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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Hagagy N, AbdElgawad H. Rapeseed plant: biostimulation effects of plant growth-promoting Actinobacteria on metabolites and antioxidant defense system under elevated CO 2 conditions. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:51-62. [PMID: 37551636 DOI: 10.1002/jsfa.12909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/17/2023] [Accepted: 08/08/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND The present study set out to evaluate the potential of plant growth-promoting Actinobacteria (PGPB) in improving some physiological and molecular parameters of rapeseed (Brassica napus L.) plants under ambient and elevated CO2 conditions by assessing some nitrogen- and sulfur-containing metabolites, antioxidant defense system and antimicrobial activity. With this aim, a pot experiment was conducted where the rapeseed plants were treated with Actinobacterium sp. strain NCO2 (OQ451136) and were grown under two levels of air CO2 concentrations: ambient CO2 (aCO2 , 410 μmol CO2 mol-1 ); and elevated CO2 (eCO2 , 710 μmol CO2 mol-1 ). RESULTS There was an increase in the photosynthetic pigments (+35-80%) and photosynthesis rate (+20-34%) in PGPB-treated plants under eCO2 compared to control plants, resulting in further growth and biomass production (+53-294%). These results were associated with an enhancement in the content of total antioxidant capacity (+15-128%), polyphenols (+21-126%) and α-tocopherols (+20-138%) under both eCO2 and PGPB application (in combination or individual application), while only the combined treatment (eCO2 + PGPB) led to a significantly higher accumulation of antioxidant enzymes (+88-197%), β-tocopherols (+177%) and flavonoids (+155%). Moreover, nitrogen- and sulfur-containing metabolites (glucosinolates and amino acids) were improved by PGPB treatment and/or CO2 levels, in which PGPB increased the amino acid-derived glucosinolate induction by eCO2 with low levels of effective sulforaphane. CONCLUSIONS Therefore, the interaction effects of beneficial Actinobacteria and eCO2 are expected to boost the level of antioxidant molecules and to have a helpful role in improving plant biomass and adaptability to complicated climate changes in the future. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Nashwa Hagagy
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Hamada AbdElgawad
- Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium
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Liu J, Qiu S, Yang L, Yang C, Xue T, Yuan Y. Germination of pecan seeds changes the microbial community. PeerJ 2023; 11:e16619. [PMID: 38107585 PMCID: PMC10725176 DOI: 10.7717/peerj.16619] [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: 08/07/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Endophytes are core of the plant-associated microbiome, and seed endophytes are closely related to the plant growth and development. Seed germination is an important part of pecan's life activities, but the composition and changes of microbes during different germination processes have not yet been revealed in pecan seeds. In order to deeply explore the characteristics of endophytes during the germination process of pecan, high-throughput sequencing was performed on seeds at four different germination stages. Findings of present study was found that the diversity and composition of microorganisms were different in different germination stages, and the microbial richness and diversity were highest in the seed endocarp break stage. It was speculated that the change of endophytes in pecan seeds was related to the germination stage. By evaluating the relationship between microbial communities, the core microbiota Cyanobacteria, Proteobacteria and Actinobacteria (bacterial) and Anthophyta and Ascomycota (fungal) core microbiota were identified in germinating pecan seeds. Finally, biomarkers in different germination processes of pecan seeds were identified by LEfSe analysis, among which Proteobacteria, Gamma proteobacteria and, Cyanobacteria and Ascomycota and Sordariomycetes were most abundant. Thus, this study will help to explore the interaction mechanism between pecan seeds and endophytes in different germination processes, and provide materials for the research and development of pecan seed endophytes.
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Affiliation(s)
- Jia Liu
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui, China
| | - Sumei Qiu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liping Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Can Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Tingting Xue
- Department of Civil and Architecture and Engineering, Chuzhou University, Anhui, China
| | - Yingdan Yuan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
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Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Mei Z, Fu Y, Wang F, Xiang L, Hu F, Harindintwali JD, Wang M, Virta M, Hashsham SA, Jiang X, Tiedje JM. Magnetic biochar/quaternary phosphonium salt reduced antibiotic resistome and pathobiome on pakchoi leaves. JOURNAL OF HAZARDOUS MATERIALS 2023; 460:132388. [PMID: 37639796 DOI: 10.1016/j.jhazmat.2023.132388] [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: 05/29/2023] [Revised: 08/04/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) in leafy vegetable is a matter of concern as they can be transferred from soil, atmosphere, and foliar sprays, and poses a potential risk to public health. While traditional disinfection technologies are effective in reducing the presence of ARGs and HPB in soil. A new technology, foliar spraying with magnetic biochar/quaternary ammonium salt (MBQ), was demonstrated and applied to the leaf surface. High-throughput quantitative PCR targeting 96 valid ARGs and 16 S rRNA sequencing were used to assess its efficacy in reducing ARGs and HPB. The results showed that spraying MBQ reduced 97.0 ± 0.81% of "high-risk ARGs", associated with seven classes of antibiotic resistance in pakchoi leaves within two weeks. Water washing could further reduce "high-risk ARGs" from pakchoi leaves by 19.8%- 24.6%. The relative abundance of HPB closely related to numerous ARGs was reduced by 15.2 ± 0.23% with MBQ application. Overall, this study identified the potential risk of ARGs from leafy vegetables and clarified the significant implications of MBQ application for human health as it offers a promising strategy for reducing ARGs and HPB in leafy vegetables.
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Affiliation(s)
- Zhi Mei
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China; Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Yuhao Fu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Leilei Xiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Hu
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jean Damascene Harindintwali
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingyi Wang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; College of Geographical Sciences, Nantong University, Nantong 226001, China
| | - Marko Virta
- Faculty of Agriculture and Forestry Department of Microbiology, University of Helsinki, 00014, Finland
| | - Syed A Hashsham
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA; Department of Civil and Environmental Engineering, Michigan State University, MI 48824, USA
| | - Xin Jiang
- CAS State Key Laboratory of Soil & Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, MI 48824, USA
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Khanal M, Bhatta BP, Malla S. Isolation and Characterization of Bacteria Associated with Onion and First Report of Onion Diseases Caused by Five Bacterial Pathogens in Texas, U.S.A. PLANT DISEASE 2023:PDIS09222206SR. [PMID: 36451309 DOI: 10.1094/pdis-09-22-2206-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.
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Affiliation(s)
- Manzeal Khanal
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Bed Prakash Bhatta
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
| | - Subas Malla
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843
- Texas A&M AgriLife Research and Extension Center, Uvalde, TX 78801
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7
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Lee W, Kim MH, Park J, Kim YJ, Kim E, Heo EJ, Kim SH, Kim G, Shin H, Kim SH, Kim HY. Seasonal Changes in the Microbial Communities on Lettuce ( Lactuca sativa L.) in Chungcheong-do, South Korea. J Microbiol Biotechnol 2023; 33:219-227. [PMID: 36524338 PMCID: PMC9998205 DOI: 10.4014/jmb.2210.10001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]
Abstract
Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.
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Affiliation(s)
- Woojung Lee
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Min-Hee Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Juyeon Park
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - You Jin Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eun Jeong Heo
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Seung Hwan Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Gyungcheon Kim
- Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Hakdong Shin
- Department of Food Science and Biotechnology, and Carbohydrate Bioproduct Research Center, College of Life Science, Sejong University, Seoul 05006, Republic of Korea
| | - Soon Han Kim
- Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
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Hou Y, Zhang X, Gao Z, Chen T, Zhang L. Relationships between fungal diversity and fruit quality of Yuluxiang pear during low temperature storage. Front Microbiol 2023; 14:1132271. [PMID: 37032901 PMCID: PMC10080050 DOI: 10.3389/fmicb.2023.1132271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/02/2023] [Indexed: 04/11/2023] Open
Abstract
Postharvest decay is an urgent problem that affects the storage of pears. Low temperature storage is one of the most important methods to reduce the prevalence of fruit diseases during storage. In this study, the microbial diversity of postharvest Yuluxiang pear (Pyrus × michauxii "Yu Lu Xiang") fruits stored at low temperature for different lengths of times was analyzed. Illumina MiSeq high-throughput sequencing was used to analyze the composition and diversity of fungal communities. The results showed that the fungi within fruit were classified into 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera based on the 97% sequence similarity level. They belonged to 6 phyla, 18 classes, 40 orders, 72 families, and 92 genera. The highest richness of fungi was obtained after 30 d of treatment. The β-diversity index showed that the fungal community composition of these fruit was significantly different at the beginning of storage compared with the different timepoints of samples at low temperature during storage. The comparison of fungal composition at the phylum level indicated that Ascomycota was dominant in the different timepoints of samples at low temperature, while Alternaria was the primary fungus at the genus level. A correlation analysis was used to further explore the correlation between fungi and fruit firmness, titratable acid, and solid soluble contents at low temperatures during storage. Aureobasidium and Didymella positively correlated with the soluble solids and hardness. Phoma positively correlated with the titratable acid, and Aspergillus positively correlated with titratable acid and hardness. This study can guide the industrial production of Yulu pear and also provide a theoretical basis to prevent and control diseases during the storage period of Yulu pear.
