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Meepagala KM, Anderson CM, Techen N, Duke SO. Pantoea ananatis, a plant growth stimulating bacterium, and its metabolites isolated from Hydrocotyle umbellata (dollarweed). PLANT SIGNALING & BEHAVIOR 2024; 19:2331894. [PMID: 38516998 PMCID: PMC10962587 DOI: 10.1080/15592324.2024.2331894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/22/2024] [Indexed: 03/23/2024]
Abstract
A bacterium growing on infected leaves of Hydrocotyle umbellata, commonly known as dollarweed, was isolated and identified as Pantoea ananatis. An ethyl acetate extract of tryptic soy broth (TSB) liquid culture filtrate of the bacterium was subjected to silica gel chromatography to isolate bioactive molecules. Indole was isolated as the major compound that gave a distinct, foul odor to the extract, together with phenethyl alcohol, phenol, tryptophol, N-acyl-homoserine lactone, 3-(methylthio)-1-propanol, cyclo(L-pro-L-tyr), and cyclo(dehydroAla-L-Leu). This is the first report of the isolation of cyclo(dehydroAla-L-Leu) from a Pantoea species. Even though tryptophol is an intermediate in the indoleacetic acid (IAA) pathway, we were unable to detect or isolate IAA. We investigated the effect of P. ananatis inoculum on the growth of plants. Treatment of Lemna paucicostata Hegelm plants with 4 × 109 colony forming units of P. ananatis stimulated their growth by ca. five-fold after 13 days. After 13 days of treatment, some control plants were browning, but treated plants were greener and no plants were browning. The growth of both Cucumis sativus (cucumber) and Sorghum bicolor (sorghum) plants was increased by ca. 20 to 40%, depending on the growth parameter and species, when the rhizosphere was treated with the bacterium after germination at the same concentration. Plant growth promotion by Pantoea ananatis could be due to the provision of the IAA precursor indole.
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Affiliation(s)
- Kumudini M. Meepagala
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
| | - Caleb M. Anderson
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, University, USA
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Natascha Techen
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
| | - Stephen O. Duke
- National Center for Natural Products Research, School of Pharmacy, University of Mississippi, University, USA
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Crosby KC, Rojas M, Sharma P, Johnson MA, Mazloom R, Kvitko BH, Smits THM, Venter SN, Coutinho TA, Heath LS, Palmer M, Vinatzer BA. Genomic delineation and description of species and within-species lineages in the genus Pantoea. Front Microbiol 2023; 14:1254999. [PMID: 38029109 PMCID: PMC10665919 DOI: 10.3389/fmicb.2023.1254999] [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: 07/08/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.
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Affiliation(s)
- Katherine C. Crosby
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Mariah Rojas
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Parul Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Marcela A. Johnson
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Theo H. M. Smits
- Environmental Genomics and System Biology Research Group, Institute of Natural Resource Sciences, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Stephanus N. Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Teresa A. Coutinho
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Lenwood S. Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, United States
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, United States
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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Howard M, Maki JJ, Connelly S, Hardy DJ, Cameron A. Complete genome sequence of a human bacteremia isolate of Kalamiella piersonii. Microbiol Resour Announc 2023; 12:e0029323. [PMID: 37650621 PMCID: PMC10508118 DOI: 10.1128/mra.00293-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/02/2023] [Indexed: 09/01/2023] Open
Abstract
The complete genome of Kalamiella piersonii clinical isolate URMC-2103A041 from human bacteremia was determined using the hybrid assembly of short- and long-read sequencing chemistry. The genome contains a 3.93 Mb chromosome, three circular plasmids, and one linear plasmid.
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Affiliation(s)
- Mondraya Howard
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Joel J. Maki
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Sara Connelly
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Dwight J. Hardy
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, USA
| | - Andrew Cameron
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
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Zhang Y, Fan Y, Zhan Y, Wang H, Li X, Wang H, Feng T, Shi L, Wang J, Wang H, Lu Z. Genomic characterization of Pantoea anthophila strain UI705 causing urinary tract infections in China. Front Cell Infect Microbiol 2023; 13:1208473. [PMID: 37520438 PMCID: PMC10375405 DOI: 10.3389/fcimb.2023.1208473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Pantoea anthophila (P. anthophila) is a Gram-negative bacterium initially isolated from Impatiens balsamina in India. P. anthophila has been characterized with low pathogenicity, and no human infections caused by this organism have been reported yet. We report the first case of urinary tract infection caused by P. anthophila in a 73-year-old man after bladder cancer surgery. Methods The bacterial isolate gained from urine was named UI705 and identified as P. anthophila by MALDI-TOF mass spectrometry. The genome sequencing and analysis were performed to further characterize the pathogenesis of the clinical isolate. Result and discussion To the best of our knowledge, this is the first report of human infection caused by P. anthophila in China. The draft genome sequence of P. anthophila UI705 provides a fundamental resource for subsequent investigation of its virulence factors, antibiotic resistance, host-pathogen interactions, and comparative genomics of genus Pantoea.
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Affiliation(s)
- Yingmiao Zhang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Fan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhan
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao Wang
- Department of Medical Laboratory, Shiyan Hospital of Integrated Traditional and Western Medicine, Shiyan, China
| | - Xun Li
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tian Feng
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lifeng Shi
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Wang
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongxin Lu
- Department of Medical Laboratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Research Institute of Wuhan, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Okhrimenko IS, Kovalev K, Petrovskaya LE, Ilyinsky NS, Alekseev AA, Marin E, Rokitskaya TI, Antonenko YN, Siletsky SA, Popov PA, Zagryadskaya YA, Soloviov DV, Chizhov IV, Zabelskii DV, Ryzhykau YL, Vlasov AV, Kuklin AI, Bogorodskiy AO, Mikhailov AE, Sidorov DV, Bukhalovich S, Tsybrov F, Bukhdruker S, Vlasova AD, Borshchevskiy VI, Dolgikh DA, Kirpichnikov MP, Bamberg E, Gordeliy VI. Mirror proteorhodopsins. Commun Chem 2023; 6:88. [PMID: 37130895 PMCID: PMC10154332 DOI: 10.1038/s42004-023-00884-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023] Open
Abstract
Proteorhodopsins (PRs), bacterial light-driven outward proton pumps comprise the first discovered and largest family of rhodopsins, they play a significant role in life on the Earth. A big remaining mystery was that up-to-date there was no described bacterial rhodopsins pumping protons at acidic pH despite the fact that bacteria live in different pH environment. Here we describe conceptually new bacterial rhodopsins which are operating as outward proton pumps at acidic pH. A comprehensive function-structure study of a representative of a new clade of proton pumping rhodopsins which we name "mirror proteorhodopsins", from Sphingomonas paucimobilis (SpaR) shows cavity/gate architecture of the proton translocation pathway rather resembling channelrhodopsins than the known rhodopsin proton pumps. Another unique property of mirror proteorhodopsins is that proton pumping is inhibited by a millimolar concentration of zinc. We also show that mirror proteorhodopsins are extensively represented in opportunistic multidrug resistant human pathogens, plant growth-promoting and zinc solubilizing bacteria. They may be of optogenetic interest.
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Affiliation(s)
- Ivan S Okhrimenko
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Lada E Petrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Alexey A Alekseev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Tatyana I Rokitskaya
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri N Antonenko
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey A Siletsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Petr A Popov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yuliya A Zagryadskaya
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | | | - Igor V Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | | | - Yury L Ryzhykau
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexey V Vlasov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Alexander I Kuklin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Andrey O Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anatolii E Mikhailov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Daniil V Sidorov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Siarhei Bukhalovich
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Fedor Tsybrov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey Bukhdruker
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Anastasiia D Vlasova
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin I Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Dubna, Russia
| | - Dmitry A Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow, Russia
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin I Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, Grenoble, France.
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Susanto M, Dunning J, Chew R. Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review. Clin Case Rep 2023; 11:e7351. [PMID: 37215972 PMCID: PMC10196424 DOI: 10.1002/ccr3.7351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/11/2022] [Accepted: 05/02/2023] [Indexed: 05/24/2023] Open
Abstract
Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.
