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Rocha J, Shapiro LR, Chimileski S, Kolter R. Complementary roles of EPS, T3SS and Expansin for virulence of Erwinia tracheiphila, the causative agent of cucurbit wilt. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600446. [PMID: 38979168 PMCID: PMC11230154 DOI: 10.1101/2024.06.24.600446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Erwinia tracheiphila (Smith) is a recently emerged plant pathogen that causes severe economic losses in cucurbit crops in temperate Eastern North America. E. tracheiphila is xylem restricted, and virulence is thought to be related to Exopolysaccharides (EPS) and biofilm formation, which occlude the passage of sap in xylem vessels and causes systemic wilt. However, the role of EPS and biofilm formation, and their contribution to disease in relation to other virulence loci are unknown. Here, we use deletion mutants to explore the roles of EPS, Hrp Type III secretion system (Hrp T3SS) and Expansin in plant colonization and virulence. Then, we quantify the expression of the genes encoding these factors during infection. Our results show that Exopolysaccharides are essential for E. tracheiphila survival in host plants, while Hrp T3SS and Expansin are dispensable for survival but needed for systemic wilt symptom development. EPS and Hrp T3SS display contrasting expression patterns in the plant, reflecting their relevance in different stages of the infection. Finally, we show that expression of the eps and hrpT3SS operons is downregulated in mildly increased temperatures, suggesting a link between expression of these virulence factors and geographic restriction of E. tracheiphila to temperate regions. Our work highlights how E. tracheiphila virulence is a complex trait where several loci are coordinated during infection. These results further shed light into the relationship between virulence factors and the ecology of this pathosystem, which will be essential for developing sustainable management strategies for this emerging pathogen.
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Affiliation(s)
- Jorge Rocha
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
- Progama de Agricultura en Zonas Áridas; Centro de Investigaciones Biológicas del Noroeste. Av. Instituto Politécnico Nacional 195, La Paz, B.C.S. México 23096
| | - Lori R Shapiro
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
| | - Scott Chimileski
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory; Woods Hole, MA, US 02543
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School. 77 Avenue Louis Pasteur, Boston MA, US 02115
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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Pilgrim J. Comparative genomics of a novel Erwinia species associated with the Highland midge ( Culicoides impunctatus). Microb Genom 2024; 10. [PMID: 38630610 DOI: 10.1099/mgen.0.001242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Erwinia (Enterobacterales: Erwiniaceae) are a group of cosmopolitan bacteria best known as the causative agents of various plant diseases. However, other species in this genus have been found to play important roles as insect endosymbionts supplementing the diet of their hosts. Here, I describe Candidatus Erwinia impunctatus (Erwimp) associated with the Highland midge Culicoides impunctatus (Diptera: Ceratopogonidae), an abundant biting pest in the Scottish Highlands. The genome of this new Erwinia species was assembled using hybrid long and short read techniques, and a comparative analysis was undertaken with other members of the genus to understand its potential ecological niche and impact. Genome composition analysis revealed that Erwimp is similar to other endophytic and ectophytic species in the genus and is unlikely to be restricted to its insect host. Evidence for an additional plant host includes the presence of a carotenoid synthesis operon implicated as a virulence factor in plant-associated members in the sister genus Pantoea. Unique features of Erwimp include several copies of intimin-like proteins which, along with signs of genome pseudogenization and a loss of certain metabolic pathways, suggests an element of host restriction seen elsewhere in the genus. Furthermore, a screening of individuals over two field seasons revealed the absence of the bacteria in Culicoides impunctatus during the second year indicating this microbe-insect interaction is likely to be transient. These data suggest that Culicoides impunctatus may have an important role to play beyond a biting nuisance, as an insect vector transmitting Erwimp alongside any conferred impacts to surrounding biota.
