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Zhang J, Lu K, Zhu L, Li N, Lin D, Cheng Y, Wang M. Inhibition of quorum sensing serves as an effective strategy to mitigate the risks of human bacterial pathogens in soil. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133272. [PMID: 38134686 DOI: 10.1016/j.jhazmat.2023.133272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023]
Abstract
The coexistence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factor genes (VFGs) in human bacterial pathogens (HBPs) increases their risks to ecological security and human health and no effective strategy is available. Herein, we demonstrated two typical quorum sensing (QS) interfering agents, 4-nitropyridine-N-oxide (4-NPO, a QS inhibitor) and Acylase Ⅰ (a quorum quenching (QQ) enzyme), effectively decreased the abundance of HBPs by 48.30% and 72.54%, respectively, which was accompanied by the reduction of VFGs, ARGs, and MGEs. The decrease in QS signals mediated by QS interfering agents disturbed bacterial communication and inhibited biofilm formation. More importantly, QS interfering agents reduced the intra-species and inter-species conjugation frequencies among bacteria, considerably inhibiting the dissemination of ARGs and VFGs via horizontal gene transfer. Furthermore, the QS interfering agents did not significantly affect the metabolic function of other nonpathogenic microorganisms in the soil. Collectively, our study provides an effective and eco-friendly strategy to mitigate the risks of HBPs in soil.
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Affiliation(s)
- Jinghan Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Kun Lu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Lin Zhu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Na Li
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Da Lin
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Yangjuan Cheng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China.
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Wang W, Luo T, Zhao Y, Yang X, Wang D, Yang G, Jin Y. Antibiotic resistance gene distribution in Shine Muscat grapes and health risk assessment of streptomycin residues in mice. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133254. [PMID: 38103297 DOI: 10.1016/j.jhazmat.2023.133254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/05/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
Antibiotic residues and antibiotic resistance genes (ARGs) in fruits and vegetables pose public health risks via the food chain, attracting increased attention. Antibiotics such as streptomycin, used directly on seedless grapes or introduced into vineyard soil through organic fertilizers. However, extensive data supporting the risk assessment of antibiotic residues and resistance in these produce remains lacking. Utilizing metagenomic sequencing, we characterized Shine Muscat grape antibiotic resistome and mobile genetic elements (MGEs). Abundant MGEs and ARGs were found in grapes, with 174 ARGs on the grape surface and 32 in the fruit. Furthermore, our data indicated that soil is not the primary source of these MGEs and ARGs. Escherichia was identified as an essential carrier and potential transmitter of ARGs. In our previous study, streptomycin residue was identified in grapes. Further short-term exposure experiments in mice revealed no severe physiological or histological damage at several environment-related concentrations. However, with increased exposure, some ARGs levels in mouse gut microbes increased, indicating a potential threat to animal health. Overall, this study provides comprehensive insights into the resistance genome and potential hosts in grapes, supporting the risk assessment of antibiotic resistance in fruits and vegetables.
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Affiliation(s)
- Weitao Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China
| | - Ting Luo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China, Hangzhou 310021, China
| | - Yao Zhao
- Xianghu Laboratory, Hangzhou 311231, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Xinyuan Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; College of Food Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Dou Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China; Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, China, Hangzhou 310021, China
| | - Guiling Yang
- Xianghu Laboratory, Hangzhou 311231, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Laboratory (Hangzhou) for Risk Assessment of Agricultural Products of Ministry of Agriculture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China.
| | - Yuanxiang Jin
- Xianghu Laboratory, Hangzhou 311231, China; College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310032, China.
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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [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] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- 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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Kahleova H, Holtz DN, Strom N, La Reau A, Kolipaka S, Schmidt N, Hata E, Znayenko-Miller T, Holubkov R, Barnard ND. A dietary intervention for postmenopausal hot flashes: A potential role of gut microbiome. An exploratory analysis. Complement Ther Med 2023; 79:103002. [PMID: 37949415 DOI: 10.1016/j.ctim.2023.103002] [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] [Received: 06/25/2023] [Revised: 10/11/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023] Open
Abstract
OBJECTIVE This study examined the role of gut microbiome changes in mediating the effects of a dietary intervention on the frequency and severity of postmenopausal vasomotor symptoms METHODS: Postmenopausal women (n = 84) reporting ≥2 moderate-to-severe hot flashes daily were randomly assigned, in 2 successive cohorts, to an intervention including a low-fat, vegan diet and cooked soybeans (½ cup [86 g] daily) or to stay on their usual diet. Over a 12-week period, frequency and severity of hot flashes were recorded with a mobile application. In a subset of 11 women, gut microbiome was analyzed at baseline and after 12 weeks of the dietary intervention (low-fat vegan diet with soybeans), using deep shotgun metagenomic sequencing. Differences in the microbiome between baseline and 12 weeks were assessed by comparing alpha diversity with Wilcoxon signed rank tests, beta diversity with permanovaFL, and taxon abundance with Wilcoxon signed rank tests. Pearson correlations were used to assess the association between changes in hot flashes and gut bacteria. RESULTS In the subset for which microbiome testing was done, total hot flashes decreased by 95 % during the dietary intervention (p = 0.007); severe hot flashes disappeared (from 0.6 to 0.0/day; p = 0.06); and moderate-to-severe hot flashes decreased by 96 % (p = 0.01). Daytime and nighttime hot flashes were reduced by 96 % (p = 0.01) and 94 % (p = 0.004), respectively. Alpha and beta diversity did not significantly differ in the intervention group between baseline and 12 weeks. Two families (Enterobacteriaceae and Veillonellaceae), 5 genera (Erysipelatoclostridium, Fusicatenibacter, Holdemanella, Intestinimonas, and Porphyromonas), and 6 species (Clostridium asparagiforme, Clostridium innocuum, Bacteroides thetaiotaomicron, Fusicatenibacter saccharivorans, Intestinimonas butyriciproducens, Prevotella corporis, and Streptococcus sp.) were differentially abundant, but after correction for multiple comparisons, these differences were no longer significant. Changes in the relative abundance of Porphyromonas and Prevotella corporis were associated with the reduction in severe day hot flashes both unadjusted (r = 0.61; p = 0.047; and r = 0.69; p = 0.02), respectively), and after adjustment for changes in body mass index (r = 0.63; p = 0.049; and r = 0.73; p = 0.02), respectively). Changes in relative abundance of Clostridium asparagiforme were associated with the reduction in total severe hot flashes (r = 0.69; p = 0.019) and severe night hot flashes (r = 0.82; p = 0.002) and the latter association remained significant after adjustment for changes in body mass index (r = 0.75; p = 0.01). CONCLUSIONS This exploratory analysis revealed potential associations between changes in vasomotor symptoms in response to a diet change and changes in the gut microbiome. Larger randomized clinical trials are needed to investigate these findings.
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Affiliation(s)
- Hana Kahleova
- Physicians Committee for Responsible Medicine, Washington, DC, USA.
| | - Danielle N Holtz
- Physicians Committee for Responsible Medicine, Washington, DC, USA
| | | | | | - Sinjana Kolipaka
- Physicians Committee for Responsible Medicine, Washington, DC, USA; Florida Atlantic University, Charles E. Schmidt College of Medicine, FL, USA
| | - Natalie Schmidt
- Physicians Committee for Responsible Medicine, Washington, DC, USA; Florida Atlantic University, Charles E. Schmidt College of Medicine, FL, USA
| | - Ellen Hata
- Physicians Committee for Responsible Medicine, Washington, DC, USA; George Washington University, Milken Institute School of Public Health, DC, USA
| | | | | | - Neal D Barnard
- Physicians Committee for Responsible Medicine, Washington, DC, USA; Adjunct faculty, George Washington University School of Medicine & Health Sciences, Washington, DC, USA
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Fan C, Zheng Y, Xue H, Xu J, Wu M, Chen L, Xu L. Different gut microbial types were found in captive striped hamsters. PeerJ 2023; 11:e16365. [PMID: 37953783 PMCID: PMC10634337 DOI: 10.7717/peerj.16365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
Background Typing analysis has become a popular approach to categorize individual differences in studies of animal gut microbial communities. However, previous definitions of gut microbial types were more understood as a passive reaction process to different external interferences, as most studies involve diverse environmental variables. We wondered whether distinct gut microbial types can also occur in animals under the same external environment. Moreover, the role of host sex in shaping gut microbiota has been widely reported; thus, the current study preliminarily explores the effects of sex on potential different microbial types. Methods Here, adult striped hamsters Cricetulus barabensis of different sexes were housed under the same controlled laboratory conditions, and their fecal samples were collected after two months to assess the gut microbiota by 16S rRNA sequencing. Results The gut microbiota of captive striped hamsters naturally separated into two types at the amplicon sequence variant (ASV) level. There was a significant difference in the Shannon index among these two types. A receiver operating characteristic (ROC) curve showed that the top 30 ASVs could effectively distinguish each type. Linear discriminant analysis of effect size (LEfSe) showed enrichment of the genera Lactobacillus, Treponema and Pygmaiobacter in one gut microbial type and enrichment of the genera Turicibacter and Ruminiclostridium in the other. The former type had higher carbohydrate metabolism ability, while the latter harbored a more complex co-occurrence network and higher amino acid metabolism ability. The gut microbial types were not associated with sex; however, we did find sex differences in the relative abundances of certain bacterial taxa, including some type-specific sex variations. Conclusions Although captive animals live in a unified environment, their gut bacteria can still differentiate into distinct types, but the sex of the hosts may not play an important role in the typing process of small-scale captive animal communities. The relevant driving factors as well as other potential types need to be further investigated to better understand host-microbe interactions.