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Gerna D, Clara D, Antonielli L, Mitter B, Roach T. Seed Imbibition and Metabolism Contribute Differentially to Initial Assembly of the Soybean Holobiont. PHYTOBIOMES JOURNAL 2022; 8:21-33. [PMID: 38818306 PMCID: PMC7616048 DOI: 10.1094/pbiomes-03-23-0019-mf] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Seed germination critically determines successful plant establishment and agricultural productivity. In the plant holobiont's life cycle, seeds are hubs for microbial communities' assembly, but what exactly shapes the holobiont during germination remains unknown. Here, 16S rRNA gene amplicon sequencing characterized the bacterial communities in embryonic compartments (cotyledons and axes) and on seed coats pre- and post-germination of four soybean (Glycine max) cultivars, in the presence or absence of exogenous abscisic acid (ABA), which prevented germination and associated metabolism of seeds that had imbibed. Embryonic compartments were metabolically profiled during germination to design minimal media mimicking the seed endosphere for bacterial growth assays. The distinction between embryonic and seed coat bacterial microbiomes of dry seeds weakened during germination, resulting in the plumule, radicle, cotyledon, and seed coat all hosting the same most abundant and structurally influential genera in germinated seeds of every cultivar. Treatment with ABA prevented the increase of bacterial microbiomes' richness, but not taxonomic homogenization across seed compartments. Growth assays on minimal media containing the most abundant metabolites that accumulated in germinated seeds revealed that seed reserve mobilization promoted enrichment of copiotrophic bacteria. Our data show that seed imbibition enabled distribution of seed-coat-derived epiphytes into embryos irrespective of germination, while germinative metabolism promoted proliferation of copiotrophic taxa, which predominated in germinated seeds.
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Affiliation(s)
- Davide Gerna
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - David Clara
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
| | - Livio Antonielli
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria Accepted for publication 17 August 2023
| | - Birgit Mitter
- Center for Health & Bioresources, Bioresources Unit, AIT Austrian Institute of Technology GmbH, 3430 Tulln, Austria Accepted for publication 17 August 2023
| | - Thomas Roach
- Department of Botany and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria
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Kim DR, Kim SH, Lee SI, Kwak YS. Microbiota Communities of Healthy and Bacterial Pustule Diseased Soybean. THE PLANT PATHOLOGY JOURNAL 2022; 38:372-382. [PMID: 35953057 PMCID: PMC9372108 DOI: 10.5423/ppj.oa.05.2022.0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Soybean is an important source of protein and for a wide range of agricultural, food, and industrial applications. Soybean is being affected by Xanthomonas citri pv. glycines, a causal pathogen of bacterial pustule disease, result in a reduction in yield and quality. Diverse microbial communities of plants are involved in various plant stresses is known. Therefore, we designed to investigate the microbial community differentiation depending on the infection of X. citri pv. glycines. The microbial community's abundance, diversity, and similarity showed a difference between infected and non-infected soybean. Microbiota community analysis, excluding X. citri pv. glycines, revealed that Pseudomonas spp. would increase the population of the infected soybean. Results of DESeq analyses suggested that energy metabolism, secondary metabolite, and TCA cycle metabolism were actively diverse in the non-infected soybeans. Additionally, Streptomyces bacillaris S8, an endophyte microbiota member, was nominated as a key microbe in the healthy soybeans. Genome analysis of S. bacillaris S8 presented that salinomycin may be the critical antibacterial metabolite. Our findings on the composition of soybean microbiota communities and the key strain information will contribute to developing biological control strategies against X. citri pv. glycines.
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Affiliation(s)
- Da-Ran Kim
- Resarch Institute of Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Su-Hyeon Kim
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Su In Lee
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Youn-Sig Kwak
- Resarch Institute of Life Science, Gyeongsang National University, Jinju 52828,
Korea
- Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828,
Korea
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11
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Rothwell MAR, Zhai Y, Pagán-Medina CG, Pérez-Díaz IM. Growth of ɣ-Proteobacteria in Low Salt Cucumber Fermentation Is Prevented by Lactobacilli and the Cover Brine Ingredients. Microbiol Spectr 2022; 10:e0103121. [PMID: 35543556 PMCID: PMC9241618 DOI: 10.1128/spectrum.01031-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/24/2022] [Indexed: 11/20/2022] Open
Abstract
This study investigated the ability of ɣ-proteobacteria, indigenous to fresh cucumber, to grow in the expressed fruit juice (CJM) and fermentation. It was hypothesized that fresh cucumbers can support prolific growth of ɣ-proteobacteria but that the cover brine composition and acid production by the competing lactobacilli in the fermentation of the fruit act as inhibitory agents. The ɣ-proteobacteria proliferated in CJM with an average maximum growth rate (μmax) of 0.3895 ± 0.0929 and doubling time (Td) of 1.885 ± 0.465/h. A significant difference was found between the ɣ-proteobacteria μmax and Td relative to Lactiplantibacillus pentosus LA0445 (0.2319 ± 0.019; 2.89/h) and Levilactobacillus brevis 7.2.43 (0.221 ± 0.015; 3.35/h) but not Lactiplantibacillus plantarum 3.2.8 (0.412 ± 0.119; 1.87/h). While inoculation level insignificantly altered the μmax and Td of the bacteria tested; it impacted the length of lag and stationary phases for the lactobacilli. Unlike the lactobacilli, the ɣ-proteobacteria were inhibited in CJM supplemented with a low salt fermentation cover brine containing calcium chloride, acetic acid and potassium sorbate. The ɣ-proteobacteria, P. agglomerans, was unable to proliferate in cucumber fermentations brined with calcium chloride at a pH of 6.0 ± 0.1 and the population of Enterobacteriaceae was outcompeted by the lactobacilli within 36 h. Together these observations demonstrate that the prolific growth of ɣ-proteobacteria in CJM is not replicated in cucumber fermentation. While the ɣ-proteobacteria growth rate is faster that most lactobacilli in CJM, their growth in cucumber fermentation is prevented by the cover brine and the acid produced by the indigenous lactobacilli. Thus, the lactobacilli indigenous to cucumber and cover brine composition influence the safety and quality of fermented cucumbers. IMPORTANCE While the abundance of specific ɣ-proteobacteria species varies among vegetable type, several harbor Enterobacteriaceae and Pseudomonadaceae that benefit the plant system. It is documented that such bacterial populations decrease in density early in vegetable fermentations. Consequently, it is assumed that they do not contribute to the quality of finished products. This study explored the viability of ɣ-proteobacteria in CJM, used as a model system, CJM supplemented with fermentation cover brine and cucumber fermentation, which are characterized by an extremely acidic endpoint pH (3.23 ± 0.17; n = 391). The data presented demonstrates that fresh cucumbers provide the nutrients needed by ɣ-proteobacteria to proliferate and reduce pH to 4.47 ± 0.12. However, ɣ-proteobacteria are unable to proliferate in cucumber fermentation. Control of ɣ-proteobacteria in fermentations depends on the cover brine constituents and the indigenous competing lactobacilli. This knowledge is of importance when developing guidelines for the safe fermentation of vegetables, particularly with low salt.
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Affiliation(s)
- Madison A. R. Rothwell
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Yawen Zhai
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Christian G. Pagán-Medina
- U.S. Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, North Carolina State University, Raleigh, North Carolina, USA
| | - Ilenys M. Pérez-Díaz
- U.S. Department of Agriculture, Agricultural Research Service, SEA Food Science and Market Quality and Handling Research Unit, North Carolina State University, Raleigh, North Carolina, USA
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12
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Brennan FP, Alsanius BW, Allende A, Burgess CM, Moreira H, Johannessen GS, Castro PML, Uyttendaele M, Truchado P, Holden NJ. Harnessing agricultural microbiomes for human pathogen control. ISME COMMUNICATIONS 2022; 2:44. [PMID: 37938739 PMCID: PMC9723689 DOI: 10.1038/s43705-022-00127-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 08/24/2023]
Affiliation(s)
- Fiona P Brennan
- Teagasc, Department of Environment, Soils and Landuse, Johnstown Castle, Wexford, Ireland.
| | - Beatrix W Alsanius
- Department of Biosystems and Technology; Microbial Horticulture Unit, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ana Allende
- Food Safety and Quality Group, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin, Ireland
| | - Helena Moreira
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Gro S Johannessen
- Section for Food Safety and Animal Health Research, Norwegian Veterinary Institute, Oslo, Norway
| | - Paula M L Castro
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Mieke Uyttendaele
- Department of Food Technology, Food Safety and Health, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Pilar Truchado
- Food Safety and Quality Group, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
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13
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Use of bacterial strains antagonistic to Escherichia coli for biocontrol of spinach: A field trial. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102862] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Dixit AR, Khodadad CLM, Hummerick ME, Spern CJ, Spencer LE, Fischer JA, Curry AB, Gooden JL, Maldonado Vazquez GJ, Wheeler RM, Massa GD, Romeyn MW. Persistence of Escherichia coli in the microbiomes of red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) - does seed sanitization matter? BMC Microbiol 2021; 21:289. [PMID: 34686151 PMCID: PMC8532290 DOI: 10.1186/s12866-021-02345-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/24/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Seed sanitization via chemical processes removes/reduces microbes from the external surfaces of the seed and thereby could have an impact on the plants' health or productivity. To determine the impact of seed sanitization on the plants' microbiome and pathogen persistence, sanitized and unsanitized seeds from two leafy green crops, red Romaine lettuce (Lactuca sativa cv. 'Outredgeous') and mizuna mustard (Brassica rapa var. japonica) were exposed to Escherichia coli and grown in controlled environment growth chambers simulating environmental conditions aboard the International Space Station. Plants were harvested at four intervals from 7 days post-germination to maturity. The bacterial communities of leaf and root were investigated using the 16S rRNA sequencing while quantitative polymerase chain reaction (qPCR) and heterotrophic plate counts were used to reveal the persistence of E. coli. RESULT E. coli was detectable for longer periods of time in plants from sanitized versus unsanitized seeds and was identified in root tissue more frequently than in leaf tissue. 16S rRNA sequencing showed dynamic changes in the abundance of members of the phylum Proteobacteria, Firmicutes, and Bacteroidetes in leaf and root samples of both leafy crops. We observed minimal changes in the microbial diversity of lettuce or mizuna leaf tissue with time or between sanitized and unsanitized seeds. Beta-diversity showed that time had more of an influence on all samples versus the E. coli treatment. CONCLUSION Our results indicated that the seed surface sanitization, a current requirement for sending seeds to space, could influence the microbiome. Insight into the changes in the crop microbiomes could lead to healthier plants and safer food supplementation.