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Affiliation(s)
- Maja Susanto
- Infectious Diseases UnitRedcliffe HospitalRedcliffeQueenslandAustralia
| | - Jacki Dunning
- Department of SurgeryAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
| | - Rusheng Chew
- Infectious Diseases UnitAlice Springs HospitalAlice SpringsNorthern TerritoryAustralia
- Faculty of MedicineUniversity of QueenslandBrisbaneQueenslandAustralia
- Centre for Tropical Medicine and Global HealthUniversity of OxfordOxfordUK
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Bragard C, Baptista P, Chatzivassiliou E, Di Serio F, Gonthier P, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas‐Cortes JA, Parnell S, Potting R, Stefani E, Thulke H, Van der Werf W, Civera AV, Yuen J, Zappalà L, Migheli Q, Vloutoglou I, Maiorano A, Streissl F, Reignault PL. Pest categorisation of Pantoea ananatis. EFSA J 2023; 21:e07849. [PMID: 36895574 PMCID: PMC9989851 DOI: 10.2903/j.efsa.2023.7849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
The EFSA Plant Health Panel performed a pest categorisation of Pantoea ananatis, a Gram-negative bacterium belonging to the Erwiniaceae family. P. ananatis is a well-defined taxonomic unit; nonetheless, its pathogenic nature is not well defined and non-pathogenic populations are known to occupy several, very different environmental niches as saprophytes, or as plant growth promoting bacteria or biocontrol agents. It is also described as a clinical pathogen causing bacteraemia and sepsis or as a member of the gut microbiota of several insects. P. ananatis is the causal agent of different diseases affecting numerous crops: in particular, centre rot of onion, bacterial leaf blight and grain discoloration of rice, leaf spot disease of maize and eucalyptus blight/dieback. A few insect species have been described as vectors of P. ananatis, among them, Frankliniella fusca and Diabrotica virgifera virgifera. This bacterium is present in several countries in Europe, Africa, Asia, North and South America, and Oceania from tropical and subtropical regions to temperate areas worldwide. P. ananatis has been reported from the EU territory, both as pathogen on rice and maize and as an environmental, non-pathogenic bacterium in rice marshes and poplar rhizosoil. It is not included in EU Commission Implementing Regulation 2019/2072. The pathogen can be detected on its host plants using direct isolation, or PCR-based methods. The main pathway for the entry of the pathogen into the EU territory is host plants for planting, including seeds. In the EU, there is a large availability of host plants, with onion, maize, rice and strawberry being the most important ones. Therefore, disease outbreaks are possible almost at any latitude, except in the most northern regions. P. ananatis is not expected to have frequent or consistent impact on crop production and is not expected to have any environmental impact. Phytosanitary measures are available to mitigate the further introduction and spread of the pathogen into the EU on some hosts. The pest does not satisfy the criteria, which are within the remit for EFSA to evaluate whether the pest meets the definition of a Union quarantine pest. P. ananatis is probably widely distributed in different ecosystems in the EU. It may impact some specific hosts such as onions while on other hosts such as rice it has been reported as a seed microbiota without causing any impact and can even be beneficial to plant growth. Hence, the pathogenic nature of P. ananatis is not fully established.
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Zrelovs N, Jansons J, Kazaka T, Kazaks A, Dislers A. Three Phages One Host: Isolation and Characterization of Pantoea agglomerans Phages from a Grasshopper Specimen. Int J Mol Sci 2023; 24:ijms24031820. [PMID: 36768143 PMCID: PMC9915841 DOI: 10.3390/ijms24031820] [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: 12/20/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
The bacterial genus Pantoea comprises species found in a variety of different environmental sources. Pantoea spp. are often recovered from plant material and are capable of both benefitting the plants and acting like phytopathogens. Some species of Pantoea (including P. agglomerans) are considered opportunistic human pathogens capable of causing various infections in immunocompromised subjects. In this study, a strain of P. agglomerans (identified by 16S rRNA gene sequencing) was isolated from a dead specimen of an unidentified Latvian grasshopper species. The retrieved strain of P. agglomerans was then used as a host for the potential retrieval of phages from the same source material. After rounds of plaque purification and propagation, three high-titer lysates corresponding to putatively distinct phages were acquired. Transmission electron microscopy revealed that one of the phages was a myophage with an unusual morphology, while the two others were typical podophages. Whole-genome sequencing (WGS) was performed for each of these isolated phages. Genome de novo assembly and subsequent functional annotation confirmed that three different strictly lytic phages were isolated. Elaborate genomic characterization of the acquired phages was performed to elucidate their place within the so-far-uncovered phage diversity.
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An X, Sun M, Ren K, Xu M, Wang Z, Li Y, Liu H, Lian B. Effect and mechanism of the improvement of coastal silt soil by application of organic fertilizer and gravel combined with Sesbania cannabina cultivation. FRONTIERS IN PLANT SCIENCE 2022; 13:1092089. [PMID: 36618651 PMCID: PMC9815860 DOI: 10.3389/fpls.2022.1092089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Jiangsu Province of China has a large area of coastal silt soil (CSS) with poor permeability, high salinity, and poor nutrients, which brings great difficulties to the development and utilization of coastal zones, so that needs to be improved as a matter of urgency. In this study, river-sand, serpentine, and organic fertilizer were used as additives in CSS, and Sesbania cannabina, a salt-tolerant cash crop, was planted in these differently treated soils. Through high-throughput sequencing, analysis of soil physico-chemical properties, and detection of plant growth status, the rhizosphere bacterial diversity of S. cannabina growing in CSS under different treatments and their environmental impact factors were studied, while exploring the effect and mechanism of organic fertilizer combined with gravel as a CSS modifier. The results implied that single application of organic fertilizer could significantly increase the fertility levels of total nitrogen (TN), total organic carbon (TOC) and Avail. P in CSS; then, the application of organic fertilizer with river-sand significantly reduced salt content and alkalinity of soil; meanwhile, in the treatment of single application of organic fertilizer and application of organic fertilizer combined with river-sand, the rhizosphere of S. cannabina enriched the bacterial communities of organic matter degradation and utilization to varying degrees. The soil moisture content and indicators related to saline-alkali soil (including total salt, electrical conductivity (EC), exchangeable sodium percentage (ESP), Avail. Na and Avail. K, etc.) were further reduced significantly by the application of organic fertilizer combined with river-sand and serpentine. The method has greatly improved the growth conditions of S. cannabina and promoted the positive development of its rhizosphere bacterial community. Among them, in the treatment of organic fertilizer combined with river-sand and serpentine, a variety of plant growth-promoting rhizobacteria (PGPR, such as Sphingomonas, Ensifer, and Rhodobacter) and nitrogen-cycle-related bacteria (such as nitrate-reduction-related bacteria, nitrogen-fixing bacteria like Ensifer, and purple non-sulfur photosynthetic bacteria like Rhodobacter) were enriched in the rhizosphere of S. cannabina; moreover, the mutual association and robustness of bacterial co-occurrence networks have been significantly enhanced. The results provide a theoretical basis and reference model for the improvement of coastal saline-alkali silt soil.
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Cross-Over Pathogenic Bacteria Detected in Infected Tomatoes ( Solanum lycopersicum L.) and Peppers ( Capsicum annuum L.) in Bulgaria. Pathogens 2022; 11:pathogens11121507. [PMID: 36558841 PMCID: PMC9783152 DOI: 10.3390/pathogens11121507] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
The ability of certain human pathogens to adapt to plants without losing their virulence toward people is a major concern today. Thus, the aim of the present work was the investigation of the presence of cross-over pathogenic bacteria in infected tomato and pepper plants. The objects of the study were 21 samples from seven different parts of the plants and three from tomato rhizosphere. In total, 26 strains were isolated, identified by MALDI-TOF, and phenotypically characterized. The PCR amplification of the rpoB gene was applied as an approach for the rapid detection of cross-over pathogens in plant samples. A great bacterial diversity was revealed from tomato samples as nine species were identified (Leclercia adecarboxylata, Pseudesherichia vulneris, Enterobacter cancerogenus, Enterobacter cloacae, Enterobacter bugandensis, Acinetobacter calcoaceticus, Pantoea agglomerans, Pantoea ananatis, and Pectobacterium carotovorum). Polymicrobial contaminations were observed in samples T2 (tomato flower) and T10 (tomato fruit). Five species were identified from pepper samples (P. agglomerans, L. adecarboxylata, Pseudomonas sp., Pseudomonas putida, and Enterococcus sp.). Antibiotic resistance patterns were assigned in accordance with EFSA recommendations. All isolates showed varying resistance to the tested antibiotics. The genetic basis for the phenotypic antibiotic resistance was not revealed. No genes for the virulence factors were found among the population. To our knowledge, this is the first overall investigation of tomato and pepper cross-over pathogenic bacterial populations in Bulgaria.
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Yu QZ, Hu MY, Wang L, Lin JQ, Fang SG. Incubation determines favorable microbial communities in Chinese alligator nests. Front Microbiol 2022; 13:983808. [PMID: 36312961 PMCID: PMC9606745 DOI: 10.3389/fmicb.2022.983808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022] Open
Abstract
Nest materials are a major heat source due to rotting promoted by microbial activity. Additionally, they are a potential microbial source given their direct contact with eggshells. Microbial dynamics during incubation have been studied in wild birds; however, similar studies in reptiles remain elusive. Here, the study characterized microbial communities in the nest materials of Chinese alligator (Alligator sinensis) using high-throughput sequencing of bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) region sequences. The results showed that significant changes in the diversity and structure of microbial communities according to different incubation periods. The diversity and richness of bacterial species increased significantly over time, but the relative abundance of the most dominant bacteria in pre-incubation period, including some pathogenic bacteria, declined after incubation. In contrast, fungal species diversity and richness decreased significantly with time. Additionally, nest material composition significantly influenced microbial community structure rather than species diversity and richness. Notably, the fungal community structure showed a stronger response than bacteria to nest material composition, which varied due to differences in plant litter composition. Our results demonstrate the significant response of microbial community diversity and structure to differences in incubation periods and nest material composition in reptiles. It is further emphasized that the importance of incubation period in the conservation of the Chinese alligator and could inform similar studies in other reptiles and birds.