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Affiliation(s)
- Chao Fan
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Yunjiao Zheng
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Huiliang Xue
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Jinhui Xu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Ming Wu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Lei Chen
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Laixiang Xu
- School of Life Sciences, Qufu Normal University, Qufu, Shandong, China
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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Sessitsch A, Wakelin S, Schloter M, Maguin E, Cernava T, Champomier-Verges MC, Charles TC, Cotter PD, Ferrocino I, Kriaa A, Lebre P, Cowan D, Lange L, Kiran S, Markiewicz L, Meisner A, Olivares M, Sarand I, Schelkle B, Selvin J, Smidt H, van Overbeek L, Berg G, Cocolin L, Sanz Y, Fernandes WL, Liu SJ, Ryan M, Singh B, Kostic T. Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet. Microbiol Mol Biol Rev 2023; 87:e0021222. [PMID: 37367231 PMCID: PMC10521359 DOI: 10.1128/mmbr.00212-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023] Open
Abstract
Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.
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Affiliation(s)
| | | | | | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Tomislav Cernava
- University of Southampton, Faculty of Environmental and Life Sciences, Southampton, United Kingdom
| | | | | | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, APC Microbiome Ireland and VistaMilk, Cork, Ireland
| | | | - Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pedro Lebre
- University of Pretoria, Pretoria, South Africa
| | - Don Cowan
- University of Pretoria, Pretoria, South Africa
| | - Lene Lange
- LL-BioEconomy, Valby, Copenhagen, Denmark
| | | | - Lidia Markiewicz
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Department of Immunology and Food Microbiology, Olsztyn, Poland
| | - Annelein Meisner
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | - Marta Olivares
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Inga Sarand
- Tallinn University of Technology, Department of Chemistry and Biotechnology, Tallinn, Estonia
| | | | | | - Hauke Smidt
- Wageningen University and Research, Laboratory of Microbiology, Wageningen, The Netherlands
| | - Leo van Overbeek
- Wageningen University and Research, Wageningen Research, Wageningen, The Netherlands
| | | | | | - Yolanda Sanz
- Institute of Agrochemistry and Food Technology, Excellence Center Severo Ochoa – Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | | | - S. J. Liu
- Chinese Academy of Sciences, Institute of Microbiology, Beijing, China
| | - Matthew Ryan
- Genetic Resources Collection, CABI, Egham, United Kingdom
| | - Brajesh Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Tanja Kostic
- AIT Austrian Institute of Technology GmbH, Tulln, Austria
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Smalla K, Kabisch J, Fiedler G, Hammerl JA, Tenhagen BA. [Health risks from crop irrigation with treated wastewater containing antibiotic residues, resistance genes, and resistant microorganisms]. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2023:10.1007/s00103-023-03710-7. [PMID: 37233812 DOI: 10.1007/s00103-023-03710-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/25/2023] [Indexed: 05/27/2023]
Abstract
This review describes the effects and potential health risks of resistant microorganisms, resistance genes, and residues of drugs and biocides that occur when re-using wastewater for crop irrigation. It focusses on specific aspects of these contaminants and their interactions, but does not provide a general risk assessment of the microbial load when using reclaimed water.Antimicrobial residues, antimicrobial resistant microorganisms, and resistance genes are frequently detected in treated wastewater. They have effects on the soil and plant-associated microbiota (total associated microorganisms) and can be taken up by plants. An interaction of residues with microorganisms is mainly expected before using the water for irrigation. However, it may also occur as a combined effect on the plant microbiome and all the abundant resistance genes (resistome). Special concerns are raised as plants are frequently consumed raw, that is, without processing that might reduce the bacterial load. Washing fruits and vegetables only has minor effects on the plant microbiome. On the other hand, cutting and other processes may support growth of microorganisms. Therefore, after such process steps, cooling of the foods is required.Further progress has to be made in the treatment of wastewater that will be used for crop irrigation with respect to removing micropollutants and microorganisms to minimize the risk of an increased exposure of consumers to transferable resistance genes and resistant bacteria.
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Affiliation(s)
- Kornelia Smalla
- Institut für Epidemiologie und Pathogendiagnostik, Julius Kühn-Institut (JKI), Braunschweig, Deutschland
| | - Jan Kabisch
- Institut für Mikrobiologie und Biotechnologie, Max Rubner-Institut (MRI), Kiel, Deutschland
| | - Gregor Fiedler
- Institut für Mikrobiologie und Biotechnologie, Max Rubner-Institut (MRI), Kiel, Deutschland
| | - Jens Andre Hammerl
- Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Deutschland
| | - Bernd-Alois Tenhagen
- Abteilung Biologische Sicherheit, Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Deutschland.
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9
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Saldarriaga JF, López JE, Díaz-García L, Montoya-Ruiz C. Changes in Lolium perenne L. rhizosphere microbiome during phytoremediation of Cd- and Hg-contaminated soils. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:49498-49511. [PMID: 36781665 PMCID: PMC10104932 DOI: 10.1007/s11356-023-25501-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/18/2023] [Indexed: 04/16/2023]
Abstract
The contamination of soil and water by metals such as mercury (Hg) and cadmium (Cd) has been increasing in recent years, because of anthropogenic activities such as mining and agriculture, respectively. In this work, the changes in the rhizosphere microbiome of Lolium perenne L. during the phytoremediation of soils contaminated with Hg and Cd were evaluated. For this, two soil types were sampled, one inoculated with mycorrhizae and one without. The soils were contaminated with Hg and Cd, and L. perenne seeds were sown and harvested after 30 days. To assess changes in the microbiome, DNA isolation tests were performed, for which samples were subjected to two-step PCR amplification with specific 16S rDNA V3-V4 primers (337F and 805R). With mycorrhizae, changes had been found in the absorption processes of metals and a new distribution. While with respect to microorganisms, families such as the Enterobacteriaceae have been shown to have biosorption and efflux effects on metals such as Hg and Cd. Mycorrhizae then improve the efficiency of removal and allow the plant to better distribute the absorbed concentrations. Overall, L. perenne is a species with a high potential for phytoremediation of Cd- and Hg-contaminated soils in the tropics. Inoculation with mycorrhizae modifies the phytoremediation mechanisms of the plant and the composition of microorganisms in the rhizosphere. Mycorrhizal inoculation and changes in the microbiome were associated with increased plant tolerance to Cd and Hg. Microorganism-assisted phytoremediation is an appropriate alternative for L. perenne.
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Affiliation(s)
- Juan F Saldarriaga
- Dept. of Civil and Environmental Engineering, Universidad de los Andes, Carrera 1Este, #19A-40, 111711, Bogotá, Colombia.
| | - Julián E López
- Facultad de Arquitectura E Ingeniería, Institución Universitaria Colegio Mayor de Antioquia, Carrera 78 # 65 - 46, 050034, Medellín, Colombia
| | - Laura Díaz-García
- Department of Chemical & Biological Engineering and Advanced Biomanufacturing Centre, University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield, S1 3JD, UK
| | - Carolina Montoya-Ruiz
- Facultad de Ciencias, Universidad Nacional de Colombia, Sede Medellín Calle, 59A #63-20, 050034, Medellín, Colombia
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10
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Yuan M, Huang Z, Malakar PK, Pan Y, Zhao Y, Zhang Z. Antimicrobial resistomes in food chain microbiomes. Crit Rev Food Sci Nutr 2023:1-22. [PMID: 36785889 DOI: 10.1080/10408398.2023.2177607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The safety and integrity of the global food system is in a constant state of flux with persistent chemical and microbial risks. While chemical risks are being managed systematically, microbial risks pose extra challenges. Antimicrobial resistant microorganism and persistence of related antibiotic resistance genes (ARGs) in the food chain adds an extra dimension to the management of microbial risks. Because the food chain microbiome is a key interface in the global health system, these microbes can affect health in many ways. In this review, we systematically summarize the distribution of ARGs in foods, describe the potential transmission pathway and transfer mechanism of ARGs from farm to fork, and discuss potential food safety problems and challenges. Modulating antimicrobial resistomes in the food chain facilitates a sustainable global food production system.
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Affiliation(s)
- Mengqi Yuan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhenhua Huang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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11
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Lastochkina OV, Allagulova CR. The Mechanisms of the Growth Promotion and Protective Effects of Endophytic PGP Bacteria in Wheat Plants Under the Impact of Drought (Review). APPL BIOCHEM MICRO+ 2023; 59:14-32. [DOI: 10.1134/s0003683823010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 06/23/2023]
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12
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Yu Y, Zhang Q, Zhang Z, Zhou S, Jin M, Zhu D, Yang X, Qian H, Lu T. Plants select antibiotic resistome in rhizosphere in early stage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 858:159847. [PMID: 36461576 DOI: 10.1016/j.scitotenv.2022.159847] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.