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Affiliation(s)
- Jack Pilgrim
- Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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4
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Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
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Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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5
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Roman-Reyna V, Sharma A, Toth H, Konkel Z, Omiotek N, Murthy S, Faith S, Slot J, Peduto Hand F, Goss EM, Jacobs JM. Live tracking of a plant pathogen outbreak reveals rapid and successive, multidecade plasmid reduction. mSystems 2024; 9:e0079523. [PMID: 38275768 PMCID: PMC10878067 DOI: 10.1128/msystems.00795-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Quickly understanding the genomic changes that lead to pathogen emergence is necessary to launch mitigation efforts and reduce harm. In this study, we tracked in real time a 2022 bacterial plant disease outbreak in U.S. geraniums (Pelargonium × hortorum) caused by Xhp2022, a novel lineage of Xanthomonas hortorum. Genomes from 31 Xhp2022 isolates from seven states showed limited chromosomal variation and all contained a single plasmid (p93). Time tree and single nucleotide polymorphism whole-genome analysis estimated that Xhp2022 emerged within the last decade. The phylogenomic analysis determined that p93 resulted from the cointegration of three plasmids (p31, p45, and p66) found sporadically across isolates from previous outbreaks. Although p93 had a 49 kb nucleotide reduction, it retained putative fitness genes, which became predominant in the 2022 outbreak. Overall, we demonstrated, through rapid whole-genome sequencing and analysis, a recent, traceable event of genome reduction for niche adaptation typically observed over millennia in obligate and fastidious pathogens.IMPORTANCEThe geranium industry, valued at $4 million annually, faces an ongoing Xanthomonas hortorum pv. pelargonii (Xhp) pathogen outbreak. To track and describe the outbreak, we compared the genome structure across historical and globally distributed isolates. Our research revealed Xhp population has not had chromosome rearrangements since 1974 and has three distinct plasmids. In 2012, we found all three plasmids in individual Xhp isolates. However, in 2022, the three plasmids co-integrated into one plasmid named p93. p93 retained putative fitness genes but lost extraneous genomic material. Our findings show that the 2022 strain group of the bacterial plant pathogen Xanthomonas hortorum underwent a plasmid reduction. We also observed several Xanthomonas species from different years, hosts, and continents have similar plasmids to p93, possibly due to shared agricultural settings. We noticed parallels between genome efficiency and reduction that we see across millennia with obligate parasites with increased niche specificity.
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Affiliation(s)
- Veronica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anuj Sharma
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Zachary Konkel
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Nicolle Omiotek
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Shashanka Murthy
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Seth Faith
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
- Applied Microbiology Services Laboratory, The Ohio State University, Columbus, Ohio, USA
| | - Jason Slot
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
| | | | - Erica M. Goss
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Jonathan M. Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
- Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
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Tembrock LR, Wilson CR, Zink FA, Timm AE, Gilligan TM, Konstantinov AS, Tishechkin AK. CO1 barcodes resolve an asymmetric biphyletic clade for Diabrotica undecimpunctata subspecies and provide nucleotide variants for differentiation from related lineages using real-time PCR. FRONTIERS IN INSECT SCIENCE 2023; 3:1168586. [PMID: 38469542 PMCID: PMC10926502 DOI: 10.3389/finsc.2023.1168586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/28/2023] [Indexed: 03/13/2024]
Abstract
Diabrotica undecimpunctata is a multivoltine polyphagous beetle species that has long been documented as a significant agricultural pest throughout its native range in North America. This beetle can vector bacterial and viral plant pathogens that result in major losses to crops such as cucumber and soybean. Many countries outside the Americas treat D. undecimpunctata as a species of quarantine importance, while in the USA only the subspecies D. u. duodecimnotata is subject to quarantine, to prevent introduction from Mexico. Identification of D. undecimpunctata on the basis of morphology alone can be complicated given the use of conflicting characters in the description of some subspecific taxa. To better understand relationships among D. undecimpunctata subspecies and other related species, we sequenced mitochondrial cytochrome oxidase 1 (CO1) and nuclear internal transcribed spacer 2 (ITS2) DNA from individuals in different subspecific taxa and across different parts of the species range using museum samples and interceptions. When our data were combined with publicly available Diabrotica data, no pattern of divergence consistent with the currently recognized subspecific designations was found. In addition, we compared phylogenetic patterns in CO1 data from the congener D. virgifera to demonstrate the utility of mitochondrial data in resolving subspecies. From the CO1 data, a diagnostic real-time PCR assay was developed that could successfully identify all haplotypes within the large D. undecimpunctata clade for use in surveys and identification at ports of entry. These findings underscore the need to resolve molecular and morphological datasets into cogent, lineage-based groupings. Such efforts will provide an evolutionary context for the study of agriculturally important attributes of Diabrotica such as host preferences, xenobiotic metabolism, and natural and anthropogenic patterns of dispersal.