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Affiliation(s)
- Anirudha R Dixit
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | | | - Mary E Hummerick
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Cory J Spern
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - LaShelle E Spencer
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Jason A Fischer
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Aaron B Curry
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | - Jennifer L Gooden
- AMENTUM Services Inc., LASSO, Kennedy Space Center, Merritt Island, FL, USA
| | | | | | - Gioia D Massa
- NASA UB, Kennedy Space Center, Merritt Island, FL, USA
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15
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Tarquinio F, Attlan O, Vanderklift MA, Berry O, Bissett A. Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds. Front Microbiol 2021; 12:703014. [PMID: 34621247 PMCID: PMC8491609 DOI: 10.3389/fmicb.2021.703014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.
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Affiliation(s)
- Flavia Tarquinio
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Océane Attlan
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia.,Sciences et Technologies, Université de la Réunion, Saint-Denis, France
| | - Mathew A Vanderklift
- Oceans and Atmosphere, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Oliver Berry
- Environomics Future Science Platform, Indian Ocean Marine Research Centre, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Crawley, WA, Australia
| | - Andrew Bissett
- Oceans and Atmosphere, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Hobart, TAS, Australia
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16
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Bashir I, War AF, Rafiq I, Reshi ZA, Rashid I, Shouche YS. Phyllosphere microbiome: Diversity and functions. Microbiol Res 2021; 254:126888. [PMID: 34700185 DOI: 10.1016/j.micres.2021.126888] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.
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Affiliation(s)
- Iqra Bashir
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India.
| | - Aadil Farooq War
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Iflah Rafiq
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
| | - Irfan Rashid
- Department of Botany, University of Kashmir, Srinagar, 190006, Jammu and Kashmir, India
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17
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Processing of leafy vegetables matters: Damage and microbial community structure from field to bag. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Liao C, Wang L. Evaluation of the bacterial populations present in Spring Mix salad and their impact on the behavior of Escherichia coli O157:H7. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Chesneau G, Torres-Cortes G, Briand M, Darrasse A, Preveaux A, Marais C, Jacques MA, Shade A, Barret M. Temporal dynamics of bacterial communities during seed development and maturation. FEMS Microbiol Ecol 2021; 96:5910485. [PMID: 32966572 DOI: 10.1093/femsec/fiaa190] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 09/17/2020] [Indexed: 12/20/2022] Open
Abstract
Seed microbiota acts as a starting point for the assembly of the plant microbiota and contributes to successful plant establishment. To date, the order and timing of microbial taxa immigration during seed development and maturation remained unknown. We investigated the temporal dynamics of seed bacterial communities in bean and radish. A high phylogenetic turnover was observed for both plant species with few taxa associated with all seed developmental stages. Greater heterogeneity in communities structure within each stage was observed for radish. While, about one-third of radish seed bacterial taxa were detected in buds, flowers and fruits, very few taxa seem to be transmitted by the floral route in bean. In the latter species, bacterial populations belonging to the P. fluorescens species complex were found either in buds, flowers and fruits or in seeds. The relative phylogenetic proximity of these bacterial populations combined with their habitat specificity led us to explore the genetic determinants involved in successful seed transmission in bean. Comparative genomic analyses of representatives bacterial strains revealed dozens of coding sequences specifically associated with seed-transmitted strains. This study provided a first glimpse on processes involved in seed microbiota assembly, which could be used for designing plant-beneficial microbial consortia.
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Affiliation(s)
- Guillaume Chesneau
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gloria Torres-Cortes
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Armelle Darrasse
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Anne Preveaux
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Coralie Marais
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Program in Ecology, Evolutionary Biology, and Behavior, The DOE Great Lakes Bioenergy Research Center, and The Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
| | - Matthieu Barret
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
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20
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Abdelfattah A, Wisniewski M, Schena L, Tack AJM. Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root. Environ Microbiol 2021; 23:2199-2214. [PMID: 33427409 DOI: 10.1111/1462-2920.15392] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/26/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
While the environment is considered the primary origin of the plant microbiome, the potential role of seeds as a source of transmitting microorganisms has not received much attention. Here we tested the hypothesis that the plant microbiome is partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in a microbe-free environment while keeping belowground and aboveground tissues separated. The microbial communities associated with the acorn's embryo and pericarp and the developing seeding's phyllosphere and root systems were analysed using amplicon sequencing of fungal ITS and bacterial 16S rDNA. Results showed that the seed microbiome is diverse and non-randomly distributed within an acorn. The microbial composition of the phyllosphere was diverse and strongly resembled the composition found in the embryo, whereas the roots and pericarp each had a less diverse and distinct microbial community. Our findings demonstrate a high level of microbial diversity and spatial partitioning of the fungal and bacterial community within both seed and seedling, indicating inheritance, niche differentiation and divergent transmission routes for the establishment of root and phyllosphere communities.
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Affiliation(s)
- Ahmed Abdelfattah
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Michael Wisniewski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden.,U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Kearneysville, West Virginia, USA
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea, Reggio Calabria, Italy.,Department of Biological Sciences, Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Ayco J M Tack
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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21
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Zhou SYD, Li H, Giles M, Neilson R, Yang XR, Su JQ. Microbial Flow Within an Air-Phyllosphere-Soil Continuum. Front Microbiol 2021; 11:615481. [PMID: 33584580 PMCID: PMC7873851 DOI: 10.3389/fmicb.2020.615481] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
The phyllosphere is populated by numerous microorganisms. Microbes from the wider environment, i.e., air and soil, are considered key contributors to phyllosphere microbial communities, but their contribution is unclear. This study seeks to address this knowledge gap by controlling the movement of microbes along the air-phyllosphere-soil continuum. Customized equipment with dual chambers was constructed that permitted airflow to enter the first chamber while the second chamber recruited filtered microbe-free air from the initial chamber. Allium schoenoprasum (chive) and Sonchus oleraceus (sow thistle) were cultivated in both chambers, and the microbial communities from air, phyllosphere, and soil samples were characterized. Shares of microbial OTUs in the equipment suggested a potential interconnection between the air, phyllosphere, and soil system. Fast expectation-maximization microbial source tracking (FEAST) suggested that soil was the major source of airborne microbial communities. In contrast, the contribution of airborne and soil microbes to phyllosphere microbial communities of either A. schoenoprasum or S. oleraceus was limited. Notably, the soilborne microbes were the only environmental sources to phyllosphere in the second chamber and could affect the composition of phyllosphere microbiota indirectly by air flow. The current study demonstrated the possible sources of phyllosphere microbes by controlling external airborne microbes in a designed microcosm system and provided a potential strategy for recruitment for phyllosphere recruitment.
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Affiliation(s)
- Shu-Yi-Dan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Madeline Giles
- Ecological Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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22
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Taffner J, Laggner O, Wolfgang A, Coyne D, Berg G. Exploring the Microbiota of East African Indigenous Leafy Greens for Plant Growth, Health, and Resilience. Front Microbiol 2020; 11:585690. [PMID: 33329455 PMCID: PMC7710512 DOI: 10.3389/fmicb.2020.585690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/30/2020] [Indexed: 01/04/2023] Open
Abstract
Indigenous leafy green vegetable crops provide a promising nutritious alternative for East African agriculture under a changing climate; they are better able to cope with biotic and abiotic stresses than cosmopolitan vegetable crops. To verify our hypothesis that the associated microbiome is involved, we studied archaeal and bacterial communities of four locally popular leafy green crops in Uganda (Bidens pilosa, Solanum scabrum, Abelmoschus esculentus, and Gynandropsis gynandra) and of four plant microhabitats (phyllosphere, root endosphere, rhizosphere, and soil) by complementary analyses of amplicon and isolate libraries. All plants shared an unusually large core microbiome, comprising 18 procaryotic families but primarily consisting of Bacillus, Sphingobium, Comamonadaceae, Pseudomonas, and one archaeon from the soil crenarchaeotic group. Microbiome composition did not differ significantly for plant species but differed for microhabitats. The diversity was, in general, higher for bacteria (27,697 ASVs/H = 6.91) than for archaea (2,995 ASVs/H = 4.91); both groups form a robust network of copiotrophic bacteria and oligotrophic archaea. Screening of selected isolates for stress and plant health protecting traits showed that strains of Bacillus and Sphingomonas spp. div. constituted a substantial portion (15-31%) of the prokaryotic plant-associated communities. Across plant species, microbiota were characterized by a high proportion of potential copiotrophic and plant-beneficial species, which was not specific by plant species. The use of identified plant-beneficial isolates could provide the basis for the development of consortia of isolates for both abiotic and biotic stress protection to improve plant and ecosystem health, ensuring food security in East Africa.
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Affiliation(s)
- Julian Taffner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Olivia Laggner
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Adrian Wolfgang
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | - Danny Coyne
- East Africa Hub, International Institute of Tropical Agriculture (IITA), Nairobi, Kenya.,Nematology Section, Department of Biology, Ghent University, Ghent, Belgium
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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23
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Hamilton A, Harper SJ, Critzer F. Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces. Microorganisms 2020; 8:microorganisms8101480. [PMID: 32993184 PMCID: PMC7601045 DOI: 10.3390/microorganisms8101480] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/24/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022] Open
Abstract
Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.