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Affiliation(s)
- Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Shuyidan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou 510650, China
| | - Mingkang Jin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 10085, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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13
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Fate of Horizontal-Gene-Transfer Markers and Beta-Lactamase Genes during Thermophilic Composting of Human Excreta. Microorganisms 2023; 11:microorganisms11020308. [PMID: 36838273 PMCID: PMC9958827 DOI: 10.3390/microorganisms11020308] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 01/26/2023] Open
Abstract
Thermophilic composting is a suitable treatment for the recycling of organic wastes for agriculture. However, using human excreta as feedstock for composting raises concerns about antibiotic resistances. We analyzed samples from the start and end of a thermophilic composting trial of human excreta, together with green cuttings and straw, with and without biochar. Beta-lactamase genes blaCTX-M, blaIMP, and blaTEM conferring resistance to broad-spectrum beta-lactam antibiotics, as well as horizontal gene transfer marker genes, intI1 and korB, were quantified using qPCR. We found low concentrations of the beta-lactamase genes in all samples, with non-significant mean decreases in blaCTX-M and blaTEM copy numbers and a mean increase in blaIMP copy numbers. The decrease in both intI1 and korB genes from start to end of composting indicated that thermophilic composting can decrease the horizontal spread of resistance genes. Thus, thermophilic composting can be a suitable treatment for the recycling of human excreta.
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14
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Wang Z, Fu C, Tian J, Wang W, Peng D, Dai X, Tian H, Zhou X, Li L, Yin H. Responses of the bacterial community of tobacco phyllosphere to summer climate and wildfire disease. FRONTIERS IN PLANT SCIENCE 2022; 13:1050967. [PMID: 36618666 PMCID: PMC9811124 DOI: 10.3389/fpls.2022.1050967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Both biotic and abiotic factors continually affect the phyllospheric ecology of plants. A better understanding of the drivers of phyllospheric community structure and multitrophic interactions is vital for developing plant protection strategies. In this study, 16S rRNA high-throughput sequencing was applied to study how summer climatic factors and bacterial wildfire disease have affected the composition and assembly of the bacterial community of tobacco (Nicotiana tabacum L.) phyllosphere. Our results indicated that three time series groups (T1, T2 and T3) formed significantly distinct clusters. The neutral community model (NCM) and beta nearest taxon index (betaNTI) demonstrated that the overall bacterial community assembly was predominantly driven by stochastic processes. Variance partitioning analysis (VPA) further showed that the complete set of the morbidity and climatic variables together could explain 35.7% of the variation of bacterial communities. The node numbers of the molecular ecological networks (MENs) showed an overall uptrend from T1 to T3. Besides, Pseudomonas is the keystone taxa in the MENs from T1 to T3. PICRUSt2 predictions revealed significantly more abundant genes of osmoprotectant biosynthesis/transport in T2, and more genes for pathogenicity and metabolizing organic substrate in T3. Together, this study provides insights into spatiotemporal patterns, processes and response mechanisms underlying the phyllospheric bacterial community.
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Affiliation(s)
- Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Changwu Fu
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Hui Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xiangping Zhou
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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15
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Xiong C, Lu Y. Microbiomes in agroecosystem: Diversity, function and assembly mechanisms. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:833-849. [PMID: 36184075 DOI: 10.1111/1758-2229.13126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Soils are a main repository of biodiversity harbouring immense diversity of microbial species that plays a central role in fundamental ecological processes and acts as the seed bank for emergence of the plant microbiome in cropland ecosystems. Crop-associated microbiomes play an important role in shaping plant performance, which includes but not limited to nutrient uptake, disease resistance, and abiotic stress tolerance. Although our understanding of structure and function of soil and plant microbiomes has been rapidly advancing, most of our knowledge comes from ecosystems in natural environment. In this review, we present an overview of the current knowledge of diversity and function of microbial communities along the soil-plant continuum in agroecosystems. To characterize the ecological mechanisms for community assembly of soil and crop microbiomes, we explore how crop host and environmental factors such as plant species and developmental stage, pathogen invasion, and land management shape microbiome structure, microbial co-occurrence patterns, and crop-microbiome interactions. Particularly, the relative importance of deterministic and stochastic processes in microbial community assembly is illustrated under different environmental conditions, and potential sources and keystone taxa of the crop microbiome are described. Finally, we highlight a few important questions and perspectives in future crop microbiome research.
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Affiliation(s)
- Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
| | - Yahai Lu
- College of Urban and Environmental Sciences, Peking University, Beijing, People's Republic of China
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16
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Zhang H, Ling H, Zhou R, Tang J, Hua R, Wu X. Contrasting dynamics of manure-borne antibiotic resistance genes in different soils. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114162. [PMID: 36252512 DOI: 10.1016/j.ecoenv.2022.114162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/21/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic resistance genes (ARGs) are important biological contamination factors in soil systems, posing direct or indirect threats to soil health, food safety and human health. The ubiquitous pollution of ARGs is usually implicated with the application of organic manures in agricultural soil ecosystem. However, little is known about the transmission and fate of ARGs after manure input concerning different soils. Herein, the transmission potential and temporal dynamics of manure-associated ARGs was characterized with three different agricultural soils collected from Jiangxi (JX), Zhejiang (ZJ), and Jilin (JL), respectively. The results show that manure input did not affect the total abundance of ARGs in the receiving soils, but remarkedly alter the compositions of ARGs in soils. The manure-associated ARGs were significantly enriched in the manure-amended soils, including genes conferring resistance to sulfonamide, aminoglycoside, tetracycline, chloramphenicol, and trimethoprim with the fold of 1.97 - 27.86. Variance partitioning analysis showed that the major variances of ARG community was explained by mobile genetic elements and bacterial profile (> 76%) but not the concentrations of heavy metals and antibiotics. Furthermore, 31, 37, and 38 ARG subtypes were identified as the potential extrinsic ARGs derived from manures in the JX, ZJ, and JL soils, respectively, including 13 shared ARG subtypes. It was also found that the manure-associated ARGs (aadA, sul1, sul2, tetC, and tetG) declined with the incubation time in the JX and ZJ soils, whereas they firstly decreased and then increased in the JL soil. The abundance of these five ARGs in the JL soil was significantly higher than that in the JX and ZJ soils. Collectively, this finding revealed that soil type was responsible for the transmission and fate of manure-associated ARGs in agroecosystem.
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Affiliation(s)
- Houpu Zhang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Hong Ling
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Ruofei Zhou
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China
| | - Jun Tang
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Rimao Hua
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China
| | - Xiangwei Wu
- College of Resources and Environment, Anhui Agricultural University, Key Laboratory of Agri-food Safety of Anhui Province, Hefei 230036, China; Research Academy of Green Development of Anhui Agricultural University, Hefei 230036, China.
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17
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Zhu D, Ding J, Wang YF, Zhu YG. Effects of Trophic Level and Land Use on the Variation of Animal Antibiotic Resistome in the Soil Food Web. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14937-14947. [PMID: 35502923 DOI: 10.1021/acs.est.2c00710] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent years, it has been increasingly recognized that soil animals are hidden reservoirs of antibiotic resistance genes (ARGs) and play a vital role in spreading ARGs in soil ecosystems. However, little is known about the variation of ARGs among different animals in the soil food web and effects of trophic levels and land uses on them. We characterized the antibiotic resistomes of 495 soil animal samples collected from six regions across China, including two different land uses. A total of 265 ARGs were detected in all animal samples, and relative abundances of ARGs in animals were significantly higher than in soils. In addition, significant differences in ARGs were observed among different animal groups. Twelve common ARGs were identified among all animal groups, accounting for 17.4% of total ARGs abundance. A positive and significant correlation was found between δ15N values (trophic level) and total ARGs abundance in animals. The relative abundance of ARGs in the soil food web from arable land was higher than forest land. Changes in soil antibiotics may indirectly affect animal resistome by altering soil ARGs. This study suggests that the risk of ARGs spreading through the food web is greater in arable than in forest ecosystems.
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Affiliation(s)
- Dong Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Ding
- School of Environmental and Material Engineering, Yantai University, 30 Qingquan Road, Yantai 264005, China
| | - Yi-Fei Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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18
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Hao Z, Wang Y, Guo X, De J. Deciphering the core seed endo-bacteriome of the highland barley in Tibet plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:1041504. [PMID: 36388601 PMCID: PMC9650301 DOI: 10.3389/fpls.2022.1041504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Highland barley (Hordeum vulgare var. nudum (L.) Hook.f., qingke) has unique physical and chemical properties and good potential for industrial applications. As the only crop that can be grown at high altitudes of 4200-4500 m, qingke is well adapted to extreme habitats at high altitudes. In this study, we analysed the seed bacterial community of 58 genotypes of qingke grown in different regions of Tibet, including qingke landraces, modern cultivars, and winter barley varieties, and characterised endophytic bacterial communities in seeds from different sources and the core endo-bacteriome of qingke. This study aim to provide a reference for the application of seed endophytes as biological inoculants for sustainable agricultural production and for considering microbe-plant interactions in breeding strategies. A total of 174 qingke seed samples from five main agricultural regions in Tibet were collected and subjected to investigation of endophytic endo-bacteriome using high-throughput sequencing and bioinformatics approaches. The phyla of endophytic bacteria in qingke seeds from different sources were similar; however, the relative proportions of each phylum were different. Different environmental conditions, growth strategies, and modern breeding processes have significantly changed the community structure of endophytic bacteria in seeds, among which the growth strategy has a greater impact on the diversity of endophytic bacteria in seeds. Seeds from different sources have conserved beneficial core endo-bacteriome. The core endo-bacteriome of qingke seeds dominated by Enterobacteriaceae may maintain qingke growth by promoting plant growth and assisting plants in resisting pests and diseases. This study reveals the core endo-bacteriome of qingke seeds and provides a basis for exploiting the endophytic endo-bacteriome of qingke seeds.