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Affiliation(s)
- Qin-Zhang Yu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Meng-Yuan Hu
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Li Wang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian-Qing Lin
- Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, Guangdong Provincial Key Laboratory of Marine Biotechnology, Institute of Marine Science, Shantou University, Shantou, China
| | - Sheng-Guo Fang
- The Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, State Conservation Center for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, China
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12
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Prasad R, Patton MJ, Floyd JL, Fortmann S, DuPont M, Harbour A, Wright J, Lamendella R, Stevens BR, Oudit GY, Grant MB. Plasma Microbiome in COVID-19 Subjects: An Indicator of Gut Barrier Defects and Dysbiosis. Int J Mol Sci 2022; 23:9141. [PMID: 36012406 PMCID: PMC9409329 DOI: 10.3390/ijms23169141] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/16/2022] Open
Abstract
The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) complications. We aimed to investigate whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n = 146) and healthy individuals (n = 47) were collected during hospitalization and routine visits. Plasma microbiome was analyzed using 16S rRNA sequencing and gut permeability markers including fatty acid binding protein 2 (FABP2), peptidoglycan (PGN), and lipopolysaccharide (LPS) in both patient cohorts. Plasma samples of both cohorts contained predominately Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria. COVID-19 subjects exhibit significant dysbiosis (p = 0.001) of the plasma microbiome with increased abundance of Actinobacteria spp. (p = 0.0332), decreased abundance of Bacteroides spp. (p = 0.0003), and an increased Firmicutes:Bacteroidetes ratio (p = 0.0003) compared to healthy subjects. The concentration of the plasma gut permeability marker FABP2 (p = 0.0013) and the gut microbial antigens PGN (p < 0.0001) and LPS (p = 0.0049) were significantly elevated in COVID-19 patients compared to healthy subjects. These findings support the notion that the intestine may represent a source for bacteremia and contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.
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Affiliation(s)
- Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Michael John Patton
- Hugh Kaul Precision Medicine Institute, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jason Levi. Floyd
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Seth Fortmann
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Mariana DuPont
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | - Angela Harbour
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
| | | | | | - Bruce R. Stevens
- Department of Physiology and Functional Genomics, University of Florida, Gainesville, FL 32611, USA
| | - Gavin Y. Oudit
- Division of Cardiology, Department of Medicine, University of Alberta, Mazankowski Alberta Heart Institute, Edmonton, AB T6G 2B7, Canada
| | - Maria B. Grant
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, 1670 University BLVD, VH490, Birmingham, AL 35294, USA
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13
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Yuvarajan S, Hameed A, Bhagwath Arun A, Kanekar S, Rekha PD. Urease-negative uropathogen Kalamiella piersonii YU22 metabolizes urea by urea carboxylase and allophanate hydrolase enzyme system. Microbiol Res 2022; 263:127142. [DOI: 10.1016/j.micres.2022.127142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
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14
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Abstract
The widely distributed, essential redox factor pyrroloquinoline quinone (PQQ, methoxatin) (1) was discovered in the mid-1960s. The breadth and depth of its biological effects are steadily being revealed, and understanding its biosynthesis at the genomic level is a continuing process. In this review, aspects of the chemistry, biology, biosynthesis, and commercial production of 1 at the gene level, and some applications, are presented from discovery through to mid-2021.
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Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, Illinois 60202, United States.,Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
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15
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Negatively regulated aerobactin and desferrioxamine E by Fur in Pantoea ananatis are required for full siderophore production and antibacterial activity, but not for virulence. Appl Environ Microbiol 2022; 88:e0240521. [PMID: 35108090 DOI: 10.1128/aem.02405-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pantoea ananatis is an emerging plant pathogen that causes disease in economically important crops such as rice, corn, onion, melon, and pineapple, and it also infects humans and insects. In this study, we identified biosynthetic gene clusters of aerobactin and desferrioxamine E (DFO-E) siderophores using the complete genome of P. ananatis PA13 isolated from rice sheath rot. P. ananatis PA13 exhibited the strongest antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). Mutants of aerobactin or DFO-E maintained antibacterial activity against E. amylovora and Y. enterocolitica, as well as in a siderophore activity assay. However, double aerobactin- and DFO-E-gene-deletion mutants completely lost siderophore and antibacterial activity. These results reveal that both siderophore biosynthetic gene clusters are essential for siderophore production and antibacterial activity in P. ananatis PA13. A ferric uptake regulator protein (Fur) mutant exhibited a significant increase in siderophore production, and a Fur-overexpressing strain completely lost antibacterial activity. Expression of the iucA, dfoJ, and foxA genes was significantly increased in the Δfur mutant background, and expression of these genes returned to wild type levels after fur compensation. These results indicate that Fur negatively regulates aerobactin and DFO-E siderophores. However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment. This study is the first to report the regulation and functional characteristics of siderophore biosynthetic genes in P. ananatis. IMPORTANCE Pantoea ananatis is a bacterium that causes diseases in several economically important crops, as well as in insects and humans. This bacterium has been studied extensively as a potentially dangerous pathogen due to its saprophytic ability. Recently, the types, biosynthetic gene clusters, and origin of the siderophores in the Pantoea genus were determined using genome comparative analyses. However, few genetic studies have investigated the characteristics and functions of siderophores in P. ananatis. The results of this study revealed that the production of aerobactin and desferrioxamine E in the rice pathogen P. ananatis PA13 is negatively regulated by Fur, and that these siderophores are essential for antibacterial activity against Erwinia amylovora and Yersinia enterocolitica (Enterobacterales). However, siderophore production was not required for P. ananatis virulence in plants, but it appears to be involved in the microbial ecology surrounding the plant environment.
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16
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Yoshimura M, Tokushige C, Maruyama JI, Kawano Y, Ishikura H, Matsunaga A, Takata T, Hiromatsu K, Yanagihara I, Togawa A, Takamatsu Y. Emerging Resistance to Beta-lactams in Pantoea ananatis Isolated from an Immunocompetent Patient with Bacteremia. Diagn Microbiol Infect Dis 2022; 102:115633. [DOI: 10.1016/j.diagmicrobio.2022.115633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 12/18/2021] [Accepted: 01/04/2022] [Indexed: 01/04/2023]
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17
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Boya BR, Kumar P, Lee JH, Lee J. Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. Microorganisms 2021; 9:microorganisms9102156. [PMID: 34683477 PMCID: PMC8537960 DOI: 10.3390/microorganisms9102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.
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18
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A Phosphonate Natural Product Made by Pantoea ananatis is Necessary and Sufficient for the Hallmark Lesions of Onion Center Rot. mBio 2021; 12:mBio.03402-20. [PMID: 33531390 PMCID: PMC7858074 DOI: 10.1128/mbio.03402-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Pantoea ananatis is the primary cause of onion center rot. Genetic data suggest that a phosphonic acid natural product is required for pathogenesis; however, the nature of the molecule is unknown. Here, we show that P. ananatis produces at least three phosphonates, two of which were purified and structurally characterized. The first, designated pantaphos, was shown to be 2-(hydroxy[phosphono]methyl)maleate; the second, a probable biosynthetic precursor, was shown to be 2-(phosphonomethyl)maleate. Purified pantaphos is both necessary and sufficient for the hallmark lesions of onion center rot. Moreover, when tested against mustard seedlings, the phytotoxic activity of pantaphos was comparable to the widely used herbicides glyphosate and phosphinothricin. Pantaphos was also active against a variety of human cell lines but was significantly more toxic to glioblastoma cells. Pantaphos showed little activity when tested against a variety of bacteria and fungi.IMPORTANCE Pantoea ananatis is a significant plant pathogen that targets a number of important crops, a problem that is compounded by the absence of effective treatments to prevent its spread. Our identification of pantaphos as the key virulence factor in onion center rot suggests a variety of approaches that could be employed to address this significant plant disease. Moreover, the general phytotoxicity of the molecule suggests that it could be developed into an effective herbicide to counter the alarming rise in herbicide-resistant weeds.