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Affiliation(s)
- Alexis Hamilton
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
- Correspondence: ; Tel.:+1-509-786-9209
| | - Scott J. Harper
- Department of Plant Pathology, Washington State University, Pullman, WA 99164, USA;
| | - Faith Critzer
- School of Food Science, Washington State University, Pullman, WA 99164, USA;
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Influence of Salt Stress on Growth of Spermosphere Bacterial Communities in Different Peanut ( Arachis hypogaea L.) Cultivars. Int J Mol Sci 2020; 21:ijms21062131. [PMID: 32244906 PMCID: PMC7139419 DOI: 10.3390/ijms21062131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 11/17/2022] Open
Abstract
Background: Exposure of seeds to high salinity can cause reduced germination and poor seedling establishment. Improving the salt tolerance of peanut (Arachis hypogaea L.) seeds during germination is an important breeding goal of the peanut industry. Bacterial communities in the spermosphere soils may be of special importance to seed germination under salt stress, whereas extant results in oilseed crop peanut are scarce. Methods: Here, bacterial communities colonizing peanut seeds with salt stress were characterized using 16S rRNA gene sequencing. Results: Peanut spermosphere was composed of four dominant genera: Bacillus, Massilia, Pseudarthrobacter, and Sphingomonas. Comparisons of bacterial community structure revealed that the beneficial bacteria (Bacillus), which can produce specific phosphatases to sequentially mineralize organic phosphorus into inorganic phosphorus, occurred in relatively higher abundance in salt-treated spermosphere soils. Further soil enzyme activity assays showed that phosphatase activity increased in salt-treated spermosphere soils, which may be associated with the shift of Bacillus. Conclusion: This study will form the foundation for future improvement of salt tolerance of peanuts at the seed germination stage via modification of the soil microbes.
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Rain induces temporary shifts in epiphytic bacterial communities of cucumber and tomato fruit. Sci Rep 2020; 10:1765. [PMID: 32020033 PMCID: PMC7000718 DOI: 10.1038/s41598-020-58671-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
Understanding weather-related drivers of crop plant-microbiome relationships is important for food security and food safety in the face of a changing climate. Cucumber and tomato are commercially important commodities that are susceptible to plant disease and have been implicated in foodborne disease outbreaks. To investigate the influence of precipitation on plant-associated microbiomes, epiphytically associated bacterial communities of cucumber and tomato samples were profiled by 16 S rRNA gene sequencing (V1-V3) in the days surrounding two rain events over a 17-day period. Following rain, α (within-sample) diversity measured on cucumber and tomato fruit surfaces, but not tomato leaf surfaces, increased significantly and remained elevated for several days. Bacterial β (between-sample) diversity on cucumber and tomato fruit responded to precipitation. In the cucumber fruit surface (carpoplane), notable shifts in the families Xanthomonadaceae, Oxalobacteriaceae, Sphingobacteriaceae and Comamonadaceae were detected following precipitation. In the tomato carpoplane, shifts were detected in the families Enterobacteriaceae and Xanthomonadaceae following the first rain event, and in the Pseudomonadaceae and Oxalobacteriaceae following the second rain event. Few taxonomic shifts were detected in the tomato leaf surface (phylloplane). Exploring rain-induced shifts in plant microbiomes is highly relevant to crop protection, food safety and agroecology, and can aid in devising ways to enhance crop resilience to stresses and climate fluctuations.
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26
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Wang Y, Wang C, Gu Y, Wang P, Song W, Ma J, Yang X. The variability of bacterial communities in both the endosphere and ectosphere of different niches in Chinese chives (Allium tuberosum). PLoS One 2020; 15:e0227671. [PMID: 31945106 PMCID: PMC6964972 DOI: 10.1371/journal.pone.0227671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/24/2019] [Indexed: 12/18/2022] Open
Abstract
Deciphering the various types of interactions between plants and their microbiomes is a hot topic for research in ecology as well as in plant sciences and agronomy. To analyse and compare the differences in microbial communities in different compartments of Chinese chives, high-throughput sequencing technology was employed to amplify and sequence the V5-V6 region of the 16S rDNA of microorganisms in the leaves, phylloplanes, stems, roots and rhizospheres of Chinese chives. The sequences were clustered by operational taxonomic units (OTUs), and the community composition of bacteria between the endosphere (inner tissues) and ectosphere (outer surfaces) of Chinese chives was analysed based on the OTU. Overall, the results indicated that the endophytic bacteria in Chinese chives mainly include Proteobacteria, Actinobacteria, and Actinomycetes. Alpha diversity index analysis and OTU number analysis showed that the bacterial diversity and richness of the underground plant compartments were higher than those of the above-ground parts. PCoA based on the OTU level showed that the vertical stratification structure of plants and compartments had significant effects on the bacterial community structure. The richness of endophytic bacteria also varied greatly among the different varieties of Chinese chive. A considerable number of endophytic bacteria form symbiotic and mutually beneficial relationships with host plants, which play an important role in regulating host growth, metabolism and stress resistance. Further investigations are needed to uncover the evolution of interactions between plants and endophytes.
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Affiliation(s)
- Yuxin Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
- * E-mail:
| | - Chaonan Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Yizhu Gu
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Pingzhi Wang
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Weitang Song
- College of Water Resources & Civil Engineering, China Agricultural University, Haidian, Beijing, China
| | - Jinhai Ma
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
| | - Xiaofei Yang
- Henan Jiuxing Institute of Biotechnology, Pingdingshan, Henan, China
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Vokou D, Genitsaris S, Karamanoli K, Vareli K, Zachari M, Voggoli D, Monokrousos N, Halley JM, Sainis I. Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem. Microorganisms 2019; 7:microorganisms7110518. [PMID: 31683878 PMCID: PMC6920919 DOI: 10.3390/microorganisms7110518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/20/2019] [Accepted: 10/29/2019] [Indexed: 01/29/2023] Open
Abstract
We explore how the phyllosphere microbial community responds to a very seasonal environment such as the Mediterranean. For this, we studied the epiphytic bacterial community of a Mediterranean ecosystem in summer and winter, expecting to detect seasonal differences at their maximum. With high-throughput sequencing (HTS), we detected the operational taxonomic units (OTUs) present in the phyllosphere and also in the surrounding air. The epiphytic community is approximately five orders of magnitude denser than the airborne one and is made almost exclusively by habitat specialists. The two communities differ considerably but Proteobacteria and Actinobacteria are dominant in both. Of the five most abundant phyllosphere OTUs, two were closely related to Sphingomonas strains, one to Methylobacterium and the other two to Rhizobiales and Burkholderiales. We found the epiphytic community to become much richer, more distinct, even and diverse, denser and more connected in summer. In contrast, there was no difference in the level of bacterial colonization of the phyllosphere between the two seasons, although there were seasonal differences for individual taxonomic groups: Firmicutes, Gemmatimonadetes and Chlroroflexi had a higher participation in summer, whereas the major Proteobacteria classes presented reverse patterns, with Betaproteobacteria increasing in summer at the expense of the prominent Alphaproteobacteria.
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Affiliation(s)
- Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Savvas Genitsaris
- School of Economics, Business Administration and Legal Studies, International Hellenic University, 57001 Thermi, Greece.
| | - Katerina Karamanoli
- School of Agriculture, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Katerina Vareli
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Marina Zachari
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Despoina Voggoli
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Nikolaos Monokrousos
- Department of Soil Science of Athens, Hellenic Agricultural Organization-Demeter, Institute of Soil and Water Resources, 14123 Lykovrisi, Greece.
| | - John Maxwell Halley
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
| | - Ioannis Sainis
- Department of Biological Applications and Technology, University of Ioannina, 45110 Ioannina, Greece.
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Patz S, Witzel K, Scherwinski AC, Ruppel S. Culture Dependent and Independent Analysis of Potential Probiotic Bacterial Genera and Species Present in the Phyllosphere of Raw Eaten Produce. Int J Mol Sci 2019; 20:ijms20153661. [PMID: 31357436 PMCID: PMC6696213 DOI: 10.3390/ijms20153661] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/05/2019] [Accepted: 07/16/2019] [Indexed: 02/06/2023] Open
Abstract
The plant phyllosphere is colonized by a complex ecosystem of microorganisms. Leaves of raw eaten vegetables and herbs are habitats for bacteria important not only to the host plant, but also to human health when ingested via meals. The aim of the current study was to determine the presence of putative probiotic bacteria in the phyllosphere of raw eaten produce. Quantification of bifidobacteria showed that leaves of Lepidium sativum L., Cichorium endivia L., and Thymus vulgaris L. harbor between 103 and 106 DNA copies per gram fresh weight. Total cultivable bacteria in the phyllosphere of those three plant species ranged from 105 to 108 CFU per gram fresh weight. Specific enrichment of probiotic lactic acid bacteria from C. endivia, T. vulgaris,Trigonella foenum-graecum L., Coriandrum sativum L., and Petroselinum crispum L. led to the isolation of 155 bacterial strains, which were identified as Pediococcus pentosaceus, Enterococcus faecium, and Bacillus species, based on their intact protein pattern. A comprehensive community analysis of the L. sativum leaves by PhyloChip hybridization revealed the presence of genera Bifidobacterium, Lactobacillus, and Streptococcus. Our results demonstrate that the phyllosphere of raw eaten produce has to be considered as a substantial source of probiotic bacteria and point to the development of vegetables and herbs with added probiotic value.
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Affiliation(s)
- Sascha Patz
- Algorithms in Bioinformatics, ZBIT Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Katja Witzel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
| | - Ann-Christin Scherwinski
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany
| | - Silke Ruppel
- Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Großbeeren, Germany.