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Affiliation(s)
| | | | | | - Ji De
- *Correspondence: Xiaofang Guo, ; Ji De,
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19
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Chen Y, Liang J, Zia A, Gao X, Wang Y, Zhang L, Xiang Q, Zhao K, Yu X, Chen Q, Penttinen P, Nyima T, Gu Y. Culture dependent and independent characterization of endophytic bacteria in the seeds of highland barley. Front Microbiol 2022; 13:981158. [PMID: 36246264 PMCID: PMC9555213 DOI: 10.3389/fmicb.2022.981158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/08/2022] [Indexed: 12/02/2022] Open
Abstract
Endophytes in the seeds of plants have shown plant growth promoting (PGP) properties. Highland barley is an economically important crop and a major part of the local diet in the Tibetan Plateau, China, with potential health benefits. We applied culture-dependent and culture-independent methods to study endophytic bacteria in the seeds of eight Highland barley varieties. Based on the seed properties, the variety Ali was clearly separated from the other varieties except the variety CM. Most of the 86 isolates were assigned into genus Bacillus. Approximately half of the isolates showed PGP properties in vitro. Compared to the not-inoculated plants, inoculation with the isolate Bacillus tequilensis LZ-9 resulted in greater length and number of roots, and in bigger aboveground and root weights. Based on the 16S rRNA gene sequencing, the seed microbiome was majorly affiliated with the phylum Proteobacteria and the family Enterobacteriaceae. Overall, the bacterial community compositions in the different varieties were different from each other, yet the between variety differences in community composition seemed relatively small. The differences in community compositions were associated with differences in the total and reducing sugar contents and viscosity of the seeds, thus possibly connected to differences in the osmotic pressure tolerance of the endophytes. The results suggested that the seed endophytes are likely to promote the growth of Highland barley since germination.
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Affiliation(s)
- Yulan Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Jinpeng Liang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Alina Zia
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xue Gao
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
| | - Yong Wang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Liangshan Tobacco Corporation of Sichuan Province, Xichang, China
| | - Lingzi Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Petri Penttinen,
| | - Tashi Nyima
- Institute of Agricultural Resources and Environmental Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, China
- Tashi Nyima,
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Chengdu, China
- Yunfu Gu,
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20
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Shen Z, Thomashow LS, Ou Y, Tao C, Wang J, Xiong W, Liu H, Li R, Shen Q, Kowalchuk GA. Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt. Research (Wash D C) 2022; 2022:9818073. [PMID: 36204250 PMCID: PMC9513836 DOI: 10.34133/2022/9818073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/22/2022] [Indexed: 11/08/2022] Open
Abstract
Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.
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Affiliation(s)
- Zongzhuan Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Linda S. Thomashow
- U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Yannan Ou
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Chengyuan Tao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Jiabao Wang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Wu Xiong
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Hongjun Liu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
| | - Rong Li
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, The Key Laboratory of Plant Immunity, Joint International Research Laboratory of Soil Health, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
- The Sanya Institute of the Nanjing Agricultural University, Sanya, Hainan Province, China
| | - George A. Kowalchuk
- Ecology and Biodiversity Group, Institute of Environmental Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, Netherlands
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21
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Yang F, Wang Y, Liu Q, Xu B, Chen H, Li Y, Wang K, Liang G, Zhang R, Jiao X, Zhang Y. High Prevalence and Varied Distribution of Antibiotic-Resistant Bacteria in the Rhizosphere and Rhizoplane of Citrus medica. Microorganisms 2022; 10:microorganisms10091708. [PMID: 36144310 PMCID: PMC9501533 DOI: 10.3390/microorganisms10091708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/20/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The plant-associated bacteria, including that in the rhizosphere and rhizoplane, play important roles in human exposure to antibiotic-resistant bacteria (ARB). The rhizosphere and rhizoplane represent two distinct environments with different selective pressures for bacterial colonization. However, whether the difference in characteristics between the rhizosphere and rhizoplane can affect the abundance and antibiotic resistance profiles of ARB colonizing, the two environments remain largely unknown. In this study, we obtained 174 bacterial isolates from the rhizosphere (113 isolates) and rhizoplane (61 isolates) of Citrus medica trees grown in a park, where humans could easily and frequently contact the trees. A very high proportion of isolates exhibited resistance to several clinically important antibiotics, including β-lactam class antibiotics and polymyxin, with several known antibiotic-resistant opportunistic pathogens, such as Micrococcus luteus, being identified. The prevalence of ARB in the rhizoplane was higher than that in the rhizosphere. While the prevalence of polymyxin-resistant isolates was higher in the rhizoplane, the prevalence of amphenicol-resistant isolates was significantly higher in the rhizosphere. In summary, our findings suggest that the rhizosphere and rhizoplane are important media for the spread of ARB, and the different characteristics between the two environments can affect the distribution of ARB.
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Affiliation(s)
- Fang Yang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yu Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Qianwen Liu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Bo Xu
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Huan Chen
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Yaomen Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Kun Wang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Guixin Liang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Ruiqi Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
| | - Xin’an Jiao
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.J.); (Y.Z.); Tel.: +86-5145-87971136 (X.J.); +86-5145-87971136 (Y.Z.)
| | - Yunzeng Zhang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, Ministry of Agriculture of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (X.J.); (Y.Z.); Tel.: +86-5145-87971136 (X.J.); +86-5145-87971136 (Y.Z.)
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22
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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23
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Leng J, Yu L, Dai Y, Leng Y, Wang C, Chen Z, Wisniewski M, Wu X, Liu J, Sui Y. Recent advances in research on biocontrol of postharvest fungal decay in apples. Crit Rev Food Sci Nutr 2022; 63:10607-10620. [PMID: 35608023 DOI: 10.1080/10408398.2022.2080638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Apple is the largest fruit crop produced in temperate regions and is a popular fruit worldwide. It is, however, susceptible to a variety of postharvest fungal pathogens, including Penicillium expansum, Botrytis cinerea, Botryosphaeria dothidea, Monilia spp., and Alternaria spp. Decays resulting from fungal infections severely reduce apple quality and marketable yield. Biological control utilizing bacterial and fungal antagonists is an eco-friendly and effective method of managing postharvest decay in horticultural crops. In the current review, research on the pathogenesis of major decay fungi and isolation of antagonists used to manage postharvest decay in apple is presented. The mode of action of postharvest biocontrol agents (BCAs), including recent molecular and genomic studies, is also discussed. Recent research on the apple microbiome and its relationship to disease management is highlighted, and the use of additives and physical treatments to enhance biocontrol efficacy of BCAs is reviewed. Biological control is a critical component of an integrated management system for the sustainable approaches to apple production. Additional research will be required to explore the feasibility of developing beneficial microbial consortia and novel antimicrobial compounds derived from BCAs for postharvest disease management, as well as genetic approaches, such as the use of CRISPR/Cas9 technology.
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Affiliation(s)
- Jinsong Leng
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Longfeng Yu
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Yuan Dai
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yan Leng
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Chaowen Wang
- School of Biotechnology and Bioengineering, West Yunnan University, Lincang, Yunan, China
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou, China
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jia Liu
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
| | - Yuan Sui
- Chongqing University of Arts and Sciences, Yongchuan, Chongqing, China
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24
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Olimi E, Kusstatscher P, Wicaksono WA, Abdelfattah A, Cernava T, Berg G. Insights into the microbiome assembly during different growth stages and storage of strawberry plants. ENVIRONMENTAL MICROBIOME 2022; 17:21. [PMID: 35484554 PMCID: PMC9052558 DOI: 10.1186/s40793-022-00415-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/17/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. RESULTS Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (107-1010 marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. CONCLUSION Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
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Affiliation(s)
- Expedito Olimi
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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25
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Berg G, Cernava T. The plant microbiota signature of the Anthropocene as a challenge for microbiome research. MICROBIOME 2022; 10:54. [PMID: 35346369 PMCID: PMC8959079 DOI: 10.1186/s40168-021-01224-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/23/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene. RESULTS Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. CONCLUSIONS Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health. Video abstract.
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Affiliation(s)
- Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria.
- Leibniz-Institute for Agricultural Engineering Potsdam, Max-Eyth-Allee 100, 14469, Potsdam, Germany.