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19
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Choi O, Kang B, Lee Y, Lee Y, Kim J. Pantoea ananatis carotenoid production confers toxoflavin tolerance and is regulated by Hfq-controlled quorum sensing. Microbiologyopen 2020; 10:e1143. [PMID: 33269542 PMCID: PMC7883899 DOI: 10.1002/mbo3.1143] [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: 10/06/2020] [Revised: 11/09/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
Carotenoids are widely used in functional foods, cosmetics, and health supplements, and their importance and scope of use are continuously expanding. Here, we characterized carotenoid biosynthetic genes of the plant‐pathogenic bacterium Pantoea ananatis, which carries a carotenoid biosynthetic gene cluster (including crtE, X, Y, I, B, and Z) on a plasmid. Reverse transcription–polymerase chain reaction (RT‐PCR) analysis revealed that the crtEXYIB gene cluster is transcribed as a single transcript and crtZ is independently transcribed in the opposite direction. Using splicing by overlap extension with polymerase chain reaction (SOE by PCR) based on asymmetric amplification, we reassembled crtE–B, crtE–B–I, and crtE–B–I–Y. High‐performance liquid chromatography confirmed that Escherichia coli expressing the reassembled crtE–B, crtE–B–I, and crtE–B–I–Y operons produced phytoene, lycopene, and β‐carotene, respectively. We found that the carotenoids conferred tolerance to UV radiation and toxoflavin. Pantoea ananatis shares rice environments with the toxoflavin producer Burkholderia glumae and is considered to be the first reported example of producing and using carotenoids to withstand toxoflavin. We confirmed that carotenoid production by P. ananatis depends on RpoS, which is positively regulated by Hfq/ArcZ and negatively regulated by ClpP, similar to an important regulatory network of E. coli (HfqArcZ →RpoS Ͱ ClpXP). We also demonstrated that Hfq‐controlled quorum signaling de‐represses EanR to activate RpoS, thereby initiating carotenoid production. Survival genes such as those responsible for the production of carotenoids of the plant‐pathogenic P. ananatis must be expressed promptly to overcome stressful environments and compete with other microorganisms. This mechanism is likely maintained by a brake with excellent performance, such as EanR.
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Affiliation(s)
- Okhee Choi
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea
| | - Byeongsam Kang
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yongsang Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, Korea
| | - Yeyeong Lee
- Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
| | - Jinwoo Kim
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Korea.,Division of Applied Life Science, Gyeongsang National University, Jinju, Korea.,Department of Plant Medicine, Gyeongsang National University, Jinju, Korea
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20
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Scheiner R, Strauß S, Thamm M, Farré-Armengol G, Junker RR. The Bacterium Pantoea ananatis Modifies Behavioral Responses to Sugar Solutions in Honeybees. INSECTS 2020; 11:insects11100692. [PMID: 33053745 PMCID: PMC7601739 DOI: 10.3390/insects11100692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
1. Honeybees, which are among the most important pollinators globally, do not only collect pollen and nectar during foraging but may also disperse diverse microbes. Some of these can be deleterious to agricultural crops and forest trees, such as the bacterium Pantoea ananatis, an emerging pathogen in some systems. P. ananatis infections can lead to leaf blotches, die-back, bulb rot, and fruit rot. 2. We isolated P. ananatis bacteria from flowers with the aim of determining whether honeybees can sense these bacteria and if the bacteria affect behavioral responses of the bees to sugar solutions. 3. Honeybees decreased their responsiveness to different sugar solutions when these contained high concentrations of P. ananatis but were not deterred by solutions from which bacteria had been removed. This suggests that their reduced responsiveness was due to the taste of bacteria and not to the depletion of sugar in the solution or bacteria metabolites. Intriguingly, the bees appeared not to taste ecologically relevant low concentrations of bacteria. 4. Synthesis and applications. Our data suggest that honeybees may introduce P. ananatis bacteria into nectar in field-realistic densities during foraging trips and may thus affect nectar quality and plant fitness.
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Affiliation(s)
- Ricarda Scheiner
- Behavioral Physiology & Sociobiology, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (M.T.)
| | - Sina Strauß
- Behavioral Physiology & Sociobiology, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (M.T.)
| | - Markus Thamm
- Behavioral Physiology & Sociobiology, Biocenter, Am Hubland, University of Würzburg, 97074 Würzburg, Germany; (S.S.); (M.T.)
| | - Gerard Farré-Armengol
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria; (G.F.-A.); (R.R.J.)
| | - Robert R. Junker
- Department of Biosciences, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria; (G.F.-A.); (R.R.J.)
- Evolutionary Ecology of Plants, Department Biodiversity of Plants, Faculty of Biology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, 35043 Marburg, Germany
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21
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Zhang H, Zhang Q, Chen S, Zhang Z, Song J, Long Z, Yu Y, Fang H. Enterobacteriaceae predominate in the endophytic microbiome and contribute to the resistome of strawberry. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 727:138708. [PMID: 32334231 DOI: 10.1016/j.scitotenv.2020.138708] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 05/21/2023]
Abstract
Antibiotic resistance genes (ARGs) harbored by plant microbiomes have been implicated as a potential risk to public health via food chain, especially directly edible fruits and vegetables. Here, we investigated the microbiome and antibiotic resistome in soil-strawberry ecosystem using shotgun metagenomic sequencing. The results showed that the enterobacterial population dominated the endophytes of strawberry fruits. Moreover, 85 subtypes of ARGs, including several clinically important ARGs, were detected in the strawberry fruit metagenomes. Additionally, host tracking analysis in combination with antibiotic-resistant bacterial isolate screening suggested that fruit-borne ARGs were mainly carried by members of the Enterobacteriaceae family. Unexpectedly, most of fruit-borne isolates were found to be resistant to several clinically important antimicrobials, e.g., erythromycin and cephalexin. Our findings provide broad insights into endophytic antibiotic resistomes of direct edible strawberry fruits and their potential hosts, and highlight the potential exposure risks of plant microbiomes to the human food chain.
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Affiliation(s)
- Houpu Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianke Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shiyu Chen
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zihan Zhang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiajin Song
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhengnan Long
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunlong Yu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Fang
- Institute of Pesticide and Environmental Toxicology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China; Key laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Zhejiang University, Hangzhou 310058, China; Key laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou 310058, China.
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22
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Kim JS, Yoon SJ, Park YJ, Kim SY, Ryu CM. Crossing the kingdom border: Human diseases caused by plant pathogens. Environ Microbiol 2020; 22:2485-2495. [PMID: 32307848 DOI: 10.1111/1462-2920.15028] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 12/16/2022]
Abstract
Interactions between pathogenic microorganisms and their hosts are varied and complex, encompassing open-field scale interactions to interactions at the molecular level. The capacity of plant pathogenic bacteria and fungi to cause diseases in human and animal systems was, until recently, considered of minor importance. However, recent evidence suggests that animal and human infections caused by plant pathogenic fungi, bacteria and viruses may have critical impacts on human and animal health and safety. This review analyses previous research on plant pathogens as causal factors of animal illness. In addition, a case study involving disruption of type III effector-mediated phagocytosis in a human cell line upon infection with an opportunistic phytopathogen, Pseudomonas syringae pv. tomato, is discussed. Further knowledge regarding the molecular interactions between plant pathogens and human and animal hosts is needed to understand the extent of disease incidence and determine mechanisms for disease prevention.
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Affiliation(s)
- Jun-Seob Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Sung-Jin Yoon
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Young-Jun Park
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
| | - Seon-Yeong Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea.,Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Choong-Min Ryu
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseng-gu, Daejeon, South Korea
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23
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Mechan Llontop ME, Hurley K, Tian L, Bernal Galeano VA, Wildschutte HK, Marine SC, Yoder KS, Vinatzer BA. Exploring Rain as Source of Biological Control Agents for Fire Blight on Apple. Front Microbiol 2020; 11:199. [PMID: 32117187 PMCID: PMC7033628 DOI: 10.3389/fmicb.2020.00199] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/28/2020] [Indexed: 01/20/2023] Open
Abstract
Poor survival on plants can limit the efficacy of Biological Control Agents (BCAs) in the field. Yet bacteria survive in the atmosphere, despite their exposure to high solar radiation and extreme temperatures. If conditions in the atmosphere are similar to, or more extreme than, the environmental conditions on the plant surface, then precipitation may serve as a reservoir of robust BCAs. To test this hypothesis, two hundred and fifty-four rain-borne isolates were screened for in vitro inhibition of Erwinia amylovora, the causal agent of fire blight, as well as of other plant pathogenic bacteria, fungi and oomycetes. Two isolates showed strong activity against E. amylovora and other plant pathogenic bacteria, while other isolates showed activity against fungal and oomycete pathogens. Survival assays suggested that the two isolates that inhibited E. amylovora were able to survive on apple blossoms and branches similarly to E. amylovora. Pathogen population size and associated fire blight symptoms were significantly reduced when detached apple blossoms were treated with the two isolates before pathogen inoculation, however, disease reduction on attached blossoms within an orchard was inconsistent. Using whole genome sequencing, the isolates were identified as Pantoea agglomerans and P. ananatis, respectively. A UV-mutagenesis screen pointed to a phenazine antibiotic D-alanylgriseoluteic acid synthesis gene cluster as being at the base of the antimicrobial activity of the P. agglomerans isolate. Our work reveals the potential of precipitation as an under-explored source of BCAs, whole genome sequencing as an effective approach to precisely identify BCAs, and UV-mutagenesis as a technically simple screen to investigate the genetic basis of BCAs. More field trials are needed to determine the efficacy of the identified BCAs in fire blight control.