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Wassermann B, Cernava T, Müller H, Berg C, Berg G. Seeds of native alpine plants host unique microbial communities embedded in cross-kingdom networks. MICROBIOME 2019; 7:108. [PMID: 31340847 PMCID: PMC6651914 DOI: 10.1186/s40168-019-0723-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/16/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds, but for native plants, complementary mechanisms are almost completely unknown. METHODS We studied the seeds of eight native plant species growing together for centuries under the same environmental conditions in Alpine meadows (Austria) by qPCR, FISH-CLSM, and amplicon sequencing targeting bacteria, archaea, and fungi. RESULTS Bacteria and fungi were determined with approx. 1010 gene copy numbers g-1 seed as abundant inhabitants. Archaea, which were newly discovered as seed endophytes, are less and represent only 1.1% of the signatures. The seed microbiome was highly diversified, and all seeds showed a species-specific, highly unique microbial signature, sharing an exceptionally small core microbiome. The plant genotype (species) was clearly identified as the main driver, while different life cycles (annual/perennial) had less impact on the microbiota composition, and fruit morphology (capsule/achene) had no significant impact. A network analysis revealed significant co-occurrence patterns for bacteria and archaea, contrasting with an independent fungal network that was dominated by mutual exclusions. CONCLUSIONS These novel insights into the native seed microbiome contribute to a deeper understanding of seed microbial diversity and phytopathological processes for plant health, and beyond that for ecosystem plasticity and diversification within plant-specific microbiota.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Christian Berg
- Institute of Biology, Department of Plant Sciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
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30
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Darlison J, Mogren L, Rosberg AK, Grudén M, Minet A, Liné C, Mieli M, Bengtsson T, Håkansson Å, Uhlig E, Becher PG, Karlsson M, Alsanius BW. Leaf mineral content govern microbial community structure in the phyllosphere of spinach (Spinacia oleracea) and rocket (Diplotaxis tenuifolia). THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 675:501-512. [PMID: 31030156 DOI: 10.1016/j.scitotenv.2019.04.254] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 06/09/2023]
Abstract
The plant microbiome is an important factor for plant health and productivity. While the impact of nitrogen (N) availability for plant growth and development is well established, its influence on the microbial phyllosphere community structure is unknown. We hypothesize that nitrogen impacts the growth and abundance of several microorganisms on the leaf surface. The bacterial and fungal communities of baby leaf spinach (Spinacia oleracea), and rocket (Diplotaxis tenuifolia) were investigated in a field trial for two years in a commercial setting. Nitrogen fertilizer was tested in four doses (basic nitrogen, basic + suboptimal, basic + commercial, basic + excess) with six replicates in each. Culture-independent (Illumina sequencing) and culture-dependent (viable count and identification of bacterial isolates) community studies were combined with monitoring of plant physiology and site weather conditions. This study found that alpha diversity of bacterial communities decreased in response to increasing nitrogen fertilizer dose, whereas viable counts showed no differences. Correspondingly, fungal communities of the spinach phyllosphere showed a decreasing pattern, whereas the decreasing diversity of fungal communities of rocket was not significant. Plant species and effects of annual variations on microbiome structure were observed for bacterial and fungal communities on both spinach and rocket. This study provides novel insights on the impact of nitrogen fertilizer regime on a nutrient scarce habitat, the phyllosphere.
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Affiliation(s)
- Julia Darlison
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden.
| | - Lars Mogren
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Anna Karin Rosberg
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Maria Grudén
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Antoine Minet
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Clarisse Liné
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Morgane Mieli
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Torbjörn Bengtsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Åsa Håkansson
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Elisabeth Uhlig
- LTH Lund University, Department of Food Technology, Box 124, SE-221 00 Lund, Sweden
| | - Paul G Becher
- Swedish University of Agricultural Sciences, Department of Plant Protection Biology, PO Box 102, SE-230 53 Alnarp, Sweden
| | - Maria Karlsson
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
| | - Beatrix W Alsanius
- Swedish University of Agricultural Sciences, Department of Biosystems and Technology, Microbial Horticulture Laboratory, PO Box 103, SE-230 53 Alnarp, Sweden
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31
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Darlison J, Mieli M, Bengtsson T, Hartmann R, Mogren L, Vågsholm I, Karlsson M, Alsanius BW. Plant species affects establishment of Escherichia coli O157:H7 gfp+ on leafy vegetables. J Appl Microbiol 2019; 127:292-305. [PMID: 31054164 DOI: 10.1111/jam.14299] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023]
Abstract
AIMS Greenhouse trials were conducted with different cultivars of baby leaf spinach, rocket and Swiss chard and inoculation of Escherichia coli O157:H7 gfp+, to determine whether plant species and cultivar have an impact on the establishment of this strain. METHODS AND RESULTS Three cultivars each of spinach, rocket and Swiss chard were spray inoculated with E. coli O157:H7 gfp+ at doses of log 7 CFU per ml. Due to the different lengths of growing period spinach and Swiss chard were spray inoculated three times and rocket five times, with final inoculation performed 3 days prior to harvest. After a growing period of 26-33 days, E. coli O157:H7 gfp+ was recovered from the leaf surface in mean populations between log 1 and 6 CFU per gram. The lowest occurrence of E. coli O157:H7 gfp+ was found on rocket leaves and the highest on spinach. There was no significant difference in the establishment of E. coli O157:H7 gfp+ between cultivars, but there were differences between plant species. Indigenous phyllosphere bacteria were pure cultured and identified with 16S rRNA gene sequencing. CONCLUSIONS Despite the same high inoculation dose of E. coli O157:H7 gfp+ on leaves, the establishment rate differed between plant species. However, plant cultivar did not affect establishment. Pantoea agglomerans dominated the identified bacterial isolates. SIGNIFICANCE AND IMPACT OF THE STUDY As previous studies are inconclusive on choice of model plant species and cultivar, we studied whether plant species or cultivar determines the fate of E. coli O157:H7 gfp+ on leafy vegetables. The findings indicate that plant species is a key determinant in the establishment of E. coli O157:H7 gfp+.
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Affiliation(s)
- J Darlison
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - M Mieli
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - T Bengtsson
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - R Hartmann
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Department of Horticultural Production Systems, Wilhelm Leibniz University, Hannover, Germany
| | - L Mogren
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - I Vågsholm
- Department of Biomedical Sciences and Veterinary Health, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - M Karlsson
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - B W Alsanius
- Department of Biosystems and Technology, Microbial Horticulture Laboratory, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Zhang Z, Kong X, Jin D, Yu H, Zhu X, Su X, Wang P, Zhang R, Jia M, Deng Y. Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew. Arch Microbiol 2019; 201:1099-1109. [PMID: 31147747 DOI: 10.1007/s00203-019-01683-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022]
Abstract
Euonymus japonicus Thunb. is a woody and ornamental plant popular in China, Europe and North America. Powdery mildew is one of the most serious diseases that affect E. japonicus growth. In this study, the diseased and apparently healthy leaves were collected from E. japonicus planted in a greenbelt in Beijing, and the effect of powdery mildew on the epiphytic microbial community was investigated by using Illumina sequencing. The results showed that the healthy leaves (HL) harbored greater bacterial and fungal diversity than diseased leaves (DL). Furthermore, both bacterial and fungal communities in DL exhibited significantly different structures from those in HL. The relative abundance of several bacterial phyla (Proteobacteria and Firmicutes) and fungal phyla (Ascomycota and Basidiomycota) were altered by powdery mildew. At the genus level, most genera decreased as powdery mildew pathogen Erysiphe increased, while the genera Kocuria and Exiguobacterium markedly increased. Leaf properties, especially protein content was found to significantly affect beta-diversity of the bacterial and fungal community. Network analysis revealed that positive bacterial interactions in DL were stronger than those in HL samples. Insights into the underlying the indigenous microbial phyllosphere populations of E. japonicus response to powdery mildew will help in the development of methods for controlling plant diseases.
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Affiliation(s)
- Zhuo Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.,Key Laboratory of Pest Management of Horticultural Crops of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Hao Yu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pei Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.,Key Laboratory of Pest Management of Horticultural Crops of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Ruiyong Zhang
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, 30655, Germany
| | - Minghong Jia
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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Torres-Cortés G, Garcia BJ, Compant S, Rezki S, Jones P, Préveaux A, Briand M, Roulet A, Bouchez O, Jacobson D, Barret M. Differences in resource use lead to coexistence of seed-transmitted microbial populations. Sci Rep 2019; 9:6648. [PMID: 31040301 PMCID: PMC6491768 DOI: 10.1038/s41598-019-42865-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/15/2019] [Indexed: 11/18/2022] Open
Abstract
Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of two phytopathogenic agents, Alternaria brassicicola Abra43 (Abra43) and Xanthomonas campestris pv. campestris 8004 (Xcc8004), on the structure and function of radish seed microbial assemblages, as well as the nutritional overlap between Xcc8004 and the seed microbiome, to find seed microbial residents capable of outcompeting this pathogen. According to taxonomic and functional inference performed on metagenomics reads, no shift in structure and function of the seed microbiome was observed following Abra43 and Xcc8004 transmission. This lack of impact derives from a limited overlap in nutritional resources between Xcc8004 and the major bacterial populations of radish seeds. However, two native seed-associated bacterial strains belonging to Stenotrophomonas rhizophila displayed a high overlap with Xcc8004 regarding the use of resources; they might therefore limit its transmission. The strategy we used may serve as a foundation for the selection of seed indigenous bacterial strains that could limit seed transmission of pathogens.