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Affiliation(s)
- Luke R. Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Christina R. Wilson
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Frida A. Zink
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Alicia E. Timm
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Todd M. Gilligan
- Pest Identification Technology Laboratory, USDA-APHIS-PPQ-Science and Technology, Fort Collins, CO, United States
| | | | - Alexey K. Tishechkin
- Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA, United States
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7
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Jenny LA, Shapiro LR, Davis CC, Jonathan Davies T, Pierce NE, Meineke E. Herbarium specimens reveal herbivory patterns across the genus Cucurbita. AMERICAN JOURNAL OF BOTANY 2023; 110:e16126. [PMID: 36633920 DOI: 10.1002/ajb2.16126] [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: 07/02/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant-insect complex is logistically difficult. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant-insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant-insect interactions that are of ecological or agricultural importance. METHODS Here, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America. RESULTS Herbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human-managed habitats. CONCLUSIONS Our study suggests that long-term evolutionary changes in habitat from xeric to mesic climates and wild to human-managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.
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Affiliation(s)
- Laura A Jenny
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Charles C Davis
- Harvard University Herbaria, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, BC V6T 1Z4, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, Gauteng, 2028, South Africa
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Emily Meineke
- Department of Entomology and Nematology, University of California, Davis, Davis, California, 95616, United States
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8
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Diwan D, Rashid MM, Vaishnav A. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiol Res 2022; 265:127180. [PMID: 36126490 DOI: 10.1016/j.micres.2022.127180] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/28/2022]
Abstract
The success of sustainable agricultural practices has now become heavily dependent on the interactions between crop plants and their associated microbiome. Continuous advancement in high throughput sequencing platforms, omics-based approaches, and gene editing technologies has remarkably accelerated this area of research. It has enabled us to characterize the interactions of plants with associated microbial communities more comprehensively and accurately. Furthermore, the genomic and post-genomic era has significantly refined our perspective toward the complex mechanisms involved in those interactions, opening new avenues for efficiently deploying the knowledge in developing sustainable agricultural practices. This review focuses on our fundamental understanding of plant-microbe interactions and the contribution of existing multi-omics approaches, including those under active development and their tremendous success in unraveling different aspects of the complex network between plant hosts and microbes. In addition, we have also discussed the importance of sustainable and eco-friendly agriculture and the associated outstanding challenges ahead.
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Affiliation(s)
- Deepti Diwan
- Washington University School of Medicine, Saint Louis, MO 63110, USA.
| | - Md Mahtab Rashid
- Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar 813210, India; Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh 221005, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh 281121, India; Department of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, Zürich CH-8008, Switzerland; Plant-Soil Interaction Group, Agroscope (Reckenholz), Reckenholzstrasse 191, Zürich 8046, Switzerland
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Tibbs-Cortes LE, Tibbs-Cortes BW, Schmitz-Esser S. Tardigrade Community Microbiomes in North American Orchards Include Putative Endosymbionts and Plant Pathogens. Front Microbiol 2022; 13:866930. [PMID: 35923389 PMCID: PMC9340075 DOI: 10.3389/fmicb.2022.866930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/20/2022] [Indexed: 11/27/2022] Open
Abstract
The microbiome of tardigrades, a phylum of microscopic animals best known for their ability to survive extreme conditions, is poorly studied worldwide and completely unknown in North America. An improved understanding of tardigrade-associated bacteria is particularly important because tardigrades have been shown to act as vectors of the plant pathogen Xanthomonas campestris in the laboratory. However, the potential role of tardigrades as reservoirs and vectors of phytopathogens has not been investigated further. This study analyzed the microbiota of tardigrades from six apple orchards in central Iowa, United States, and is the first analysis of the microbiota of North American tardigrades. It is also the first ever study of the tardigrade microbiome in an agricultural setting. We utilized 16S rRNA gene amplicon sequencing to characterize the tardigrade community microbiome across four contrasts: location, substrate type (moss or lichen), collection year, and tardigrades vs. their substrate. Alpha diversity of the tardigrade community microbiome differed significantly by location and year of collection but not by substrate type. Our work also corroborated earlier findings, demonstrating that tardigrades harbor a distinct microbiota from their environment. We also identified tardigrade-associated taxa that belong to genera known to contain phytopathogens (Pseudomonas, Ralstonia, and the Pantoea/Erwinia complex). Finally, we observed members of the genera Rickettsia and Wolbachia in the tardigrade microbiome; because these are obligate intracellular genera, we consider these taxa to be putative endosymbionts of tardigrades. These results suggest the presence of putative endosymbionts and phytopathogens in the microbiota of wild tardigrades in North America.