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Affiliation(s)
| | - Kelly Hurley
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Long Tian
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Hans K. Wildschutte
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States
| | - Sasha C. Marine
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States
| | - Keith S. Yoder
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
- Alson H. Smith Jr. Agricultural Research and Extension Center, Virginia Tech, Winchester, VA, United States
| | - Boris A. Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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24
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, Davies R, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 11: suitability of taxonomic units notified to EFSA until September 2019. EFSA J 2020; 18:e05965. [PMID: 32874211 PMCID: PMC7448003 DOI: 10.2903/j.efsa.2020.5965] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Qualified presumption of safety (QPS) was developed to provide a generic safety evaluation for biological agents to support EFSA's Scientific Panels. The taxonomic identity, body of knowledge, safety concerns and antimicrobial resistance are assessed. Safety concerns identified for a taxonomic unit (TU) are where possible to be confirmed at strain or product level, reflected by 'qualifications'. No new information was found that would change the previously recommended QPS TUs and their qualifications. The list of microorganisms notified to EFSA was updated with 54 biological agents, received between April and September 2019; 23 already had QPS status, 14 were excluded from the QPS exercise (7 filamentous fungi, 6 Escherichia coli, Sphingomonas paucimobilis which was already evaluated). Seventeen, corresponding to 16 TUs, were evaluated for possible QPS status, fourteen of these for the first time, and Protaminobacter rubrum, evaluated previously, was excluded because it is not a valid species. Eight TUs are recommended for QPS status. Lactobacillus parafarraginis and Zygosaccharomyces rouxii are recommended to be included in the QPS list. Parageobacillus thermoglucosidasius and Paenibacillus illinoisensis can be recommended for the QPS list with the qualification 'for production purposes only' and absence of toxigenic potential. Bacillus velezensis can be recommended for the QPS list with the qualification 'absence of toxigenic potential and the absence of aminoglycoside production ability'. Cupriavidus necator, Aurantiochytrium limacinum and Tetraselmis chuii can be recommended for the QPS list with the qualification 'production purposes only'. Pantoea ananatis is not recommended for the QPS list due to lack of body of knowledge in relation to its pathogenicity potential for plants. Corynebacterium stationis, Hamamotoa singularis, Rhodococcus aetherivorans and Rhodococcus ruber cannot be recommended for the QPS list due to lack of body of knowledge. Kodamaea ohmeri cannot be recommended for the QPS list due to safety concerns.
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Soutar CD, Stavrinides J. Molecular validation of clinical Pantoea isolates identified by MALDI-TOF. PLoS One 2019; 14:e0224731. [PMID: 31682625 PMCID: PMC6827907 DOI: 10.1371/journal.pone.0224731] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/20/2019] [Indexed: 12/13/2022] Open
Abstract
The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.
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Affiliation(s)
- Craig D. Soutar
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
- * E-mail:
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Grode AS, Brisco-McCann E, Wiriyajitsonboom P, Hausbeck MK, Szendrei Z. Managing Onion Thrips can Limit Bacterial Stalk and Leaf Necrosis in Michigan Onion Fields. PLANT DISEASE 2019; 103:938-943. [PMID: 30893026 DOI: 10.1094/pdis-07-18-1271-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Onion thrips (Thrips tabaci) is a major insect pest of onion and it has been identified as a likely vector of Pantoea agglomerans (bacterial stalk and leaf necrosis), a relatively new pathogen to Michigan's onion industry. Our objective was to develop an integrated insect and disease management program by examining the efficacy of bactericides and insecticides alone and in combination to limit bacterial stalk and leaf necrosis caused by P. agglomerans. We also examined the association of onion thrips and disease incidence in the field, because thrips are known to transmit this pathogen. In the pesticide trial, insecticides reduced both thrips abundance and bacterial stalk and leaf necrosis incidence whereas bactericides alone did not reduce disease severity. Positive correlations among thrips population density, numbers of thrips positive for P. agglomerans, and bacterial stalk and leaf necrosis incidence in onion fields were determined. This study suggests that onion thrips feeding can facilitate the development of bacterial stalk and leaf necrosis in Michigan's commercial onion fields, and results from the pesticide trials indicate that thrips feeding damage is positively correlated with disease incidence. Therefore, in order to reduce bacterial stalk and leaf necrosis incidence in onion, management efforts should include reducing onion thrips populations through the use of insecticides and other cultural practices.
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Affiliation(s)
- A S Grode
- 1 Department of Entomology, Michigan State University, East Lansing, MI 48824, U.S.A
| | - E Brisco-McCann
- 2 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.; and
| | - P Wiriyajitsonboom
- 3 Department of Microbiology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - M K Hausbeck
- 2 Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A.; and
| | - Z Szendrei
- 1 Department of Entomology, Michigan State University, East Lansing, MI 48824, U.S.A
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Giorgio A, De Bonis S, Balestrieri R, Rossi G, Guida M. The Isolation and Identification of Bacteria on Feathers of Migratory Bird Species. Microorganisms 2018; 6:microorganisms6040124. [PMID: 30563109 PMCID: PMC6313546 DOI: 10.3390/microorganisms6040124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 11/28/2022] Open
Abstract
Worldwide, bacteria are the most ubiquitous microorganisms, and it has been extensively demonstrated that migratory wild birds can increase bacterial global scale dispersion through long-distance migration and dispersal. The microbial community hosted by wild birds can be highly diverse, including pathogenic strains that can contribute to infections and disease spread. This study focused on feather and plumage bacteria within bird microbial communities. Samples were collected during ornithological activities in a bird ringing station. Bacterial identification was carried out via DNA barcoding of the partial 16S rRNA gene. Thirty-seven isolates of bacteria were identified on the chest feathers of 60 migratory birds belonging to three trans-Saharan species: Muscicapastriata, Hippolaisicterina, and Sylviaborin. Our results demonstrate the possibility of bacterial transfer, including pathogens, through bird migration between very distant countries. The data from the analysis of plumage bacteria can aid in the explanation of phenomena such as migratory birds’ fitness or the development of secondary sexual traits. Moreover, these results have deep hygienic–sanitary implications, since many bird species have synanthropic behaviors during their migration that increase the probability of disease spread.
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Affiliation(s)
- Antonella Giorgio
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia ed. 7, 80126 Napoli (NA), Italy.
| | - Salvatore De Bonis
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia ed. 7, 80126 Napoli (NA), Italy.
| | - Rosario Balestrieri
- Consiglio Nazionale delle Ricerche, Istituto di Biologia Agroambientale e Forestale, Via Salaria km 29, 300, 00015 Monterotondo (RM), Italy.
- Associazione per la Ricerca, la Divulgazione e l'Educazione Ambientale (ARDEA), Via Ventilabro 6, 80126 Napoli (NA), Italy.
| | - Giovanni Rossi
- Freshwater Science Group; Dipartimento di Scienze Biologiche, Geologiche ed Ambientali (BiGeA); Alma Mater Studiorum-Università di Bologna, Via Selmi 3, 40126 Bologna (BO), Italy.
- Hydrosynergy S.C.-Environmental Monitoring and Applied Ecology, Via Roma 11, 40068 San Lazzaro di Savena (BO), Italy.
| | - Marco Guida
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, Via Cinthia ed. 7, 80126 Napoli (NA), Italy.
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Soutar CD, Stavrinides J. The evolution of three siderophore biosynthetic clusters in environmental and host-associating strains of Pantoea. Mol Genet Genomics 2018; 293:1453-1467. [PMID: 30027301 DOI: 10.1007/s00438-018-1477-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/13/2018] [Indexed: 12/22/2022]
Abstract
For many pathogenic members of the Enterobacterales, siderophores play an important role in virulence, yet the siderophores of the host-associating members of the genus Pantoea remain unexplored. We conducted a genome-wide survey of environmental and host-associating strains of Pantoea to identify known and candidate siderophore biosynthetic clusters. Our analysis identified three clusters homologous to those of enterobactin, desferrioxamine, and aerobactin that were prevalent among Pantoea species. Using both phylogenetic and comparative genomic approaches, we demonstrate that the enterobactin-like cluster was present in the common ancestor of all Pantoea, with evidence for three independent losses of the cluster in P. eucalypti, P. eucrina, and the P. ananatis-P. stewartii lineage. The desferrioxamine biosynthetic cluster, previously described and characterized in Pantoea, was horizontally acquired from its close relative Erwinia, with phylogenetic evidence that these transfer events were ancient and occurred between ancestral lineages. The aerobactin cluster was identified in three host-associating species groups, P. septica, P. ananatis, and P. stewartii, with strong evidence for horizontal acquisition from human-pathogenic members of the Enterobacterales. Our work identifies and describes the key siderophore clusters in Pantoea, shows three distinct evolutionary processes driving their diversification, and provides a foundation for exploring the roles that these siderophores may play in human opportunistic infections.
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Affiliation(s)
- Craig D Soutar
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, SK, S4S0A2, Canada.