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Affiliation(s)
- G Torres-Cortés
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR4207 QuaSaV, 49071, Beaucouzé, France.
| | - B J Garcia
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - S Compant
- AIT Austrian Institute of Technology GmbH, Center for Health and Bioresources, Bioresources Unit, Konrad Lorenz Straße 24, A-3430, Tulln, Austria
| | - S Rezki
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR4207 QuaSaV, 49071, Beaucouzé, France
| | - P Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - A Préveaux
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR4207 QuaSaV, 49071, Beaucouzé, France
| | - M Briand
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR4207 QuaSaV, 49071, Beaucouzé, France
| | - A Roulet
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - O Bouchez
- INRA, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - D Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - M Barret
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR4207 QuaSaV, 49071, Beaucouzé, France
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34
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Fogler K, Guron GKP, Wind LL, Keenum IM, Hession WC, Krometis LA, Strawn LK, Pruden A, Ponder MA. Microbiota and Antibiotic Resistome of Lettuce Leaves and Radishes Grown in Soils Receiving Manure-Based Amendments Derived From Antibiotic-Treated Cows. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00022] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Impact of weather conditions, leaf age and irrigation water disinfection on the major epiphytic bacterial genera of baby spinach grown in an open field. Food Microbiol 2018; 78:46-52. [PMID: 30497607 DOI: 10.1016/j.fm.2018.09.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/27/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022]
Abstract
The effects of factors such as weather conditions, leaf age and irrigation water disinfection on the main bacterial genera (total bacterial, Enterobacteriaceae and Pseudomonas) of baby spinach were studied. Culture-dependent and independent quantification techniques were compared. Cultivation was carried out over two consecutive trials in commercial open field divided in two plots: 1) baby spinach irrigated with untreated surface water and 2) baby spinach irrigated with chlorine dioxide (ClO2) treated water. In all the cases, higher concentrations of bacteria were detected using molecular quantification in comparison with culture dependent techniques. Based on the obtained results, wind speed, solar radiation and relative humidity seem to have an impact on the levels of total bacterial, Enterobacteriaceae and Pseudomonas during cultivation of baby spinach. However, further studies would be needed to confirm this tendency. Water disinfection treatments (ClO2), when applied to irrigation water, impacted differently the bacterial genera evaluated in the present study. Thus, although no significant effects were observed in total bacterial enumerations of baby spinach irrigated with ClO2 treated water; significant reductions were detected in Enterobacteriaceae (19%) and Pseudomonas spp. (14%) levels. These results were also confirmed using specific culture-dependent methods. On the other hand, leaf age did not influence the levels of the main bacterial genera of baby spinach. Considering that, a large proportion of foodborne and pathogenic bacteria associated to fresh produce belong to the Enterobacteriaceae family and Pseudomonas genera, reductions in these bacterial groups could be beneficial. However, these groups are very diverse, making difficult to link the measurement of Enterobacteriaceae and Pseudomonas levels with the presence/abundance of potential pathogenic and spoilage microorganisms.
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Analysis of Bacterial Communities in White Clover Seeds via High-Throughput Sequencing of 16S rRNA Gene. Curr Microbiol 2018; 76:187-193. [DOI: 10.1007/s00284-018-1607-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/24/2018] [Indexed: 01/16/2023]
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Escobar Rodríguez C, Mitter B, Antonielli L, Trognitz F, Compant S, Sessitsch A. Roots and Panicles of the C4 Model Grasses Setaria viridis (L). and S. pumila Host Distinct Bacterial Assemblages With Core Taxa Conserved Across Host Genotypes and Sampling Sites. Front Microbiol 2018; 9:2708. [PMID: 30483233 PMCID: PMC6240606 DOI: 10.3389/fmicb.2018.02708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/23/2018] [Indexed: 01/22/2023] Open
Abstract
Virtually all studied plant tissues are internally inhabited by endophytes. Due to their relevance for plant growth and health, bacterial microbiota of crop plants have been broadly studied. In plant microbiome research the root is the most frequently addressed environment, whereas the ecology of microbiota associated with reproductive organs still demands investigation. In this work, we chose the model grasses Setaria viridis and Setaria pumila to better understand the drivers shaping bacterial communities associated with panicles (representing a reproductive organ) as compared to those associated with roots. We collected wild individuals of both grass species from 20 different locations across Austria and investigated the bacterial assemblages within roots and ripe grain-harboring panicles by 16S rRNA gene-based Illumina sequencing. Furthermore, plant samples were subjected to genotyping by genetic diversity-focused Genotyping by Sequencing. Overall, roots hosted more diverse microbiota than panicles. Both the plant organ and sampling site significantly shaped the root and panicle-associated microbiota, whereas the host genotype only affected root communities. In terms of community structure, root-specific assemblages were highly diverse and consisted of conserved bacterial taxa. In contrast, panicle-specific communities were governed by Gammaproteobacteria, were less diverse and highly origin-dependent. Among OTUs found in both plant tissues, relative abundances of Gammaproteobacteria were higher in panicles, whereas Rhizobiales dominated root communities. We further identified core and non-core taxa within samples of both Setaria species. Non-core taxa included members of the Saccharibacteria and Legionelalles, while core communities encompassed eleven OTUs of seven bacterial orders, together with a set of ten panicle-enriched OTUs. These communities were widespread across root and panicle samples from all locations, hinting toward an evolved form of mutualism through potential vertical transmission of these taxa within Setaria species.
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Affiliation(s)
- Carolina Escobar Rodríguez
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Birgit Mitter
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Livio Antonielli
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Friederike Trognitz
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Stéphane Compant
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Angela Sessitsch
- Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Vienna, Austria
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Purahong W, Orrù L, Donati I, Perpetuini G, Cellini A, Lamontanara A, Michelotti V, Tacconi G, Spinelli F. Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1563. [PMID: 30464766 PMCID: PMC6234494 DOI: 10.3389/fpls.2018.01563] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 10/05/2018] [Indexed: 05/20/2023]
Abstract
Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.
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Affiliation(s)
- Witoon Purahong
- Department of Soil Ecology, Helmholtz Center for Environmental Research - UFZ, Halle, Germany
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Irene Donati
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Giorgia Perpetuini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | - Antonio Cellini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
| | | | - Vania Michelotti
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Gianni Tacconi
- CREA Research Centre for Genomics and Bioinformatics – Fiorenzuola d’Arda, Italy
| | - Francesco Spinelli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – Università di Bologna, Bologna, Italy
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Carvalho SD, Castillo JA. Influence of Light on Plant-Phyllosphere Interaction. FRONTIERS IN PLANT SCIENCE 2018; 9:1482. [PMID: 30369938 PMCID: PMC6194327 DOI: 10.3389/fpls.2018.01482] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 09/21/2018] [Indexed: 05/11/2023]
Abstract
Plant-phyllosphere interactions depend on microbial diversity, the plant host and environmental factors. Light is perceived by plants and by microorganisms and is used as a cue for their interaction. Photoreceptors respond to narrow-bandwidth wavelengths and activate specific internal responses. Light-induced plant responses include changes in hormonal levels, production of secondary metabolites, and release of volatile compounds, which ultimately influence plant-phyllosphere interactions. On the other hand, microorganisms contribute making some essential elements (N, P, and Fe) biologically available for plants and producing growth regulators that promote plant growth and fitness. Therefore, light directly or indirectly influences plant-microbe interactions. The usage of light-emitting diodes in plant growth facilities is helping increasing knowledge in the field. This progress will help define light recipes to optimize outputs on plant-phyllosphere communications. This review describes research advancements on light-regulated plant-phyllosphere interactions. The effects of full light spectra and narrow bandwidth-wavelengths from UV to far-red light are discussed.
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Affiliation(s)
- Sofia D. Carvalho
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - José A. Castillo
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí, Ecuador
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Mogren L, Windstam S, Boqvist S, Vågsholm I, Söderqvist K, Rosberg AK, Lindén J, Mulaosmanovic E, Karlsson M, Uhlig E, Håkansson Å, Alsanius B. The Hurdle Approach-A Holistic Concept for Controlling Food Safety Risks Associated With Pathogenic Bacterial Contamination of Leafy Green Vegetables. A Review. Front Microbiol 2018; 9:1965. [PMID: 30197634 PMCID: PMC6117429 DOI: 10.3389/fmicb.2018.01965] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023] Open
Abstract
Consumers appreciate leafy green vegetables such as baby leaves for their convenience and wholesomeness and for adding a variety of tastes and colors to their plate. In Western cuisine, leafy green vegetables are usually eaten fresh and raw, with no step in the long chain from seed to consumption where potentially harmful microorganisms could be completely eliminated, e.g., through heating. A concerning trend in recent years is disease outbreaks caused by various leafy vegetable crops and one of the most important foodborne pathogens in this context is Shiga toxin-producing Escherichia coli (STEC). Other pathogens such as Salmonella, Shigella, Yersinia enterocolitica and Listeria monocytogenes should also be considered in disease risk analysis, as they have been implicated in outbreaks associated with leafy greens. These pathogens may enter the horticultural value network during primary production in field or greenhouse via irrigation, at harvest, during processing and distribution or in the home kitchen/restaurant. The hurdle approach involves combining several mitigating approaches, each of which is insufficient on its own, to control or even eliminate pathogens in food products. Since the food chain system for leafy green vegetables contains no absolute kill step for pathogens, use of hurdles at critical points could enable control of pathogens that pose a human health risk. Hurdles should be combined so as to decrease the risk due to pathogenic microbes and also to improve microbial stability, shelf-life, nutritional properties and sensory quality of leafy vegetables. The hurdle toolbox includes different options, such as physical, physiochemical and microbial hurdles. The goal for leafy green vegetables is multi-target preservation through intelligently applied hurdles. This review describes hurdles that could be used for leafy green vegetables and their biological basis, and identifies prospective hurdles that need attention in future research.