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476, Potsdam, Germany.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
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26
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. ENVIRONMENTAL MICROBIOME 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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27
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Adi Wicaksono W, Reisenhofer-Graber T, Erschen S, Kusstatscher P, Berg C, Krause R, Cernava T, Berg G. Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens? J Adv Res 2022; 43:109-121. [PMID: 36585101 PMCID: PMC9811327 DOI: 10.1016/j.jare.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them. OBJECTIVE We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria. METHODS Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays. RESULTS A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces. CONCLUSIONS Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | | | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Christian Berg
- Institute of Plant Sciences, Karl-Franzens-University, Graz, Austria.
| | - Robert Krause
- Department of Internal Medicine, Medical University of Graz, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; BioTechMed Graz, Inter-university Cooperation Platform, Graz, Austria; Leibniz Institute for Agricultural Engineering and Bioeconomy Potsdam, Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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28
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Hou J, Mao D, Zhang Y, Huang R, Li L, Wang X, Luo Y. Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127220. [PMID: 34844350 DOI: 10.1016/j.jhazmat.2021.127220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yulin Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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29
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Köberl M, Kusstatscher P, Wicaksono WA, Mpiira S, Kalyango F, Staver C, Berg G. Increased Yield and High Resilience of Microbiota Representatives With Organic Soil Amendments in Smallholder Farms of Uganda. FRONTIERS IN PLANT SCIENCE 2022; 12:815377. [PMID: 35185962 PMCID: PMC8847376 DOI: 10.3389/fpls.2021.815377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Organic matter inputs positively affect soil fertility and quality but management effects on the soil and plant microbiome are less understood. Therefore, we studied the response of microbial colonization of the East African highland banana cultivar "Mpologoma" (AAA genome) under different mulch and manure treatments on three representative smallholder farms in Uganda. In general, the gammaproteobacterial community appeared stable with no significant response to organic matter inputs after 24 months of treatment. Significant differences (p < 0.05) in the plant-associated carpo-, phyllo-, and rhizosphere microbial community composition and diversity were found among individual sampled farms, independent of added soil inputs. Across farms, banana fruit harbored a richer and more balanced gammaproteobacterial community than the rhizo- and endospheres. Gammaproteobacterial beta diversity was shaped by the microenvironment (44%) as well as the sampling site (4%). Global effects of treatments in the rhizosphere analyzed using linear discriminant analysis effect size showed significantly enriched genera, such as Enterobacter, under manure and mulch treatments. As shown in previous works, bunch size and total yield were highly increased with manure and mulch, however, our results highlight general short-term microbial stability of Ugandan banana cropping systems with increases in the gammaproteobacterial community.
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Affiliation(s)
- Martina Köberl
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Samuel Mpiira
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | - Francis Kalyango
- National Agricultural Research Laboratories, National Agricultural Research Organisation, Kampala, Uganda
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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Suhadolnik MLS, Costa PS, Paiva MC, Salim ACDM, Barbosa FAR, Lobo FP, Nascimento AMA. Spatiotemporal dynamics of the resistome and virulome of riverine microbiomes disturbed by a mining mud tsunami. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150936. [PMID: 34678365 DOI: 10.1016/j.scitotenv.2021.150936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Aquatic ecosystems are highly vulnerable to anthropogenic activities. However, it remains unclear how the microbiome responds to press disturbance events in these ecosystems. We examined the impact of the world's largest mining disaster (Brazil, 2015) on sediment microbiomes in two disturbed rivers compared to an undisturbed river during 390 days post-disturbance. The diversity and structure of the virulome and microbiome, and of antibiotic and metal resistomes, consistently differed between the disturbed and undisturbed rivers, particularly at day 7 post-disturbance. 684 different ARGs were predicted, 38% were exclusive to the disturbed rivers. Critical antibiotic resistance genes (ARGs), e.g., mcr and ereA2, were significantly more common in the disturbed microbiomes. 401 different ARGs were associated with mobile genetic elements (MGEs), 95% occurred in the disturbed rivers. While plasmids were the most common MGEs with a broad spectrum of ARGs, spanning 16 antibiotic classes, integrative conjugative elements (ICEs) and integrons disseminated ARGs associated with aminoglycoside and tetracycline, and aminoglycoside and beta-lactam, respectively. A significant increase in the relative abundance of class 1 integrons, ICEs, and pathogens was identified at day 7 in the disturbed microbiomes, 72-, 14- and 3- fold higher, respectively, compared with the undisturbed river. Mobile ARGs associated with ESKAPEE group pathogens, while metal resistance genes and virulence factor genes in nonpathogenic hosts predominated in all microbiomes. Network analysis showed highly interconnected ARGs in the disturbed communities, including genes targeting antibiotics of last resort. Interactions between copper and beta-lactam/aminoglycoside/macrolide resistance genes, mostly mobile and critical, were also uncovered. We conclude that the mud tsunami resulted in resistome expansion, enrichment of pathogens, and increases in promiscuous and mobile ARGs. From a One Health perspective, mining companies need to move toward more environmentally friendly and socially responsible mining practices to reduce risks associated with pathogens and critical and mobile ARGs.
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Affiliation(s)
- Maria Luíza Soares Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Patrícia Silva Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | | | | | | | - Francisco Pereira Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil.
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Leonard SR, Simko I, Mammel MK, Richter TKS, Brandl MT. Seasonality, shelf life and storage atmosphere are main drivers of the microbiome and E. coli O157:H7 colonization of post-harvest lettuce cultivated in a major production area in California. ENVIRONMENTAL MICROBIOME 2021; 16:25. [PMID: 34930479 PMCID: PMC8686551 DOI: 10.1186/s40793-021-00393-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/30/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures. RESULTS Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO2 levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival. CONCLUSIONS The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO2 promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California.
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Affiliation(s)
- Susan R Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA, USA
| | - Mark K Mammel
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Taylor K S Richter
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD, USA
| | - Maria T Brandl
- Produce Safety and Microbiology Research Unit, US Department of Agriculture, Agricultural Research Service, Albany, CA, USA.
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The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 2021; 11:24017. [PMID: 34911987 PMCID: PMC8674285 DOI: 10.1038/s41598-021-03334-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 11/24/2021] [Indexed: 12/15/2022] Open
Abstract
Plant microbiomes have been extensively studied for their agricultural relevance on growth promotion and pathogenesis, but little is known about their role as part of the diet when fresh fruits and vegetables are consumed raw. Most studies describing these communities are based on 16S rRNA gene amplicon surveys, limiting our understanding of the taxonomic resolution at the species level and functional capabilities. In this study, we characterized microbes colonizing tomatoes, spinach, brined olives, and dried figs using shotgun metagenomics. We recovered metagenome-assembled genomes of novel lactic acid bacteria from green olives and identified high intra- and inter-specific diversity of Pseudomonas in tomatoes. All samples were colonized by Pseudomonas, consistent with other reports with distinct community structure. Functional characterization showed the presence of enzymes involved in vitamin and short chain fatty acid metabolism and degradation of diverse carbohydrate substrates including plant fibers. The dominant bacterial members were isolated, sequenced, and mapped to its metagenome confirming their identity and indicating the microbiota is culturable. Our results reveal high genetic diversity, previously uncultured genera, and specific functions reflecting a likely plant host association. This study highlights the potential that plant microbes can play when consumed as part of our diet and proposes these as transient contributors to the gut microbiome.
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Chen X, Krug L, Yang M, Berg G, Cernava T. The Himalayan Onion (Allium wallichii Kunth) Harbors Unique Spatially Organized Bacterial Communities. MICROBIAL ECOLOGY 2021; 82:909-918. [PMID: 33723621 PMCID: PMC8551121 DOI: 10.1007/s00248-021-01728-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Plant-associated microorganisms are known to contribute with various beneficial functions to the health and productivity of their hosts, yet the microbiome of most plants remains unexplored. This especially applies to wild relatives of cultivated plants, which might harbor beneficial microorganisms that were lost during intensive breeding. We studied bacterial communities of the Himalayan onion (Allium wallichii Kunth), a wild relative of onion native to mountains in East Asia. The bacterial community structure was assessed in different plant microhabitats (rhizosphere, endosphere, anthosphere) by sequencing of 16S rRNA gene fragment amplicons. Targeted bioinformatic analyses were implemented in order to identify unique features in each habitat and to map the overall community in the first representative of the Amaryllidaceae plant family. The highest bacterial diversity was found for bulk soil (Shannon index, H' 9.3) at the high-altitude sampling location. It was followed by the plant rhizosphere (H' 8.9) while communities colonizing flowers (H' 6.1) and the endosphere (H' 6.5 and 5.6) where less diverse. Interestingly, we observed a non-significant rhizosphere effect. Another specificity of the microbiome was its high evenness in taxonomic distribution, which was so far not observed in plant microbiomes. Pseudomonas was identified among additional 10 bacterial genera as a plant-specific signature. The first insights into the microbiome of a plant in the widespread Allium genus will facilitate upcoming comparisons with its domesticated relatives while additionally providing a detailed microbiome mapping of the plant's microhabitats to facilitate bioresource mining.
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Affiliation(s)
- Xiaoyulong Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, 550025, China
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China
- Key Laboratory of Agricultural Microbiology, Guizhou University, Guiyang, 550025, China
- College of Science, Tibet University, Lhasa, 850012, China
| | - Lisa Krug
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Maofa Yang
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria
| | - Tomislav Cernava
- College of Tobacco Science, Guizhou University, Guiyang, 550025, China.