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Genome Sequence of Pantoea ananatis SGAir0210, Isolated from Outdoor Air in Singapore. GENOME ANNOUNCEMENTS 2018; 6:6/27/e00643-18. [PMID: 29976614 PMCID: PMC6033981 DOI: 10.1128/genomea.00643-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore. The genome was assembled from long reads generated by single-molecule real-time sequencing complemented with short reads. Pantoea ananatis SGAir0210 was isolated from outdoor air collected in Singapore. The genome was assembled from long reads generated by single-molecule real-time sequencing complemented with short reads. The genome size was approximately 4.81 Mb, with 4,303 protein-coding genes, 80 tRNAs, and 22 rRNAs identified.
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Saticioglu IB, Duman M, Altun S. Antimicrobial resistance and molecular characterization of Pantoea agglomerans isolated from rainbow trout ( Oncorhynchus mykiss ) fry. Microb Pathog 2018; 119:131-136. [DOI: 10.1016/j.micpath.2018.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/12/2018] [Accepted: 04/12/2018] [Indexed: 10/17/2022]
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Stice SP, Stumpf SD, Gitaitis RD, Kvitko BH, Dutta B. Pantoea ananatis Genetic Diversity Analysis Reveals Limited Genomic Diversity as Well as Accessory Genes Correlated with Onion Pathogenicity. Front Microbiol 2018; 9:184. [PMID: 29491851 PMCID: PMC5817063 DOI: 10.3389/fmicb.2018.00184] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
Pantoea ananatis is a member of the family Enterobacteriaceae and an enigmatic plant pathogen with a broad host range. Although P. ananatis strains can be aggressive on onion causing foliar necrosis and onion center rot, previous genomic analysis has shown that P. ananatis lacks the primary virulence secretion systems associated with other plant pathogens. We assessed a collection of fifty P. ananatis strains collected from Georgia over three decades to determine genetic factors that correlated with onion pathogenic potential. Previous genetic analysis studies have compared strains isolated from different hosts with varying diseases potential and isolation sources. Strains varied greatly in their pathogenic potential and aggressiveness on different cultivated Allium species like onion, leek, shallot, and chive. Using multi-locus sequence analysis (MLSA) and repetitive extragenic palindrome repeat (rep)-PCR techniques, we did not observe any correlation between onion pathogenic potential and genetic diversity among strains. Whole genome sequencing and pan-genomic analysis of a sub-set of 10 strains aided in the identification of a novel series of genetic regions, likely plasmid borne, and correlating with onion pathogenicity observed on single contigs of the genetic assemblies. We named these loci Onion Virulence Regions (OVR) A-D. The OVR loci contain genes involved in redox regulation as well as pectate lyase and rhamnogalacturonase genes. Previous studies have not identified distinct genetic loci or plasmids correlating with onion foliar pathogenicity or pathogenicity on a single host pathosystem. The lack of focus on a single host system for this phytopathgenic disease necessitates the pan-genomic analysis performed in this study.
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Affiliation(s)
- Shaun P. Stice
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Spencer D. Stumpf
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Ron D. Gitaitis
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
- The Plant Center, University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria. Front Microbiol 2018; 9:113. [PMID: 29467735 PMCID: PMC5808187 DOI: 10.3389/fmicb.2018.00113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/17/2018] [Indexed: 12/21/2022] Open
Abstract
Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea, the four lineages within the genus, as well as its sister-genus Tatumella. This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella, various traits involved in nutrient cycling were identified within Pantoea, providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetic, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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Weller‐Stuart T, De Maayer P, Coutinho T. Pantoea ananatis: genomic insights into a versatile pathogen. MOLECULAR PLANT PATHOLOGY 2017; 18:1191-1198. [PMID: 27880983 PMCID: PMC6638271 DOI: 10.1111/mpp.12517] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
UNLABELLED Pantoea ananatis, a bacterium that is well known for its phytopathogenic characteristics, has been isolated from a myriad of ecological niches and hosts. Infection of agronomic crops, such as maize and rice, can result in substantial economic losses. In the last few years, much of the research performed on P. ananatis has been based on the sequencing and analysis of the genomes of strains isolated from different environments and with different lifestyles. In this review, we summarize the advances made in terms of pathogenicity determinants of phytopathogenic strains of P. ananatis and how this bacterium is able to adapt and survive in such a wide variety of habitats. The diversity and adaptability of P. ananatis can largely be attributed to the plasticity of its genome and the integration of mobile genetic elements on both the chromosome and plasmid. Furthermore, we discuss the recent interest in this species in various biotechnological applications. TAXONOMY Domain Bacteria; Class Gammaproteobacteria; Family Enterobacteriaceae; genus Pantoea; species ananatis. DISEASE SYMPTOMS Pantoea ananatis causes disease on a wide range of plants, and symptoms can range from dieback and stunted growth in Eucalyptus seedlings to chlorosis and bulb rotting in onions. DISEASE CONTROL Currently, the only methods of control of P. ananatis on most plant hosts are the use of resistant clones and cultivars or the eradication of infected plant material. The use of lytic bacteriophages on certain host plants, such as rice, has also achieved a measure of success.
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Affiliation(s)
- Tania Weller‐Stuart
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
| | - Pieter De Maayer
- School of Molecular and Cell BiologyUniversity of the WitwatersrandJohannesburg2050South Africa
| | - Teresa Coutinho
- Forestry and Agricultural Biotechnology Institute (FABI), Department of MicrobiologyUniversity of PretoriaPretoria0002South Africa
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Raphael E, Riley LW. Infections Caused by Antimicrobial Drug-Resistant Saprophytic Gram-Negative Bacteria in the Environment. Front Med (Lausanne) 2017; 4:183. [PMID: 29164118 PMCID: PMC5670356 DOI: 10.3389/fmed.2017.00183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/12/2017] [Indexed: 11/25/2022] Open
Abstract
Background Drug-resistance genes found in human bacterial pathogens are increasingly recognized in saprophytic Gram-negative bacteria (GNB) from environmental sources. The clinical implication of such environmental GNBs is unknown. Objectives We conducted a systematic review to determine how often such saprophytic GNBs cause human infections. Methods We queried PubMed for articles published in English, Spanish, and French between January 2006 and July 2014 for 20 common environmental saprophytic GNB species, using search terms “infections,” “human infections,” “hospital infection.” We analyzed 251 of 1,275 non-duplicate publications that satisfied our selection criteria. Saprophytes implicated in blood stream infection (BSI), urinary tract infection (UTI), skin and soft tissue infection (SSTI), post-surgical infection (PSI), osteomyelitis (Osteo), and pneumonia (PNA) were quantitatively assessed. Results Thirteen of the 20 queried GNB saprophytic species were implicated in 674 distinct infection episodes from 45 countries. The most common species included Enterobacter aerogenes, Pantoea agglomerans, and Pseudomonas putida. Of these infections, 443 (66%) had BSI, 48 (7%) had SSTI, 36 (5%) had UTI, 28 (4%) had PSI, 21 (3%) had PNA, 16 (3%) had Osteo, and 82 (12%) had other infections. Nearly all infections occurred in subjects with comorbidities. Resistant strains harbored extended-spectrum beta-lactamase (ESBL), carbapenemase, and metallo-β-lactamase genes recognized in human pathogens. Conclusion These observations show that saprophytic GNB organisms that harbor recognized drug-resistance genes cause a wide spectrum of infections, especially as opportunistic pathogens. Such GNB saprophytes may become increasingly more common in healthcare settings, as has already been observed with other environmental GNBs such as Acinetobacter baumannii and Pseudomonas aeruginosa.
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Affiliation(s)
- Eva Raphael
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
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Palmer M, Steenkamp ET, Coetzee MPA, Chan WY, van Zyl E, De Maayer P, Coutinho TA, Blom J, Smits THM, Duffy B, Venter SN. Phylogenomic resolution of the bacterial genus Pantoea and its relationship with Erwinia and Tatumella. Antonie van Leeuwenhoek 2017; 110:1287-1309. [PMID: 28255640 DOI: 10.1007/s10482-017-0852-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 02/23/2017] [Indexed: 11/29/2022]
Abstract
Investigation of the evolutionary relationships between related bacterial species and genera with a variety of lifestyles have gained popularity in recent years. For analysing the evolution of specific traits, however, a robust phylogeny is essential. In this study we examined the evolutionary relationships among the closely related genera Erwinia, Tatumella and Pantoea, and also attempted to resolve the species relationships within Pantoea. To accomplish this, we used the whole genome sequence data for 35 different strains belonging to these three genera, as well as nine outgroup taxa. Multigene datasets consisting of the 1039 genes shared by these 44 strains were then generated and subjected to maximum likelihood phylogenetic analyses, after which the results were compared to those using conventional multi-locus sequence analysis (MLSA) and ribosomal MLSA (rMLSA) approaches. The robustness of the respective phylogenies was then explored by considering the factors typically responsible for destabilizing phylogenetic trees. We found that the nucleotide datasets employed in the MLSA, rMLSA and 1039-gene datasets contained significant levels of homoplasy, substitution saturation and differential codon usage, all of which likely gave rise to the observed lineage specific rate heterogeneity. The effects of these factors were much less pronounced in the amino acid dataset for the 1039 genes, which allowed reconstruction of a fully supported and resolved phylogeny. The robustness of this amino acid tree was also supported by different subsets of the 1039 genes. In contrast to the smaller datasets (MLSA and rMLSA), the 1039 amino acid tree was also not as sensitive to long-branch attraction. The robust and well-supported evolutionary hypothesis for the three genera, which confidently resolved their various inter- and intrageneric relationships, represents a valuable resource for future studies. It will form the basis for studies aiming to understand the forces driving the divergence and maintenance of lineages, species and biological traits in this important group of bacteria.