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Affiliation(s)
- Lars Mogren
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Sofia Windstam
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Department of Biological Sciences, SUNY Oswego, Oswego, NY, United States
| | - Sofia Boqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ivar Vågsholm
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Karin Söderqvist
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Anna K. Rosberg
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Julia Lindén
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Emina Mulaosmanovic
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Maria Karlsson
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Elisabeth Uhlig
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Åsa Håkansson
- Department of Food Technology, Engineering and Nutrition, Lund University, Lund, Sweden
| | - Beatrix Alsanius
- Microbial Horticulture, Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Truchado P, Gil MI, Suslow T, Allende A. Impact of chlorine dioxide disinfection of irrigation water on the epiphytic bacterial community of baby spinach and underlying soil. PLoS One 2018; 13:e0199291. [PMID: 30020939 PMCID: PMC6051574 DOI: 10.1371/journal.pone.0199291] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 06/05/2018] [Indexed: 12/13/2022] Open
Abstract
The contamination of pathogenic bacteria through irrigation water is a recognized risk factor for fresh produce. Irrigation water disinfection is an intervention strategy that could be applied to reduce the probability of microbiological contamination of crops. Disinfection treatments should be applied ensuring minimum effective doses, which are efficient in inhibiting the microbial contamination while avoiding formation and accumulation of chemical residues. Among disinfection technologies available for growers, chlorine dioxide (ClO2) represents, after sodium hypochlorite, an alternative disinfection treatment, which is commercially applied by growers in the USA and Spain. However, in most of the cases, the suitability of this treatment has been tested against pathogenic bacteria and low attention have been given to the impact of chemical residues on the bacterial community of the vegetable tissue. The aim of this study was to (i) to evaluate the continual application of chlorine dioxide (ClO2) as a water disinfection treatment of irrigation water during baby spinach growth in commercial production open fields, and (ii) to determine the subsequent impact of these treatments on the bacterial communities in water, soil, and baby spinach. To gain insight into the changes in the bacterial community elicited by ClO2, samples of treated and untreated irrigation water as well as the irrigated soil and baby spinach were analyzed using Miseq® Illumina sequencing platform. Next generation sequencing and multivariate statistical analysis revealed that ClO2 treatment of irrigation water did not affect the diversity of the bacterial community of water, soil and crop, but significant differences were observed in the relative abundance of specific bacterial genera. This demonstrates the different susceptibility of the bacteria genera to the ClO2 treatment. Based on the obtained results it can be concluded that the phyllosphere bacterial community of baby spinach was more influenced by the soil bacteria community rather than that of irrigation water. In the case of baby spinach, the use of low residual ClO2 concentrations (approx. 0.25 mg/L) to treat irrigation water decreased the relative abundance of Pseudomonaceae (2.28-fold) and Enterobacteriaceae (2.5-fold) when comparing treated versus untreated baby spinach. Members of these two bacterial families are responsible for food spoilage and foodborne illnesses. Therefore, a reduction of these bacterial families might be beneficial for the crop and for food safety. In general it can be concluded that the constant application of ClO2 as a disinfection treatment for irrigation water only caused changes in two bacterial families of the baby spinach and soil microbiota, without affecting the major phyla and classes. The significance of these changes in the bacterial community should be further evaluated.
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Affiliation(s)
- Pilar Truchado
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - María Isabel Gil
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
| | - Trevor Suslow
- Department of Plant Science, University of California, One Shields Avenue, Mann Laboratory, Davis, CA, United States of America
| | - Ana Allende
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, Spain
- * E-mail:
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42
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Torres-Cortés G, Bonneau S, Bouchez O, Genthon C, Briand M, Jacques MA, Barret M. Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence. FRONTIERS IN PLANT SCIENCE 2018; 9:902. [PMID: 30008730 PMCID: PMC6034153 DOI: 10.3389/fpls.2018.00902] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/07/2018] [Indexed: 05/03/2023]
Abstract
Microbial interactions occurring on and around seeds are especially important for plant fitness since seed-borne microorganisms are the initial source of inoculum for the plant microbiota. In this study, we analyze structural and functional changes occurring within the plant microbiota at these early stages of the plant cycle, namely germination and emergence. To this purpose, we performed shotgun DNA sequencing of microbial assemblages associated to seeds, germinating seeds and seedlings of two plant species: bean and radish. We observed an enrichment of Enterobacteriales and Pseudomonadales during emergence and a set of functional traits linked to copiotrophy that could be responsible for this selection as a result of an increase of nutrient availability after germination. Representative bacterial isolates of taxa that are selected in seedlings showed indeed faster bacterial growth rate in comparison to seed-associated bacteria isolates. Finally, binning of metagenomics contigs results in the reconstruction of population genomes of the major bacterial taxa associated to the samples. Together, our results demonstrate that, although seed microbiota varied across plant species, nutrient availability during germination elicits changes of the composition of microbial communities by potentially selecting microbial groups with functional traits linked to copiotrophy. The data presented here represents the first attempts to empirically assess changes in the microbial community during plant emergence and moves us toward a more holistic understanding of the plant microbiome.
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Affiliation(s)
| | - Sophie Bonneau
- IRHS, INRA, Agrocampus Ouest, Université d’Angers, Beaucouzé, France
| | | | | | - Martial Briand
- IRHS, INRA, Agrocampus Ouest, Université d’Angers, Beaucouzé, France
| | | | - Matthieu Barret
- IRHS, INRA, Agrocampus Ouest, Université d’Angers, Beaucouzé, France
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43
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Zhang Z, Luo L, Tan X, Kong X, Yang J, Wang D, Zhang D, Jin D, Liu Y. Pumpkin powdery mildew disease severity influences the fungal diversity of the phyllosphere. PeerJ 2018; 6:e4559. [PMID: 29629242 PMCID: PMC5885987 DOI: 10.7717/peerj.4559] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/09/2018] [Indexed: 01/01/2023] Open
Abstract
Phyllosphere microbiota play a crucial role in plant-environment interactions and their microbial community and function are influenced by biotic and abiotic factors. However, there is little research on how pathogens affect the microbial community of phyllosphere fungi. In this study, we collected 16 pumpkin (Cucurbita moschata) leaf samples which exhibited powdery mildew disease, with a severity ranging from L1 (least severe) to L4 (most severe). The fungal community structure and diversity was examined by Illumina MiSeq sequencing of the internal transcribed spacer (ITS) region of ribosomal RNA genes. The results showed that the fungal communities were dominated by members of the Basidiomycota and Ascomycota. The Podosphaera was the most dominant genus on these infected leaves, which was the key pathogen responsible for the pumpkin powdery mildew. The abundance of Ascomycota and Podosphaera increased as disease severity increased from L1 to L4, and was significantly higher at disease severity L4 (P < 0.05). The richness and diversity of the fungal community increased from L1 to L2, and then declined from L2 to L4, likely due to the biotic pressure (i.e., symbiotic and competitive stresses among microbial species) at disease severity L4. Our results could give new perspectives on the changes of the leaf microbiome at different pumpkin powdery mildew disease severity.
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Affiliation(s)
- Zhuo Zhang
- Hunan Academy of Agricultural Sciences, Hunan Plant Protection Institute, Changsha, Hunan, China
| | - Luyun Luo
- Hunan Academy of Agricultural Sciences, Hunan Plant Protection Institute, Changsha, Hunan, China.,College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Xinqiu Tan
- Hunan Academy of Agricultural Sciences, Hunan Plant Protection Institute, Changsha, Hunan, China
| | - Xiao Kong
- Chinese Academy of Sciences Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jianguo Yang
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Duanhua Wang
- Vegetable Research Institute, Hunan Academy of Agricultural Science, Changsha, Hunan, China
| | - Deyong Zhang
- Hunan Academy of Agricultural Sciences, Hunan Plant Protection Institute, Changsha, Hunan, China
| | - Decai Jin
- Chinese Academy of Sciences Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yong Liu
- Hunan Academy of Agricultural Sciences, Hunan Plant Protection Institute, Changsha, Hunan, China
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Kim MJ, Jeon CW, Cho G, Kim DR, Kwack YB, Kwak YS. Comparison of Microbial Community Structure in Kiwifruit Pollens. THE PLANT PATHOLOGY JOURNAL 2018; 34:143-149. [PMID: 29628821 PMCID: PMC5880359 DOI: 10.5423/ppj.nt.12.2017.0281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 05/29/2023]
Abstract
Flowers of kiwifruit are morphologically hermaphroditic and survivable binucleate pollen is produced by the male flowers. In this study, we investigated microbial diversity in kiwifruit pollens by analyzing amplicon sequences of 16S rRNA. Four pollen samples were collected: 'NZ' was imported from New Zealand, 'CN' from China in year of 2014, respectively. 'KR13' and 'KR14' were collected in 2013' and 2014' in South Korea. Most of the identified bacterial phyla in the four different pollens were Proteobacteria, Actinobacteria and Firmicutes. However, the imported and the domestic pollen samples showed different aspects of microbial community structures. The domestic pollens had more diverse in diversity than the imported samples. Among top 20 OTUs, Pseudomonas spp. was the most dominant specie. Interestingly, a bacterial pathogen of kiwifruit canker, Pseudomonas syringae pv. actinidiae was detected in 'NZ' by the specific PCR. This study provides insights microbial distribution and community structure information in kiwifruit pollen.
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Affiliation(s)
- Min-Jung Kim
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | - Chang-Wook Jeon
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Gyongjun Cho
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
| | - Da-Ran Kim
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
| | | | - Youn-Sig Kwak
- Department of Plant Medicine, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju 52828,
Korea
- Dvision of Applied Life Science (BK21plus), Gyeongsang National University, Jinju 52828,
Korea
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45
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Correa-Galeote D, Bedmar EJ, Arone GJ. Maize Endophytic Bacterial Diversity as Affected by Soil Cultivation History. Front Microbiol 2018; 9:484. [PMID: 29662471 PMCID: PMC5890191 DOI: 10.3389/fmicb.2018.00484] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/28/2018] [Indexed: 11/20/2022] Open
Abstract
The bacterial endophytic communities residing within roots of maize (Zea mays L.) plants cultivated by a sustainable management in soils from the Quechua maize belt (Peruvian Andes) were examined using tags pyrosequencing spanning the V4 and V5 hypervariable regions of the 16S rRNA. Across four replicate libraries, two corresponding to sequences of endophytic bacteria from long time maize-cultivated soils and the other two obtained from fallow soils, 793 bacterial sequences were found that grouped into 188 bacterial operational taxonomic units (OTUs, 97% genetic similarity). The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from fallow soils. A mean of 30 genera were found in the fallow soil libraries and 47 were in those from the maize-cultivated soils. Both alpha and beta diversity indexes showed clear differences between bacterial endophytic populations from plants with different soil cultivation history and that the soils cultivated for long time requires a higher diversity of endophytes. The number of sequences corresponding to main genera Sphingomonas, Herbaspirillum, Bradyrhizobium and Methylophilus in the maize-cultivated libraries were statistically more abundant than those from the fallow soils. Sequences of genera Dyella and Sreptococcus were significantly more abundant in the libraries from the fallow soils. Relative abundance of genera Burkholderia, candidatus Glomeribacter, Staphylococcus, Variovorax, Bacillus and Chitinophaga were similar among libraries. A canonical correspondence analysis of the relative abundance of the main genera showed that the four libraries distributed in two clearly separated groups. Our results suggest that cultivation history is an important driver of endophytic colonization of maize and that after a long time of cultivation of the soil the maize plants need to increase the richness of the bacterial endophytes communities.