- Institute of Environmental Biotechnology, Graz University of Technology, 8010, Graz, Austria.
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Wisser RJ, Oppenheim SJ, Ernest EG, Mhora TT, Dumas MD, Gregory NF, Evans TA, Donofrio NM. Genome assembly of a Mesoamerican derived variety of lima bean: a foundational cultivar in the Mid-Atlantic USA. G3 GENES|GENOMES|GENETICS 2021; 11:6326801. [PMID: 34542584 PMCID: PMC8527486 DOI: 10.1093/g3journal/jkab207] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022]
Abstract
Lima bean, Phaseolus lunatus, is closely related to common bean and is high in fiber and protein, with a low glycemic index. Lima bean is widely grown in the state of Delaware, where late summer and early fall weather are conducive to pod production. The same weather conditions also promote diseases such as pod rot and downy mildew, the latter of which has caused previous epidemics. A better understanding of the genes underlying resistance to this and other pathogens is needed to keep this industry thriving in the region. Our current study sought to sequence, assemble, and annotate a commercially available cultivar called Bridgeton, which could then serve as a reference genome, a basis of comparison to other Phaseolus taxa, and a resource for the identification of potential resistance genes. Combined efforts of sequencing, linkage, and comparative analysis resulted in a 623 Mb annotated assembly for lima bean, as well as a better understanding of an evolutionarily dynamic resistance locus in legumes.
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Affiliation(s)
- Randall J Wisser
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
- Laboratoire d’Ecophysiologie des Plantes sous Stress Environnementaux, INRAE, Univ. Montpellier, SupAgro, 34060 Montpellier, France
| | - Sara J Oppenheim
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Emmalea G Ernest
- Cooperative Extension, University of Delaware, Georgetown, DE 19947, USA
| | - Terence T Mhora
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Michael D Dumas
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Nancy F Gregory
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Thomas A Evans
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Nicole M Donofrio
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
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Fan X, Fu Y, Nie Y, Matsumoto H, Wang Y, Hu T, Pan Q, Lv T, Fang H, Xu H, Wang Y, Ge H, Zhu G, Liu Y, Wang Q, Wang M. Keystone taxa-mediated bacteriome response shapes the resilience of the paddy ecosystem to fungicide triadimefon contamination. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126061. [PMID: 34229385 DOI: 10.1016/j.jhazmat.2021.126061] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/18/2021] [Accepted: 05/04/2021] [Indexed: 05/22/2023]
Abstract
The increasing input of fungicides has emerged as a global concern for agroecosystem stability and sustainability. Agroecosystem resilience has been linked to microbiome response, however, is not well understood. Focusing on a widespread triazole-class fungicide triadimefon in the paddy ecosystem, we characterized that the soils and sediments were dominant triadimefon reservoirs with the peak level at 195 μg kg-1 and 31.3 μg kg-1, respectively, but essential for the resilience of paddy ecosystem to triadimefon. In paddy simulation models, the half-life of triadimefon in soil-sediment was 8.4-28.9 days, while it was prolonged to 86.6-115.5 days after elimination of resident microbial community. Phospholipid fatty acid profiling and high-throughput sequencing showed that the distinctive bacterial community responses contributed to variable degradation of triadimefon in paddy soils and sediments. Sphingomonas and Xanthomonas were identified as positive responders of the keystone taxa in the responsive bacteriome, whereas Enterobacter were negative responders that declined over time. Synthetic assemblages combined with quantitative polymerase chain reaction further validated that Sphingomonas and Xanthomonas were involved in sustaining soil-sediment resilience to triadimefon contamination. Collectively, our results revealed that the shaping of soil and sediment bacteriomes was responsible for the resilience of the paddy agroecosystem to fungicide contamination.
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Affiliation(s)
- Xiaoyan Fan
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yan Fu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Ningbo Academy of Agricultural Sciences, Ningbo 315040, China
| | - Yanxia Nie
- Ecology and Environmental Sciences Center, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Haruna Matsumoto
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yue Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tingting Hu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Pan
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tianxing Lv
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongda Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Haorong Xu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yi Wang
- Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Hang Ge
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yihua Liu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Qiangwei Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengcen Wang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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Xu H, Chen Z, Huang R, Cui Y, Li Q, Zhao Y, Wang X, Mao D, Luo Y, Ren H. Antibiotic Resistance Gene-Carrying Plasmid Spreads into the Plant Endophytic Bacteria using Soil Bacteria as Carriers. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:10462-10470. [PMID: 34114802 DOI: 10.1021/acs.est.1c01615] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Applications of animal manure and treated wastewater could enrich antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in the plant microbiome. However, the mechanistic studies of the transmission of ARB and ARGs from the environment to plant endophytic bacteria were few. Herein, a genetically engineered fluorescent Escherichia coli harboring a conjugative RP4 plasmid that carries three ARGs was used to trace its spread into Arabidopsis thaliana interior in a tetracycline-amended hydroponic system in the absence or presence of a simulated soil bacterial community. Confocal microscope observation demonstrated that E. coli was internalized into plant tissues and the carried RP4 plasmid was transferred into plant endophytic bacteria. More importantly, we observed that soil bacteria inhibited the internalization of E. coli but substantially promoted RP4 plasmid spread into the plant microbiome. The altered RP4-carrying bacterial community composition in the plant microbiome and the increased core-shared RP4-carrying bacteria number between plant interior and exterior in the presence of soil bacteria collectively confirmed that soil bacteria, especially Proteobacteria, might capture RP4 from E. coli and then translocate into plant microbiome, resulting in the increased RP4 plasmid spread in the plant endophytes. Overall, our findings provided important insights into the dissemination of ARB and ARGs from the environment to the plant microbiome.
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Affiliation(s)
- Han Xu
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Zeyou Chen
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yuxiao Cui
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
- Municipal Experimental Teaching Demonstration Center for Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Qiang Li
- College of Agriculture and Forestry Science, Linyi University, Linyi 276000, Shandong, China
| | - Yanhui Zhao
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China
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Kim SH, Do H, Cho G, Kim DR, Kwak YS. Bacterial Community Structure and the Dominant Species in Imported Pollens for Artificial Pollination. THE PLANT PATHOLOGY JOURNAL 2021; 37:299-306. [PMID: 34111919 PMCID: PMC8200575 DOI: 10.5423/ppj.nt.02.2021.0029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Pollination is an essential process for plants to carry on their generation. Pollination is carried out in various ways depending on the type of plant species. Among them, pollination by insect pollinator accounts for the most common. However, these pollinators have be decreasing in population density due to environmental factors. Therefore, use of artificial pollination is increasing. However, there is a lack of information on microorganisms present in the artificial pollens. We showed the composition of bacteria structure present in the artificial pollens of apple, kiwifruit, peach and pear, and contamination of high-risk pathogens was investigated. Acidovorax spp., Pantoea spp., Erwinia spp., Pseudomonas spp., and Xanthomonas spp., which are classified as potential high-risk pathogens, have been identified in imported pollens. This study presented the pollen-associated bacterial community structure, and the results are expected to be foundation for strengthening biosecurity in orchard industry.
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Affiliation(s)
- Su-Hyeon Kim
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Heeil Do
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Gyeongjun Cho
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Da-Ran Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
| | - Youn-Sig Kwak
- Division of Applied Life Science, Gyeongsang National University, Jinju 52828, Korea
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea
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38
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Moisture‐dependent
engineering properties of arugula seed relevant in mechanical processing and bulk handling. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13704] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Anzalone A, Di Guardo M, Bella P, Ghadamgahi F, Dimaria G, Zago R, Cirvilleri G, Catara V. Bioprospecting of Beneficial Bacteria Traits Associated With Tomato Root in Greenhouse Environment Reveals That Sampling Sites Impact More Than the Root Compartment. FRONTIERS IN PLANT SCIENCE 2021; 12:637582. [PMID: 33927735 PMCID: PMC8078776 DOI: 10.3389/fpls.2021.637582] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/10/2021] [Indexed: 05/06/2023]
Abstract
Tomato is subject to several diseases that affect both field- and greenhouse-grown crops. To select cost-effective potential biocontrol agents, we used laboratory throughput screening to identify bacterial strains with versatile characteristics suitable for multipurpose uses. The natural diversity of tomato root-associated bacterial communities was bioprospected under a real-world environment represented by an intensive tomato cultivation area characterized by extraseasonal productions in the greenhouse. Approximately 400 tomato root-associated bacterial isolates, in majority Gram-negative bacteria, were isolated from three compartments: the soil close to the root surface (rhizosphere, R), the root surface (rhizoplane, RP), and the root interior (endorhizosphere, E). A total of 33% of the isolates produced siderophores and were able to solubilize phosphates and grow on NA with 8% NaCl. A total of 30% of the root-associated bacteria showed antagonistic activity against all the tomato pathogens tested, i.e., Clavibacter michiganesis pv. michiganensis, Pseudomonas syringae pv. tomato, Pseudomonas corrugata and Xanthomonas euvesicatoria pv. perforans, and Fusarium oxysporum f. sp. lycopersici. We found that the sampling site rather than the root compartment of isolation influenced bacterial composition in terms of analyzed phenotype. This was demonstrated through a diversity analysis including general characteristics and PGPR traits, as well as biocontrol activity in vitro. Analysis of 16S rRNA gene (rDNA) sequencing of 77 culturable endophytic bacteria that shared multiple beneficial activity revealed a predominance of bacteria in Bacillales, Enterobacteriales, and Pseudomonadales. Their in vitro antagonistic activity showed that Bacillus species were significantly more active than the isolates in the other taxonomic group. In planta activity against phytopathogenic bacteria of a subset of Bacillus and Pseudomonas isolates was also assessed.