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Affiliation(s)
- Laura E. Tibbs-Cortes
- Department of Agronomy, Iowa State University, Ames, IA, United States
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
- *Correspondence: Laura E. Tibbs-Cortes,
| | - Bienvenido W. Tibbs-Cortes
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
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10
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LaSarre B, Olawole OI, Paulsen AA, Halverson LJ, Gleason ML, Beattie GA. Complete Genome Sequences of Four Strains of Erwinia tracheiphila: A Resource for Studying a Bacterial Plant Pathogen with a Highly Complex Genome. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:500-504. [PMID: 35491948 DOI: 10.1094/mpmi-01-22-0008-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Breah LaSarre
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Olakunle I Olawole
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Ashley A Paulsen
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Larry J Halverson
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Mark L Gleason
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
| | - Gwyn A Beattie
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011-1101, U.S.A
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11
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Catlin NS, Josephs EB. The important contribution of transposable elements to phenotypic variation and evolution. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102140. [PMID: 34883307 DOI: 10.1016/j.pbi.2021.102140] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Transposable elements (TEs) are responsible for significant genomic variation in plants. Our understanding of the evolutionary forces shaping TE polymorphism has lagged behind other mutations because of the difficulty of accurately identifying TE polymorphism in short-read population genomic data. However, new approaches allow us to quantify TE polymorphisms in population datasets and address fundamental questions about the evolution of these polymorphisms. Here, we discuss how insertional biases shape where, when, and how often TEs insert throughout the genome. Next, we examine mechanisms by which TEs can affect phenotype. Finally, we evaluate current evidence for selection on TE polymorphisms. All together, it is clear that TEs are important, but underappreciated, contributors to intraspecific phenotypic variation, and that understanding the dynamics governing TE polymorphism is crucial for evolutionary biologists interested in the maintenance of variation.
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Affiliation(s)
- Nathan S Catlin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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12
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Phylogenomic analysis of the Erwiniaceae supports reclassification of Kalamiella piersonii to Pantoea piersonii comb. nov. and Erwinia gerundensis to the new genus Duffyella gen. nov. as Duffyella gerundensis comb. nov. Mol Genet Genomics 2022; 297:213-225. [PMID: 34988605 DOI: 10.1007/s00438-021-01829-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/27/2021] [Indexed: 01/20/2023]
Abstract
To better understand the taxonomy of Erwinia in the context of the Erwiniaceae family, we carried out a taxogenomic analysis of the Erwiniaceae, a family that was created following the taxonomic revision of the family, Enterobacteriaceae. There has been no systematic analysis of this family, including the agriculturally relevant genus, Erwinia. Our analyses focused on 80 strains of Erwinia along with 37 strains representing 7 other genera in the family. We identified 308 common proteins, generated a genome-level phylogeny and carried out Average Nucleotide Identity, Average Amino Acid Identity and Percentage of Conserved Protein analyses. We show that multiple strains of Erwinia cannot be assigned to established species groups and that both Erwinia gerundensis and "Erwinia mediterraneensis" are not members of Erwinia. We propose the creation of the genus Duffyella gen. nov. and the reclassification of Erwinia gerundensis to this genus as the type species, Duffyella gerundensis comb. nov. Furthermore, divergence between other species within Erwinia as measured by Average Amino Acid Identity is greater than the divergence between Erwinia and other genera, supporting the possible subdivision of the genus Erwinia into at least two genera. Our analyses also suggest that there is no basis for the establishment of the genus Kalamiella within the Erwiniaceae or the taxonomic revision of the Pantoea septica lineage. Therefore, we propose reclassifying Kalamiella piersonii as Pantoea piersonii comb. nov. Our study provides new insight into the diversity of the Erwiniaceae and provides a solid foundation for advancing taxonomic revision of this broadly relevant family.