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Affiliation(s)
- Marike Palmer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Martin P A Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI),, University of Pretoria, Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Elritha van Zyl
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Pieter De Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Teresa A Coutinho
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jochen Blom
- Computational Genomics, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Stephanus N Venter
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
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Acevedo FE, Peiffer M, Tan CW, Stanley BA, Stanley A, Wang J, Jones AG, Hoover K, Rosa C, Luthe D, Felton G. Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:127-137. [PMID: 28027025 DOI: 10.1094/mpmi-11-16-0240-r] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Mechanical damage caused by insect feeding along with components present in insect saliva and oral secretions are known to induce jasmonic acid-mediated defense responses in plants. This study investigated the effects of bacteria from oral secretions of the fall armyworm Spodoptera frugiperda on herbivore-induced defenses in tomato and maize plants. Using culture-dependent methods, we identified seven different bacterial isolates belonging to the family Enterobacteriacea from the oral secretions of field-collected caterpillars. Two isolates, Pantoea ananatis and Enterobacteriaceae-1, downregulated the activity of the plant defensive proteins polyphenol oxidase and trypsin proteinase inhibitors (trypsin PI) but upregulated peroxidase (POX) activity in tomato. A Raoultella sp. and a Klebsiella sp. downregulated POX but upregulated trypsin PI in this plant species. Conversely, all of these bacterial isolates upregulated the expression of the herbivore-induced maize proteinase inhibitor (mpi) gene in maize. Plant treatment with P. ananatis and Enterobacteriaceae-1 enhanced caterpillar growth on tomato but diminished their growth on maize plants. Our results highlight the importance of herbivore-associated microbes and their ability to mediate insect plant interactions differently in host plants fed on by the same herbivore.
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Affiliation(s)
- Flor E Acevedo
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
| | - Michelle Peiffer
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
| | - Ching-Wen Tan
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
| | - Bruce A Stanley
- 2 Section of Research Resources, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, 17033, U.S.A
| | - Anne Stanley
- 2 Section of Research Resources, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, 17033, U.S.A
| | - Jie Wang
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
- 3 Department of Ecology, South China Agricultural University, Guangzhou, Guangdong 510640, China
| | - Asher G Jones
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
| | - Kelli Hoover
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
| | - Cristina Rosa
- 4 Department of Plant Pathology, The Pennsylvania State University, 321 Buckhout Lab; and
| | - Dawn Luthe
- 5 Department of Plant Science, The Pennsylvania State University, 216 Agricultural Sciences and Industries Building
| | - Gary Felton
- 1 Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, 16802, U.S.A
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Duron O, Noël V. A wide diversity of Pantoea lineages are engaged in mutualistic symbiosis and cospeciation processes with stinkbugs. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:715-727. [PMID: 27362408 DOI: 10.1111/1758-2229.12432] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 05/20/2016] [Indexed: 05/27/2023]
Abstract
Pantoea are emerging as widespread bacteria engaged in associations with a variety of hosts, including plants, insects and humans. Recently, mutualistic Pantoea gut symbionts have also been reported in pentatomid stinkbugs. In the present study, we examine the incidence and evolutionary history of these Pantoea symbionts in pentatomid stinkbug populations from 14 species, characterising the processes that shape their diversity. We identify midgut crypts of pentatomid stinkbugs as harboring a remarkable diversity of Pantoea. Present in 10 of the 14 sampled host species, multi-locus typing revealed the presence of 10 novel Panteoa lineages, all highly differentiated from the known Panteoa species. Rearing experiments of two pentatomid stinkbug species confirmed that these novel Panteoa are maternally inherited through egg smearing and engaged in mutualistic interactions with their hosts. Phylogenetic investigations further revealed that the Pantoea evolutionary history in pentatomid stinkbugs was notably complex: it has been shaped not only by horizontal transfers with frequent host turnover but also by strict vertical transmission over long evolutionary periods, resulting in host-symbiont codiversification.
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Affiliation(s)
- Olivier Duron
- Laboratoire MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (UMR5290) - Université de Montpellier - Institut de Recherche pour le Développement (UR224), Montpellier, France
| | - Valérie Noël
- Laboratoire MIVEGEC (Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle), Centre National de la Recherche Scientifique (UMR5290) - Université de Montpellier - Institut de Recherche pour le Développement (UR224), Montpellier, France
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Palmer M, de Maayer P, Poulsen M, Steenkamp ET, van Zyl E, Coutinho TA, Venter SN. Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites. Stand Genomic Sci 2016; 11:23. [PMID: 26937267 PMCID: PMC4774006 DOI: 10.1186/s40793-016-0144-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 01/20/2016] [Indexed: 02/02/2023] Open
Abstract
The genus Pantoea incorporates many economically and clinically important species. The plant-associated species, Pantoea agglomerans and Pantoea vagans, are closely related and are often isolated from similar environments. Plasmids conferring certain metabolic capabilities are also shared amongst these two species. The genomes of two isolates obtained from fungus-growing termites in South Africa were sequenced, assembled and annotated. A high number of orthologous genes are conserved within and between these species. The difference in genome size between P. agglomerans MP2 (4,733,829 bp) and P. vagans MP7 (4,598,703 bp) can largely be attributed to the differences in plasmid content. The genome sequences of these isolates may shed light on the common traits that enable P. agglomerans and P. vagans to co-occur in plant- and insect-associated niches.
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Affiliation(s)
- Marike Palmer
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Pieter de Maayer
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002 South Africa
| | - Michael Poulsen
- />Department of Biology, Centre for Social Evolution, Section for Ecology and Evolution, University of Copenhagen, Univeritetsparken 15, 2100 Copenhagen East, Denmark
| | - Emma T. Steenkamp
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Elritha van Zyl
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Teresa A. Coutinho
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
| | - Stephanus N. Venter
- />Department of Microbiology and Plant Pathology and the Genome Research Institute, University of Pretoria, Pretoria, 0002 South Africa
- />DST-NRF Centre of Excellence in Tree Health Biotechnology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, 0002 South Africa
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A Novel Glycolipid Biosurfactant Confers Grazing Resistance upon Pantoea ananatis BRT175 against the Social Amoeba Dictyostelium discoideum. mSphere 2016; 1:mSphere00075-15. [PMID: 27303689 PMCID: PMC4863597 DOI: 10.1128/msphere.00075-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 12/01/2015] [Indexed: 11/20/2022] Open
Abstract
Pantoea is a versatile genus of bacteria with both plant- and animal-pathogenic strains, some of which have been suggested to cause human infections. There is, however, limited knowledge on the potential determinants used for host association and pathogenesis in animal systems. In this study, we used the model host Dictyostelium discoideum to show that isolates of Pantoea ananatis exhibit differential grazing susceptibility, with some being resistant to grazing by the amoebae. We carried out a high-throughput genetic screen of one grazing-resistant isolate, P. ananatis BRT175, using the D. discoideum pathosystem to identify genes responsible for the resistance phenotype. Among the 26 candidate genes involved in grazing resistance, we identified rhlA and rhlB, which we show are involved in the biosynthesis of a biosurfactant that enables swarming motility in P. ananatis BRT175. Using liquid chromatography-mass spectrometry (LC-MS), the biosurfactant was shown to be a glycolipid with monohexose-C10-C10 as the primary congener. We show that this novel glycolipid biosurfactant is cytotoxic to the amoebae and is capable of compromising cellular integrity, leading to cell lysis. The production of this biosurfactant may be important for bacterial survival in the environment and could contribute to the establishment of opportunistic infections. IMPORTANCE The genetic factors used for host interaction by the opportunistic human pathogen Pantoea ananatis are largely unknown. We identified two genes that are important for the production of a biosurfactant that confers grazing resistance against the social amoeba Dictyostelium discoideum. We show that the biosurfactant, which exhibits cytotoxicity toward the amoebae, is a glycolipid that incorporates a hexose rather than rhamnose. The production of this biosurfactant may confer a competitive advantage in the environment and could potentially contribute to the establishment of opportunistic infections.
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Genome Sequence of Pantoea ananatis Strain CFH 7-1, Which Is Associated with a Vector-Borne Cotton Fruit Disease. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01029-15. [PMID: 26358602 PMCID: PMC4566184 DOI: 10.1128/genomea.01029-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pantoea ananatis is a bacterium with versatile niches that vary from pathogenic to beneficial. We present the genome of strain CFH 7-1, which was recovered from a diseased greenhouse cotton boll previously caged with a field-collected cotton fleahopper (Pseudatomoscelis seriatus). These data will assist in deciphering the infection process.
