomato crop under two different spray water regimes, and therefore represents an important step forward towards the development of science-based metrics for Good Agricultural Practices.
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Affiliation(s)
- Adriana Telias
- Plant Science and Landscape Architecture Department, University of Maryland, College Park, MD 21201, USA.
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Yashiro E, Spear R, McManus P. Culture-dependent and culture-independent assessment of bacteria in the apple phyllosphere. J Appl Microbiol 2011; 110:1284-96. [DOI: 10.1111/j.1365-2672.2011.04975.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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