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13
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Provorov NA. Symbiotic Models for Reconstruction of Organellogenesis. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421010117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Rocha J, Shapiro LR, Kolter R. A horizontally acquired expansin gene increases virulence of the emerging plant pathogen Erwinia tracheiphila. Sci Rep 2020; 10:21743. [PMID: 33303810 PMCID: PMC7729394 DOI: 10.1038/s41598-020-78157-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/09/2020] [Indexed: 12/16/2022] Open
Abstract
Erwinia tracheiphila is a bacterial plant pathogen that causes a fatal wilt infection in some cucurbit crop plants. Wilt symptoms are thought to be caused by systemic bacterial colonization through xylem that impedes sap flow. However, the genetic determinants of within-plant movement are unknown for this pathogen species. Here, we find that E. tracheiphila has horizontally acquired an operon with a microbial expansin (exlx) gene adjacent to a glycoside hydrolase family 5 (gh5) gene. Plant inoculation experiments with deletion mutants in the individual genes (Δexlx and Δgh5) and the full operon (Δexlx-gh5) resulted in decreased severity of wilt symptoms, decreased mortality rate, and impaired systemic colonization compared to the Wt strain. Co-inoculation experiments with Wt and Δexlx-gh5 rescued the movement defect of the mutant strain, suggesting that expansin and GH5 function extracellularly. Together, these results show that expansin-GH5 contributes to systemic movement through xylem, leading to rapid wilt symptom development and higher rates of plant death. The presence of expansin genes in diverse species of bacterial and fungal wilt-inducing pathogens suggests that microbial expansin proteins may be an under-appreciated virulence factor for many pathogen species.
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Affiliation(s)
- Jorge Rocha
- Department of Microbiology, Harvard Medical School, Boston, MA, USA.
- Conacyt-Centro de Investigación y Desarrollo en Agrobiotecnología Alimentaria, San Agustin Tlaxiaca, 42163, Hidalgo, Mexico.
| | - Lori R Shapiro
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Roberto Kolter
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
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15
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McCann HC. Skirmish or war: the emergence of agricultural plant pathogens. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:147-152. [PMID: 32712539 DOI: 10.1016/j.pbi.2020.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 06/12/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Understanding the ecological and evolutionary processes underlying the emergence of infectious disease is critically important in guiding prevention, management and breeding strategies. Novel pathogen lineages may arise within agricultural environments, wild hosts or from non-host associated disease reservoirs. Although the source of most disease outbreaks remains unknown, environmental and zoonotic origins are frequently identified in mammalian pathosystems and expanded sampling of plant pathosystems reveals important links with wild populations. This review describes key ecological and evolutionary processes underlying disease emergence, with particular emphasis on shifts from wild reservoirs to cultivated hosts and genetic mechanisms driving host adaption subsequent to emergence.
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Affiliation(s)
- Honour C McCann
- New Zealand Institute for Advanced Study, Massey University, Albany, New Zealand; Max Planck Institute for Developmental Biology, Tübingen, Germany.
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16
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Chase WR, Zhaxybayeva O, Rocha J, Cosgrove DJ, Shapiro LR. Global cellulose biomass, horizontal gene transfers and domain fusions drive microbial expansin evolution. THE NEW PHYTOLOGIST 2020; 226:921-938. [PMID: 31930503 DOI: 10.1111/nph.16428] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/19/2019] [Indexed: 05/23/2023]
Abstract
Plants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that nonenzymatically loosen noncovalent bonding between cellulose microfibrils. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct a comprehensive phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cell wall cellulose, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi inhabit varied ecological contexts, mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Overall, expansins are unexpectedly widespread in bacteria and eukaryotes, and the contribution of these genes to microbial ecological interactions with plants and algae has probbaly been underappreciated.
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Affiliation(s)
- William R Chase
- Department of Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
- Department of Computer Science, Dartmouth College, Hanover, NH, 03755, USA
| | - Jorge Rocha
- Department of Microbiology and Immunology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - Lori R Shapiro
- Department of Microbiology and Immunology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
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17
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Polsinelli I, Borruso L, Caliandro R, Triboli L, Esposito A, Benini S. A genome-wide analysis of desferrioxamine mediated iron uptake in Erwinia spp. reveals genes exclusive of the Rosaceae infecting strains. Sci Rep 2019; 9:2818. [PMID: 30808981 PMCID: PMC6391442 DOI: 10.1038/s41598-019-39787-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/29/2019] [Indexed: 11/17/2022] Open
Abstract
Erwinia amylovora is the etiological agent of fire blight, a devastating disease which is a global threat to commercial apple and pear production. The Erwinia genus includes a wide range of different species belonging to plant pathogens, epiphytes and even opportunistic human pathogens. The aim of the present study is to understand, within the Erwinia genus, the genetic differences between phytopathogenic strains and those strains not reported to be phytopathogenic. The genes related to the hydroxamate siderophores iron uptake have been considered due to their potential druggability. In E. amylovora siderophore-mediated iron acquisition plays a relevant role in the progression of Fire blight. Here we analyzed the taxonomic relations within Erwinia genus and the relevance of the genes related to the siderophore-mediated iron uptake pathway. The results of this study highlight the presence of a well-defined sub-group of Rosaceae infecting species taxonomically and genetically related with a high number of conserved core genes. The analysis of the complete ferrioxamine transport system has led to the identification of two genes exclusively present in the Rosaceae infecting strains.