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Affiliation(s)
- Alice Anzalone
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Palermo, Italy
| | - Farideh Ghadamgahi
- Department of Plant Protection, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Giulio Dimaria
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | | | - Gabriella Cirvilleri
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
| | - Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, Catania, Italy
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40
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Kavamura VN, Mendes R, Bargaz A, Mauchline TH. Defining the wheat microbiome: Towards microbiome-facilitated crop production. Comput Struct Biotechnol J 2021; 19:1200-1213. [PMID: 33680361 PMCID: PMC7902804 DOI: 10.1016/j.csbj.2021.01.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 12/17/2022] Open
Abstract
Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.
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Affiliation(s)
- Vanessa N. Kavamura
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariúna, SP, Brazil
| | - Adnane Bargaz
- Agrobiosciences, Mohammed VI Polytechnic University, Benguerir, Morocco
| | - Tim H. Mauchline
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, Hertfordshire, UK
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41
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Wicaksono WA, Kusstatscher P, Erschen S, Reisenhofer-Graber T, Grube M, Cernava T, Berg G. Antimicrobial-specific response from resistance gene carriers studied in a natural, highly diverse microbiome. MICROBIOME 2021; 9:29. [PMID: 33504360 PMCID: PMC7841911 DOI: 10.1186/s40168-020-00982-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 12/16/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into natural environments, we exposed lichen thalli of Peltigera polydactylon, which represent defined, highly diverse miniature ecosystems, to clinical (colistin, tetracycline), and non-clinical (glyphosate, alkylpyrazine) antimicrobials. We studied microbiome responses by analysing DNA- and RNA-based amplicon libraries and metagenomic datasets. RESULTS The analyzed samples consisted of the thallus-forming fungus that is associated with cyanobacteria as well as other diverse and abundant bacterial communities (up to 108 16S rRNA gene copies ng-1 DNA) dominated by Alphaproteobacteria and Bacteroidetes. Moreover, the natural resistome of this meta-community encompassed 728 AMR genes spanning 30 antimicrobial classes. Following 10 days of exposure to the selected antimicrobials at four different concentrations (full therapeutic dosage and a gradient of sub-therapeutic dosages), we observed statistically significant, antimicrobial-specific shifts in the structure and function but not in bacterial abundances within the microbiota. We observed a relatively lower response after the exposure to the non-clinical compared to the clinical antimicrobial compounds. Furthermore, we observed specific bacterial responders, e.g., Pseudomonas and Burkholderia to clinical antimicrobials. Interestingly, the main positive responders naturally occur in low proportions in the lichen holobiont. Moreover, metagenomic recovery of the responders' genomes suggested that they are all naturally equipped with specific genetic repertoires that allow them to thrive and bloom when exposed to antimicrobials. Of the responders, Sphingomonas, Pseudomonas, and Methylobacterium showed the highest potential. CONCLUSIONS Antimicrobial exposure resulted in a microbial dysbiosis due to a bloom of naturally low abundant taxa (positive responders) with specific AMR features. Overall, this study provides mechanistic insights into community-level responses of a native microbiota to antimicrobials and suggests novel strategies for AMR prediction and management. Video Abstract.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Peter Kusstatscher
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Sabine Erschen
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Martin Grube
- Institute of Biology, University of Graz, Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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42
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Xiong C, Zhu YG, Wang JT, Singh B, Han LL, Shen JP, Li PP, Wang GB, Wu CF, Ge AH, Zhang LM, He JZ. Host selection shapes crop microbiome assembly and network complexity. THE NEW PHYTOLOGIST 2021; 229:1091-1104. [PMID: 32852792 DOI: 10.1111/nph.16890] [Citation(s) in RCA: 221] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 08/13/2020] [Indexed: 05/20/2023]
Abstract
Plant microbiomes are essential to host health and productivity but the ecological processes that govern crop microbiome assembly are not fully known. Here we examined bacterial communities across 684 samples from soils (rhizosphere and bulk soil) and multiple compartment niches (rhizoplane, root endosphere, phylloplane, and leaf endosphere) in maize (Zea mays)-wheat (Triticum aestivum)/barley (Hordeum vulgare) rotation system under different fertilization practices at two contrasting sites. Our results demonstrate that microbiome assembly along the soil-plant continuum is shaped predominantly by compartment niche and host species rather than by site or fertilization practice. From soils to epiphytes to endophytes, host selection pressure sequentially increased and bacterial diversity and network complexity consequently reduced, with the strongest host effect in leaf endosphere. Source tracking indicates that crop microbiome is mainly derived from soils and gradually enriched and filtered at different plant compartment niches. Moreover, crop microbiomes were dominated by a few dominant taxa (c. 0.5% of bacterial phylotypes), with bacilli identified as the important biomarker taxa for wheat and barley and Methylobacteriaceae for maize. Our work provides comprehensive empirical evidence on host selection, potential sources and enrichment processes for crop microbiome assembly, and has important implications for future crop management and manipulation of crop microbiome for sustainable agriculture.
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Affiliation(s)
- Chao Xiong
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Brajesh Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Gui-Bao Wang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, 655000, China
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - An-Hui Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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43
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Obermeier MM, Wicaksono WA, Taffner J, Bergna A, Poehlein A, Cernava T, Lindstaedt S, Lovric M, Müller Bogotá CA, Berg G. Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance. ISME JOURNAL 2020; 15:921-937. [PMID: 33177608 PMCID: PMC8027415 DOI: 10.1038/s41396-020-00822-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/30/2022]
Abstract
The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.
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Affiliation(s)
- Melanie Maria Obermeier
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Alessandro Bergna
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
| | - Anja Poehlein
- Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University of Göttingen, Grisebachstrasse 8, 37077, Göttingen, Germany
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Stefanie Lindstaedt
- Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, 8010, Graz, Austria
| | - Mario Lovric
- Know-Center GmbH, Research Center for Data-Driven Business & Big Data Analytics, Infeldgasse 13/VI, 8010, Graz, Austria
| | - Christina Andrea Müller Bogotá
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria. .,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria.,ACIB GmbH, Krenngasse 37/II, 8010, Graz, Austria
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44
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Chen YM, Holmes EC, Chen X, Tian JH, Lin XD, Qin XC, Gao WH, Liu J, Wu ZD, Zhang YZ. Diverse and abundant resistome in terrestrial and aquatic vertebrates revealed by transcriptional analysis. Sci Rep 2020; 10:18870. [PMID: 33139761 PMCID: PMC7608656 DOI: 10.1038/s41598-020-75904-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Despite increasing evidence that antibiotic resistant pathogens are shared among humans and animals, the diversity, abundance and patterns of spread of antibiotic resistance genes (ARGs) in wildlife remains unclear. We identified 194 ARGs associated with phenotypic resistance to 13 types of antibiotic in meta-transcriptomic data generated from a broad range of lower vertebrates residing in both terrestrial and aquatic habitats. These ARGs, confirmed by PCR, included those that shared high sequence similarity to clinical isolates of public health concern. Notably, the lower vertebrate resistome varied by ecological niche of the host sampled. The resistomes in marine fish shared high similarity and were characterized by very high abundance, distinct from that observed in other habitats. An assessment of ARG mobility found that ARGs in marine fish were frequently co-localized with mobile elements, indicating that they were likely spread by horizontal gene transfer. Together, these data reveal the remarkable diversity and transcriptional levels of ARGs in lower vertebrates, and suggest that these wildlife species might play an important role in the global spread of ARGs.