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Walterson AM, Stavrinides J. Pantoea:insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiol Rev 2015; 39:968-84. [DOI: 10.1093/femsre/fuv027] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/31/2022] Open
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De Maayer P, Chan WY, Martin DAJ, Blom J, Venter SN, Duffy B, Cowan DA, Smits THM, Coutinho TA. Integrative conjugative elements of the ICEPan family play a potential role in Pantoea ananatis ecological diversification and antibiosis. Front Microbiol 2015; 6:576. [PMID: 26106378 PMCID: PMC4458695 DOI: 10.3389/fmicb.2015.00576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 12/31/2022] Open
Abstract
Pantoea ananatis is a highly versatile enterobacterium isolated from diverse environmental sources. The ecological diversity of this species may be attributed, in part, to the acquisition of mobile genetic elements. One such element is an Integrative and Conjugative Element (ICE). By means of in silico analyses the ICE elements belonging to a novel family, ICEPan, were identified in the genome sequences of five P. ananatis strains and characterized. PCR screening showed that ICEPan is prevalent among P. ananatis strains isolated from different environmental sources and geographic locations. Members of the ICEPan family share a common origin with ICEs of other enterobacteria, as well as conjugative plasmids of Erwinia spp. Aside from core modules for ICEPan integration, maintenance and dissemination, the ICEPan contain extensive non-conserved islands coding for proteins that may contribute toward various phenotypes such as stress response and antibiosis, and the highly diverse ICEPan thus plays a major role in the diversification of P. ananatis. An island is furthermore integrated within an ICEPan DNA repair-encoding locus umuDC and we postulate its role in stress-induced dissemination and/or expression of the genes on this island.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Microbiology, University of Pretoria Pretoria, South Africa
| | - Wai-Yin Chan
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Douglas A J Martin
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen Giessen, Germany
| | - Stephanus N Venter
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria Pretoria, South Africa ; Department of Genetics, University of Pretoria Pretoria, South Africa
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zürich University of Applied Sciences Wädenswil, Switzerland
| | - Teresa A Coutinho
- Department of Microbiology, University of Pretoria Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria Pretoria, South Africa
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De Maayer P, Chan WY, Rubagotti E, Venter SN, Toth IK, Birch PRJ, Coutinho TA. Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts. BMC Genomics 2014; 15:404. [PMID: 24884520 PMCID: PMC4070556 DOI: 10.1186/1471-2164-15-404] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms. Results The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors. Conclusions P. ananatis has an ‘open’ pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-404) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pieter De Maayer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria 0002, South Africa.
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Levine JA, Hansen AM, Michalski JM, Hazen TH, Rasko DA, Kaper JB. H-NST induces LEE expression and the formation of attaching and effacing lesions in enterohemorrhagic Escherichia coli. PLoS One 2014; 9:e86618. [PMID: 24466172 PMCID: PMC3897749 DOI: 10.1371/journal.pone.0086618] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/17/2013] [Indexed: 11/19/2022] Open
Abstract
Background Enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli are important causes of morbidity and mortality worldwide. These enteric pathogens contain a type III secretion system (T3SS) responsible for the attaching and effacing (A/E) lesion phenotype. The T3SS is encoded by the locus of enterocyte effacement (LEE) pathogenicity island. The H-NS-mediated repression of LEE expression is counteracted by Ler, the major activator of virulence gene expression in A/E pathogens. A regulator present in EPEC, H-NST, positively affects expression of H-NS regulon members in E. coli K-12, although the effect of H-NST on LEE expression and virulence of A/E pathogens has yet-to-be determined. Results We examine the effect of H-NST on LEE expression and A/E lesion formation on intestinal epithelial cells. We find that H-NST positively affects the levels of LEE-encoded proteins independently of ler and induces A/E lesion formation. We demonstrate H-NST binding to regulatory regions of LEE1 and LEE3, the first report of DNA-binding by H-NST. We characterize H-NST mutants substituted at conserved residues including Ala16 and residues Arg60 and Arg63, which are part of a potential DNA-binding domain. The single mutants A16V, A16L, R60Q and the double mutant R60Q/R63Q exhibit a decreased effect on LEE expression and A/E lesion formation. DNA mobility shift assays reveal that these residues are important for H-NST to bind regulatory LEE DNA targets. H-NST positively affects Ler binding to LEE DNA in the presence of H-NS, and thereby potentially helps Ler displace H-NS bound to DNA. Conclusions H-NST induces LEE expression and A/E lesion formation likely by counteracting H-NS-mediated repression. We demonstrate that H-NST binds to DNA and identify arginine residues that are functionally important for DNA-binding. Our study suggests that H-NST provides an additional means for A/E pathogens to alleviate repression of virulence gene expression by H-NS to promote virulence capabilities.
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Affiliation(s)
- Jonathan A. Levine
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Graduate Program in Biochemistry and Molecular Biology, University of Maryland, Baltimore, Maryland, United States of America
| | - Anne-Marie Hansen
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jane M. Michalski
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David A. Rasko
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - James B. Kaper
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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Abstract
The enterobacterium Pantoea ananatis is an ecologically versatile species. It has been found in the environment, as plant epiphyte and endophyte, as an emerging phytopathogen, and as a presumptive, opportunistic human pathogen. Here, we report the complete genome sequence of P. ananatis LMG 5342, isolated from a human wound.
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Pantoea ananatis as a cause of corneal infiltrate after rice husk injury. J Clin Microbiol 2012; 50:2163-4. [PMID: 22461671 DOI: 10.1128/jcm.06743-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report a case of an agricultural worker presenting with corneal infiltrate following ocular injury with a rice husk. On examination, a superficial corneal foreign body was removed and sent for culture, which grew Pantoea ananatis. This is, to our knowledge, the first clinical case report of Pantoea ananatis causing corneal infiltrate.
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Kirzinger MWB, Nadarasah G, Stavrinides J. Insights into cross-kingdom plant pathogenic bacteria. Genes (Basel) 2011; 2:980-97. [PMID: 24710301 PMCID: PMC3927606 DOI: 10.3390/genes2040980] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 11/02/2011] [Accepted: 11/07/2011] [Indexed: 01/29/2023] Open
Abstract
Plant and human pathogens have evolved disease factors to successfully exploit their respective hosts. Phytopathogens utilize specific determinants that help to breach reinforced cell walls and manipulate plant physiology to facilitate the disease process, while human pathogens use determinants for exploiting mammalian physiology and overcoming highly developed adaptive immune responses. Emerging research, however, has highlighted the ability of seemingly dedicated human pathogens to cause plant disease, and specialized plant pathogens to cause human disease. Such microbes represent interesting systems for studying the evolution of cross-kingdom pathogenicity, and the benefits and tradeoffs of exploiting multiple hosts with drastically different morphologies and physiologies. This review will explore cross-kingdom pathogenicity, where plants and humans are common hosts. We illustrate that while cross-kingdom pathogenicity appears to be maintained, the directionality of host association (plant to human, or human to plant) is difficult to determine. Cross-kingdom human pathogens, and their potential plant reservoirs, have important implications for the emergence of infectious diseases.
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Affiliation(s)
- Morgan W B Kirzinger
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada.
| | - Geetanchaly Nadarasah
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada.
| | - John Stavrinides
- Department of Biology, University of Regina, 3737 Wascana Parkway, Regina, Saskatchewan S4S0A2, Canada.
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Strope PK, Nickerson KW, Harris SD, Moriyama EN. Molecular evolution of urea amidolyase and urea carboxylase in fungi. BMC Evol Biol 2011; 11:80. [PMID: 21447149 PMCID: PMC3073912 DOI: 10.1186/1471-2148-11-80] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 03/29/2011] [Indexed: 11/16/2022] Open
Abstract
Background Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms. Results Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina. Conclusions We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay.
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Affiliation(s)
- Pooja K Strope
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
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Holden N, Pritchard L, Toth I. Colonization outwith the colon: plants as an alternative environmental reservoir for human pathogenic enterobacteria. FEMS Microbiol Rev 2009; 33:689-703. [PMID: 19076238 DOI: 10.1111/j.1574-6976.2008.00153.x] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Members of the Enterobacteriaceae have the capacity to adapt to a wide variety of environments and can be isolated from a range of host species across biological kingdoms. Bacteria that are pathogenic to animals, in particular humans, are increasingly found to be transmitted through the food chain by fruits and vegetables. Rather than simply contaminating plant surfaces, there is a growing body of evidence to show that these bacteria actively interact with plants and can colonize them as alternative hosts. This review draws together evidence from studies that investigate proven and potential mechanisms involved in colonization of plants by human pathogenic enterobacteria.
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Affiliation(s)
- Nicola Holden
- Department of Plant Pathology, Scottish Crop Research Institute, Invergowrie, Dundee, UK.
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