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Affiliation(s)
- Ivan Polsinelli
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Luigimaria Borruso
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Rosanna Caliandro
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Luca Triboli
- Centre for Integrative Biology, University of Trento, via Sommarive n. 9, 38123, Povo, Trento, Italy
| | - Alfonso Esposito
- Centre for Integrative Biology, University of Trento, via Sommarive n. 9, 38123, Povo, Trento, Italy.
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy.
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18
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Draft Genome Sequence of an Erwinia tracheiphila Isolate from an Infected Muskmelon (Cucumis melo). Microbiol Resour Announc 2018; 7:MRA01058-18. [PMID: 30533754 PMCID: PMC6256489 DOI: 10.1128/mra.01058-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/04/2018] [Indexed: 02/01/2023] Open
Abstract
Erwinia tracheiphila is a bacterial plant pathogen emerging in eastern North America. To aid in understanding genetic variation within E. tracheiphila, here we sequence the first reference genome of an infected muskmelon (Cucumis melo). Erwinia tracheiphila is a bacterial plant pathogen emerging in eastern North America. To aid in understanding genetic variation within E. tracheiphila, here we sequence the first reference genome of an infected muskmelon (Cucumis melo). The genome assembles into a single chromosomal contig, three plasmid contigs, and one bacteriophage contig.
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19
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Shapiro LR, Paulson JN, Arnold BJ, Scully ED, Zhaxybayeva O, Pierce NE, Rocha J, Klepac-Ceraj V, Holton K, Kolter R. An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. mBio 2018; 9:e01307-18. [PMID: 30279283 PMCID: PMC6168856 DOI: 10.1128/mbio.01307-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/17/2018] [Indexed: 12/14/2022] Open
Abstract
Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits, an economically important phytopathogen affecting an economically important phytopathogen affecting few cultivated Cucurbitaceae few cultivated Cucurbitaceae host plant species in temperate eastern North America. However, essentially nothing is known about E. tracheiphila population structure or genetic diversity. To address this shortcoming, a representative collection of 88 E. tracheiphila isolates was gathered from throughout its geographic range, and their genomes were sequenced. Phylogenomic analysis revealed three genetic clusters with distinct hrpT3SS virulence gene repertoires, host plant association patterns, and geographic distributions. Low genetic heterogeneity within each cluster suggests a recent population bottleneck followed by population expansion. We showed that in the field and greenhouse, cucumber (Cucumis sativus), which was introduced to North America by early Spanish conquistadors, is the most susceptible host plant species and the only species susceptible to isolates from all three lineages. The establishment of large agricultural populations of highly susceptible C. sativus in temperate eastern North America may have facilitated the original emergence of E. tracheiphila into cucurbit agroecosystems, and this introduced plant species may now be acting as a highly susceptible reservoir host. Our findings have broad implications for agricultural sustainability by drawing attention to how worldwide crop plant movement, agricultural intensification, and locally unique environments may affect the emergence, evolution, and epidemic persistence of virulent microbial pathogens.IMPORTANCEErwinia tracheiphila is a virulent phytopathogen that infects two genera of cucurbit crop plants, Cucurbita spp. (pumpkin and squash) and Cucumis spp. (muskmelon and cucumber). One of the unusual ecological traits of this pathogen is that it is limited to temperate eastern North America. Here, we complete the first large-scale sequencing of an E. tracheiphila isolate collection. From phylogenomic, comparative genomic, and empirical analyses, we find that introduced Cucumis spp. crop plants are driving the diversification of E. tracheiphila into multiple lineages. Together, the results from this study show that locally unique biotic (plant population) and abiotic (climate) conditions can drive the evolutionary trajectories of locally endemic pathogens in unexpected ways.