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Affiliation(s)
- David Correa-Galeote
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Eulogio J Bedmar
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín, Agencia Estatal Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Gregorio J Arone
- Department of Agricultural Sciences, National University of Huancavelica, Huancavelica, Peru
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Malinich EA, Bauer CE. The plant growth promoting bacterium Azospirillum brasilense is vertically transmitted in Phaseolus vulgaris (common bean). Symbiosis 2018. [DOI: 10.1007/s13199-018-0539-2] [Citation(s) in RCA: 16] [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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47
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Lozano YM, Armas C, Hortal S, Casanoves F, Pugnaire FI. Disentangling above- and below-ground facilitation drivers in arid environments: the role of soil microorganisms, soil properties and microhabitat. THE NEW PHYTOLOGIST 2017; 216:1236-1246. [PMID: 28262957 DOI: 10.1111/nph.14499] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/11/2017] [Indexed: 05/22/2023]
Abstract
Nurse plants promote establishment of other plant species by buffering climate extremes and improving soil properties. Soil biota plays an important role, but an analysis to disentangle the effects of soil microorganisms, soil properties and microclimate on facilitation is lacking. In three microhabitats (gaps, small and large Retama shrubs), we placed six microcosms with sterilized soil, two per soil origin (i.e. from each microhabitat). One in every pair received an alive, and the other a sterile, inoculum from its own soil. Seeds of annual plants were sown into the microcosms. Germination, survival and biomass were monitored. Soil bacterial communities were characterized by pyrosequencing. Germination in living Retama inoculum was nearly double that of germination in sterile inoculum. Germination was greater under Retama canopies than in gaps. Biomass was up to three times higher in nurse than in gap soils. Soil microorganisms, soil properties and microclimate showed a range of positive to negative effects on understory plants depending on species identity and life stage. Nurse soil microorganisms promoted germination, but the effect was smaller than the positive effects of soil properties and microclimate under nurses. Nurse below-ground environment (soil properties and microorganisms) promoted plant growth and survival more than nurse microhabitat.
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Affiliation(s)
- Yudi M Lozano
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| | - Cristina Armas
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| | - Sara Hortal
- Western Sydney University, Hawkesbury Institute for the Environment, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Fernando Casanoves
- Unidad de Bioestadística del Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Turrialba, 7170, Costa Rica
| | - Francisco I Pugnaire
- Estación Experimental de Zonas Áridas, Spanish National Research Council (EEZA-CSIC), Carretera de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
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Jongman M, Chidamba L, Korsten L. Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing. J Appl Microbiol 2017; 123:1043-1053. [PMID: 28795469 DOI: 10.1111/jam.13558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/14/2017] [Accepted: 07/24/2017] [Indexed: 11/30/2022]
Abstract
AIMS To investigate the influence of irrigation water microbial quality on leafy green vegetables produced in commercial and small-scale farms as well as homestead gardens using pyrosequencing. METHODS AND RESULTS Next generation sequencing analysis of the V1-V3 hypervariable region of bacterial 16S rDNA was used to compare bacterial diversity in irrigation water sources and on leafy vegetables. In all samples (12) analysed, the phylum Proteobacteria (64·5%), class Gammaproteobacteria (56·6%) and genus Aeromonas (14·4%) were found to be dominant. Of the total Escherichia sequences detected in tested samples, lettuce (16·3%) from the one commercial farm harboured more sequences than cabbage from the small-scale farm (1·3%) or homestead gardens (1·9%). Escherichia sequences were detected in both irrigation water (4·6%) and on cabbage (1·3%) samples from the small-scale farm. The genus Salmonella was absent in borehole water but was detected in the holding dam water (<1%) from commercial farm A. Salmonella sequences were present in river water (<1%) and on cabbages (1·9%) from the small-scale farm but were not detected on cabbage samples from the one commercial farm or the homestead gardens. CONCLUSION Water sources quality used for irrigation greatly influences the microbial dynamics of the irrigated crop. SIGNIFICANCE AND IMPACT OF THE STUDY Microbial biomes in irrigation water and on leafy greens were described with pyrosequencing and revealed insights into prevalence of potential and opportunistic pathogens across different production systems.
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Affiliation(s)
- M Jongman
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
| | - L Chidamba
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
| | - L Korsten
- Department of Plant and Soil Sciences, University of Pretoria, P/Bag X20 Hatfield, Pretoria, South Africa
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49
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Uhlig E, Olsson C, He J, Stark T, Sadowska Z, Molin G, Ahrné S, Alsanius B, Håkansson Å. Effects of household washing on bacterial load and removal of Escherichia coli from lettuce and "ready-to-eat" salads. Food Sci Nutr 2017; 5:1215-1220. [PMID: 29188050 PMCID: PMC5694878 DOI: 10.1002/fsn3.514] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 12/03/2022] Open
Abstract
Customer demands for fresh salads are increasing, but leafy green vegetables have also been linked to food‐borne illness due to pathogens such as Escherichia coli O157:H7. As a safety measure, consumers often wash leafy vegetables in water before consumption. In this study, we analyzed the efficiency of household washing to reduce the bacterial content. Romaine lettuce and ready‐to‐eat mixed salad were washed several times in flowing water at different rates and by immersing the leaves in water. Lettuce was also inoculated with E. coli before washing. Only washing in a high flow rate (8 L/min) resulted in statistically significant reductions (p < .05), “Total aerobic count” was reduced by 80%, and Enterobacteriaceae count was reduced by 68% after the first rinse. The number of contaminating E. coli was not significantly reduced. The dominating part of the culturable microbiota of the washed lettuce was identified by rRNA 16S sequencing of randomly picked colonies. The majority belonged to Pseudomonadaceae, but isolates from Enterobacteriaceae and Staphylococcaceaceae were also frequently found. This study shows the inefficiency of tap water washing methods available for the consumer when it comes to removal of bacteria from lettuce. Even after washing, the lettuce contained high levels of bacteria that in a high dose and under certain circumstances may constitute a health risk.
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Affiliation(s)
- Elisabeth Uhlig
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Crister Olsson
- Department of Biosystems and Technology Swedish University of Agricultural Sciences Alnarp Sweden
| | - Jiayi He
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Therese Stark
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Zuzanna Sadowska
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Göran Molin
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Siv Ahrné
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
| | - Beatrix Alsanius
- Department of Biosystems and Technology Swedish University of Agricultural Sciences Alnarp Sweden
| | - Åsa Håkansson
- Department of Food Technology, Engineering and Nutrition Lund University Lund Sweden
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Truchado P, Gil MI, Reboleiro P, Rodelas B, Allende A. Impact of solar radiation exposure on phyllosphere bacterial community of red-pigmented baby leaf lettuce. Food Microbiol 2017; 66:77-85. [PMID: 28576376 DOI: 10.1016/j.fm.2017.03.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 03/24/2017] [Accepted: 03/29/2017] [Indexed: 11/27/2022]
Abstract
Solar radiation has been identified as a stress factor affecting phyllosphere associated bacteria colonization and survival during primary production. In the present study, the impact of different solar radiation doses on the phyllosphere microbiota of red-pigmented baby leaf lettuce cultivated in open field under commercial conditions was evaluated. Four weeks before harvest, the growing field was divided into four plots; each one was consecutively covered with one-week-interval with a light-excluding plastic to reduce the sunlight exposure. Four different solar radiation treatments were generated and cumulative photosynthetically active radiation (PAR) was used to differentiate treatments as follows: 4889 ± 428 μmol/m2/s (uncovered), 4265 ± 356 μmol/m2/s (covered for 1 week), 3602 ± 225 μmol/m2/s (covered for 2 weeks) and 3115 ± 313 μmol/m2/s (covered for 3 weeks). The size and composition of the phyllosphere bacterial community were determined by cultivation-depended (plate count) and independent (qPCR) techniques. Exposure to decreased levels of cumulative PAR did not produce significant differences in total bacterial community size, regardless of the chosen quantification techniques. However, total bacteria size quantified by qPCR was around 3.5 orders of magnitude higher than those obtained by plate count. The observed differences between cultivation-depended and independent techniques could be attributed to the presence of non-viable or viable but non-culturable (VBNC) bacteria. The bacterial community structure was analyzed using temperature gradient gel electrophoresis (TGGE), and significant differences were detected when the four solar treatment were compared. A qPCR approach was applied to the quantification of specific bacterial phyla and classes, previously identified in the phyllosphere of plants available literature, confirming that Proteobacteria, Bacteroidetes, Actinobacterias and Firmicutes were the most abundantly represented phyla in lettuce. Treatment comparison revealed higher proportions of Gammaproteobacteria as opposed to the Betaproteobacteria on the lettuce exposed to the lowest cumulative PAR dose (3115 ± 313 μmol/m2/s). The obtained results demonstrated that the solar radiation is a relevant environmental factor influencing the relative abundance of specific-groups of phyllosphere-associated bacteria in pigmented baby leaf lettuce.
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Affiliation(s)
- Pilar Truchado
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - M Isabel Gil
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain
| | - Patricia Reboleiro
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, Granada, Spain; Instituto del Agua, Universidad de Granada, Granada, Spain
| | - Belén Rodelas
- Departamento de Microbiología, Facultad de Farmacia, Universidad de Granada, Granada, Spain; Instituto del Agua, Universidad de Granada, Granada, Spain
| | - Ana Allende
- Research Group on Quality, Safety and Bioactivity of Plant Foods, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 30100, Murcia, Spain.
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