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Affiliation(s)
- Yan-Mei Chen
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Edward C Holmes
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- School of Life and Environmental Sciences and School of Medical Sciences, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, Australia
| | - Xiao Chen
- College of Marine Sciences, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jun-Hua Tian
- Wuhan Center for Disease Control and Prevention, Wuhan, Hubei, China
| | - Xian-Dan Lin
- Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang, China
| | - Xin-Cheng Qin
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Wen-Hua Gao
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Jing Liu
- Department of Zoonosis, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Changping Beijing, China
| | - Zhong-Dao Wu
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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45
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Shukla SP, Beran F. Gut microbiota degrades toxic isothiocyanates in a flea beetle pest. Mol Ecol 2020; 29:4692-4705. [PMID: 33006166 DOI: 10.1111/mec.15657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/04/2020] [Accepted: 09/22/2020] [Indexed: 11/30/2022]
Abstract
Microbial symbionts of herbivorous insects have been suggested to aid in the detoxification of plant defense compounds; however, quantitative studies on microbial contribution to plant toxin degradation remain scarce. Here, we demonstrate microbiome-mediated degradation of plant-derived toxic isothiocyanates in the cabbage stem flea beetle Psylliodes chrysocephala, a major pest of oilseed rape. Suppression of microbiota in antibiotic-fed beetles resulted in up to 11.3-fold higher levels of unmetabolized isothiocyanates compared to control beetles but did not affect other known detoxification pathways in P. chrysocephala. We characterized the microbiome of laboratory-reared and field-collected insects using 16S rRNA amplicon sequencing and isolated bacteria belonging to the three core genera Pantoea, Acinetobacter and Pseudomonas. Only Pantoea isolates rapidly degraded isothiocyanates in vitro, and restored isothiocyanate degradation in vivo when reintroduced in antibiotic-fed beetles. Pantoea was consistently present across beetle life stages and in field and lab populations. In addition, Pantoea was detected in undamaged tissues of the host plant Brassica rapa, indicating that P. chrysocephala could possibly acquire an isothiocyanate detoxifying bacterium through their diet. Our results demonstrate that both insect endogenous mechanisms and the microbiota can contribute to the detoxification of plant defense compounds and together they can better account for the fate of ingested plant metabolites.
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Affiliation(s)
- Shantanu P Shukla
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany.,Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Franziska Beran
- Research Group Sequestration and Detoxification in Insects, Max Planck Institute for Chemical Ecology, Jena, Germany
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46
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Wang M, Cernava T. Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2020; 4:100061. [PMID: 36157708 PMCID: PMC9487991 DOI: 10.1016/j.ese.2020.100061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 05/11/2023]
Abstract
Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.
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Affiliation(s)
- Mengcen Wang
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, 310058, China
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Corresponding author.
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47
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Noble AS, Noe S, Clearwater MJ, Lee CK. A core phyllosphere microbiome exists across distant populations of a tree species indigenous to New Zealand. PLoS One 2020; 15:e0237079. [PMID: 32790769 PMCID: PMC7425925 DOI: 10.1371/journal.pone.0237079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/19/2020] [Indexed: 12/30/2022] Open
Abstract
The phyllosphere microbiome is increasingly recognised as an influential component of plant physiology, yet it remains unclear whether stable host-microbe associations generally exist in the phyllosphere. Leptospermum scoparium (mānuka) is a tea tree indigenous to New Zealand, and honey derived from mānuka is widely known to possess unique antimicrobial properties. However, the host physiological traits associated with these antimicrobial properties vary widely, and the specific cause of such variation has eluded scientists despite decades of research. Notably, the mānuka phyllosphere microbiome remains uncharacterised, and its potential role in mediating host physiology has not been considered. Working within the prevailing core microbiome conceptual framework, we hypothesise that the phyllosphere microbiome of mānuka exhibits specific host association patterns congruent with those of a microbial community under host selective pressure (null hypothesis: the mānuka phyllosphere microbiome is recruited stochastically from the surrounding environment). To examine our hypothesis, we characterised the phyllosphere and associated soil microbiomes of five distinct and geographically distant mānuka populations across the North Island of New Zealand. We identified a habitat-specific and relatively abundant core microbiome in the mānuka phyllosphere, which was persistent across all samples. In contrast, non-core phyllosphere microorganisms exhibited significant variation across individual host trees and populations that was strongly driven by environmental and spatial factors. Our results demonstrate the existence of a dominant and ubiquitous core microbiome in the phyllosphere of mānuka, supporting our hypothesis that phyllosphere microorganisms of mānuka exhibit specific host association and potentially mediate physiological traits of this nationally and culturally treasured indigenous plant. In addition, our results illustrate biogeographical patterns in mānuka phyllosphere microbiomes and offer insight into factors contributing to phyllosphere microbiome assembly.
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Affiliation(s)
- Anya S. Noble
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Stevie Noe
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Charles K. Lee
- School of Science, University of Waikato, Hamilton, New Zealand
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48
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Zhang H, Zhang Q, Chen S, Zhang Z, Song J, Long Z, Yu Y, Fang H. Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138708. [PMID: 32334231 DOI: 10.1016/j.scitotenv.2020.138708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.
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Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shiyu Chen
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zihan Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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49
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Guo W, Zhou M, Ma T, Bi S, Wang W, Zhang Y, Huang X, Guan LL, Long R. Survey of rumen microbiota of domestic grazing yak during different growth stages revealed novel maturation patterns of four key microbial groups and their dynamic interactions. Anim Microbiome 2020; 2:23. [PMID: 33499950 PMCID: PMC7807461 DOI: 10.1186/s42523-020-00042-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 06/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development and maturation of rumen microbiota across the lifetime of grazing yaks remain unexplored due to the varied lifestyles and feed types of yaks as well as the challenges of obtaining samples. In addition, the interactions among four different rumen microbial groups (bacteria, archaea, fungi and protozoa) in the rumen of yak are not well defined. In this study, the rumen microbiota of full-grazing yaks aged 7 days to 12 years old was assessed to determine the maturation patterns of these four microbial groups and the dynamic interactions among them during different growth stages. RESULTS The rumen microbial groups (bacteria, archaea, protozoa and fungi) varied through the growth of yaks from neonatal (7 days) to adult (12 years), and the bacterial and archaeal groups were more sensitive to changes in growth stages compared to the two eukaryotic microbial groups. The age-discriminatory taxa within each microbial group were identified with the random forest model. Among them, Olsenella (bacteria), Group 10 sp., belonging to the family Methanomassiliicoccaceae (archaea), Orpinomyces (fungi), and Dasytricha (protozoa) contributed the most to discriminating the age of the rumen microbiota. Moreover, we found that the rumen archaea reached full maturation at 5 approximately years of age, and the other microbial groups matured between 5 and 8 years of age. The intra-interactions patterns and keystone species within each microbial group were identified by network analysis, and the inter-interactions among the four microbial groups changed with growth stage. Regarding the inter-interactions among the four microbial groups, taxa from bacteria and protozoa, including Christensenellaceae R-7 group, Prevotella 1, Trichostomatia, Ruminococcaceae UCG-014 and Lachnospiraceae, were the keystone species in the network based on betweenness centrality scores. CONCLUSIONS This study depicted a comprehensive view of rumen microbiota changes in different growth stages of grazing yaks. The results revealed the unique microbiota maturation trajectory and the intra- and inter-interactions among bacteria, archaea, fungi and protozoa in the rumen of grazing yaks across the lifetime of yaks. The information obtained in this study is vital for the future development of strategies to manipulate rumen microbiota in grazing yaks for better growth and performance in the harsh Qinghai-Tibetan Plateau ecosystem.
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Affiliation(s)
- Wei Guo
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Tao Ma
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
- Key laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Sisi Bi
- School of Life Sciences, Lanzhou University, Lanzhou, 730020 China
| | - Weiwei Wang
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
| | - Ying Zhang
- School of Public Health, Lanzhou University, Lanzhou, 730020 China
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, Lanzhou, 730020 China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5 Canada
| | - Ruijun Long
- College of Pastoral Agriculture Science and Technology, State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Lanzhou, 730020 China
- School of Life Sciences, Lanzhou University, Lanzhou, 730020 China
- International Centre for Tibetan Plateau Ecosystem Management, Lanzhou University, Lanzhou, 730020 China
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Shen Y, Nie J, Kuang L, Zhang J, Li H. DNA sequencing, genomes and genetic markers of microbes on fruits and vegetables. Microb Biotechnol 2020; 14:323-362. [PMID: 32207561 PMCID: PMC7936329 DOI: 10.1111/1751-7915.13560] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/01/2020] [Accepted: 03/02/2020] [Indexed: 12/20/2022] Open
Abstract
The development of DNA sequencing technology has provided an effective method for studying foodborne and phytopathogenic microorganisms on fruits and vegetables (F & V). DNA sequencing has successfully proceeded through three generations, including the tens of operating platforms. These advances have significantly promoted microbial whole‐genome sequencing (WGS) and DNA polymorphism research. Based on genomic and regional polymorphisms, genetic markers have been widely obtained. These molecular markers are used as targets for PCR or chip analyses to detect microbes at the genetic level. Furthermore, metagenomic analyses conducted by sequencing the hypervariable regions of ribosomal DNA (rDNA) have revealed comprehensive microbial communities in various studies on F & V. This review highlights the basic principles of three generations of DNA sequencing, and summarizes the WGS studies of and available DNA markers for major bacterial foodborne pathogens and phytopathogenic fungi found on F & V. In addition, rDNA sequencing‐based bacterial and fungal metagenomics are summarized under three topics. These findings deepen the understanding of DNA sequencing and its application in studies of foodborne and phytopathogenic microbes and shed light on strategies for the monitoring of F & V microbes and quality control.
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Affiliation(s)
- Youming Shen
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jiyun Nie
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China.,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lixue Kuang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Jianyi Zhang
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
| | - Haifei Li
- Institute of Pomology, Chinese Academy of Agricultural Sciences/Laboratory of Quality & Safety Risk Assessment for Fruit (Xingcheng), Ministry of Agriculture and Rural Affairs/Quality Inspection and Test Center for Fruit and Nursery Stocks (Xingcheng), Ministry of Agriculture and Rural Affairs, Xingcheng, 125100, China
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