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Affiliation(s)
- Lori R Shapiro
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., San Francisco, California, USA
| | - Brian J Arnold
- Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Erin D Scully
- Stored Product Insect and Engineering Research Unit, USDA-ARS Center for Grain and Animal Health Research, Manhattan, Kansas, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Computer Science, Dartmouth College, Hanover, New Hampshire, USA
| | - Naomi E Pierce
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jorge Rocha
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
- CIDEA Consortium Conacyt-Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Mexico
| | - Vanja Klepac-Ceraj
- Department of Biological Sciences, Wellesley College, Wellesley, Massachusetts, USA
| | - Kristina Holton
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Roberto Kolter
- Department of Microbiology and Immunology, Harvard Medical School, Boston, Massachusetts, USA
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20
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Arens DK, Brady TS, Carter JL, Pape JA, Robinson DM, Russell KA, Staley LA, Stettler JM, Tateoka OB, Townsend MH, Whitley KV, Wienclaw TM, Williamson TL, Johnson SM, Grose JH. Characterization of two related Erwinia myoviruses that are distant relatives of the PhiKZ-like Jumbo phages. PLoS One 2018; 13:e0200202. [PMID: 29979759 PMCID: PMC6034870 DOI: 10.1371/journal.pone.0200202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 06/21/2018] [Indexed: 12/25/2022] Open
Abstract
Bacteriophages are a major force in the evolution of bacteria due to their sheer abundance as well as their ability to infect and kill their hosts and to transfer genetic material. Bacteriophages that infect the Enterobacteriaceae family are of particular interest because this bacterial family contains dangerous animal and plant pathogens. Herein we report the isolation and characterization of two jumbo myovirus Erwinia phages, RisingSun and Joad, collected from apple trees. These two genomes are nearly identical with Joad harboring two additional putative gene products. Despite mass spectrometry data that support the putative annotation, 43% of their gene products have no significant BLASTP hit. These phages are also more closely related to Pseudomonas and Vibrio phages than to published Enterobacteriaceae phages. Of the 140 gene products with a BLASTP hit, 81% and 63% of the closest hits correspond to gene products from Pseudomonas and Vibrio phages, respectively. This relatedness may reflect their ecological niche, rather than the evolutionary history of their host. Despite the presence of over 800 Enterobacteriaceae phages on NCBI, the uniqueness of these two phages highlights the diversity of Enterobacteriaceae phages still to be discovered.
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Affiliation(s)
- Daniel K. Arens
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - T. Scott Brady
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - John L. Carter
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Jenny A. Pape
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - David M. Robinson
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Kerri A. Russell
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Lyndsay A. Staley
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Jason M. Stettler
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, United States of America
| | - Olivia B. Tateoka
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Michelle H. Townsend
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Kiara V. Whitley
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Trevor M. Wienclaw
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Taryn L. Williamson
- Plant and Wildlife Sciences Department, Brigham Young University, Provo, Utah, United States of America
| | - Steven M. Johnson
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
| | - Julianne H. Grose
- Microbiology and Molecular Biology Department, Brigham Young University, Provo, Utah, United States of America
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21
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Where are we going with genomics in plant pathogenic bacteria? Genomics 2018; 111:729-736. [PMID: 29678682 DOI: 10.1016/j.ygeno.2018.04.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
Abstract
Genome sequencing is commonly used in research laboratories right now thanks to the rise of high-throughput sequencing with higher speed and output-to-cost ratios. Here, we summarized the application of genomics in different aspects of plant bacterial pathosystems. Genomics has been used in studying the mechanisms of plant-bacteria interactions, and host specificity. It also helps with taxonomy, study of non-cultured bacteria, identification of causal agent, single cell sequencing, population genetics, and meta-transcriptomic. Overall, genomics has significantly improved our understanding of plant-microbe interaction.
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22
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Andrade-Domínguez A, Kolter R, Shapiro LR. Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila. GENOME ANNOUNCEMENTS 2018; 6:e00127-18. [PMID: 29472340 PMCID: PMC5824000 DOI: 10.1128/genomea.00127-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/20/2022]
Abstract
Erwinia tracheiphila is the causal agent of bacterial wilt of cucurbits. Here, we report the genome sequence of the temperate phage EtG, which was isolated from an E. tracheiphila-infected cucumber plant. Phage EtG has a linear 30,413-bp double-stranded DNA genome with cohesive ends and 45 predicted open reading frames.
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Affiliation(s)
- Andrés Andrade-Domínguez
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lori R Shapiro
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, USA
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23
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Borruso L, Salomone-Stagni M, Polsinelli I, Schmitt AO, Benini S. Conservation of Erwinia amylovora pathogenicity-relevant genes among Erwinia genomes. Arch Microbiol 2017; 199:1335-1344. [PMID: 28695265 PMCID: PMC5663808 DOI: 10.1007/s00203-017-1409-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/10/2017] [Accepted: 07/03/2017] [Indexed: 11/28/2022]
Abstract
The Erwinia genus comprises species that are plant pathogens, non-pathogen, epiphytes, and opportunistic human pathogens. Within the genus, Erwinia amylovora ranks among the top 10 plant pathogenic bacteria. It causes the fire blight disease and is a global threat to commercial apple and pear production. We analyzed the presence/absence of the E. amylovora genes reported to be important for pathogenicity towards Rosaceae within various Erwinia strains genomes. This simple bottom-up approach, allowed us to correlate the analyzed genes to pathogenicity, host specificity, and make useful considerations to drive targeted studies.
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Affiliation(s)
- Luigimaria Borruso
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Marco Salomone-Stagni
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Ivan Polsinelli
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy
| | - Armin Otto Schmitt
- Department of Nutztierwissenschaften, Breeding Informatics, Georg-August-Universität Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany
| | - Stefano Benini
- Bioorganic Chemistry and Bio-Crystallography Laboratory (B2Cl), Faculty of Science and Technology, Free University of Bolzano, Piazza Università 5, 39100, Bolzano, Italy.
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24
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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25
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De Maayer P, Aliyu H, Vikram S, Blom J, Duffy B, Cowan DA, Smits THM, Venter SN, Coutinho TA. Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii. Front Microbiol 2017; 8:1755. [PMID: 28959245 PMCID: PMC5603701 DOI: 10.3389/fmicb.2017.01755] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022] Open
Abstract
Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular and Cell Biology, University of the WitwatersrandJohannesburg, South Africa
| | - Habibu Aliyu
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Jochen Blom
- Department of Bioinformatics and Systems Biology, Justus-Liebig-University GiessenGiessen, Germany
| | - Brion Duffy
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Theo H. M. Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied SciencesWinterthur, Switzerland
| | - Stephanus N. Venter
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Teresa A. Coutinho
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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26
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Brader G, Compant S, Vescio K, Mitter B, Trognitz F, Ma LJ, Sessitsch A. Ecology and Genomic Insights into Plant-Pathogenic and Plant-Nonpathogenic Endophytes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:61-83. [PMID: 28489497 DOI: 10.1146/annurev-phyto-080516-035641] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plants are colonized on their surfaces and in the rhizosphere and phyllosphere by a multitude of different microorganisms and are inhabited internally by endophytes. Most endophytes act as commensals without any known effect on their plant host, but multiple bacteria and fungi establish a mutualistic relationship with plants, and some act as pathogens. The outcome of these plant-microbe interactions depends on biotic and abiotic environmental factors and on the genotype of the host and the interacting microorganism. In addition, endophytic microbiota and the manifold interactions between members, including pathogens, have a profound influence on the function of the system plant and the development of pathobiomes. In this review, we elaborate on the differences and similarities between nonpathogenic and pathogenic endophytes in terms of host plant response, colonization strategy, and genome content. We furthermore discuss environmental effects and biotic interactions within plant microbiota that influence pathogenesis and the pathobiome.
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Affiliation(s)
- Günter Brader
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Stéphane Compant
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Kathryn Vescio
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
| | - Birgit Mitter
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Friederike Trognitz
- Center for Health and Bioresources, Bioresources Unit, Austrian Institute of Technology (AIT), 3430 Tulln, Austria
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
| | - Angela Sessitsch
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003;
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McCann HC, Li L, Liu Y, Li D, Pan H, Zhong C, Rikkerink EH, Templeton MD, Straub C, Colombi E, Rainey PB, Huang H. Origin and Evolution of the Kiwifruit Canker Pandemic. Genome Biol Evol 2017; 9:932-944. [PMID: 28369338 PMCID: PMC5388287 DOI: 10.1093/gbe/evx055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2017] [Indexed: 12/18/2022] Open
Abstract
Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.
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Affiliation(s)
- Honour C. McCann
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Li Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Yifei Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Hui Pan
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Erik H.A. Rikkerink
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Matthew D. Templeton
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, New Zealand
| | - Christina Straub
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Elena Colombi
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231 PSL Research University, Paris, France
| | - Hongwen Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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