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Topalović O, Radaković ZS, Elhady A, Bredenbruch S, Heuer H. Investigations on Microbes Attached to the Cuticle of Phytonematodes. Methods Mol Biol 2024; 2756:257-270. [PMID: 38427298 DOI: 10.1007/978-1-0716-3638-1_7] [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: 03/02/2024]
Abstract
Nematodes form various associations with soil microbiome. Experimental studies on nematode-attached microbes can improve mechanistic understanding of these associations and lead to new discoveries relevant for the field of nematode biocontrol. Microbial attachment to the surface of phytonematodes is very specific and influenced by a multitude of factors, including the designation of nematodes and microbes, environmental and biological factors in soil, time of incubation, and the ratio and evolutionary trajectories between nematodes and microbes. Here, we describe how the classical nematological and microbiological techniques can be coupled with the advanced molecular tools to study the microbial attachment to phytonematodes in soil. We focus on the characterization of nematode-attached microbes using classical microbiological approaches and high-throughput amplicon sequencing and on the effects of nematode-attached microbes on plant defense responses.
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Affiliation(s)
- Olivera Topalović
- Department of Biology, Section of Terrestrial Ecology, University of Copenhagen, Copenhagen, Denmark.
| | - Zoran S Radaković
- Laboratory of Insect and Nematode Management, Corteva Agriscience Research, Center Eschbach, Eschbach, Germany
| | - Ahmed Elhady
- Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Germany
| | - Sandra Bredenbruch
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES-Molecular Phytomedicine, Bonn, Germany
| | - Holger Heuer
- Epidemiology and Pathogen Diagnostics, Julius Kuehn Institute, Braunschweig, Germany
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2
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Davies KG, Mohan S, Phani V, Srivastava A. Exploring the mechanisms of host-specificity of a hyperparasitic bacterium ( Pasteuria spp.) with potential to control tropical root-knot nematodes ( Meloidogyne spp.): insights from Caenorhabditis elegans. Front Cell Infect Microbiol 2023; 13:1296293. [PMID: 38173791 PMCID: PMC10761439 DOI: 10.3389/fcimb.2023.1296293] [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: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 01/05/2024] Open
Abstract
Plant-parasitic nematodes are important economic pests of a range of tropical crops. Strategies for managing these pests have relied on a range of approaches, including crop rotation, the utilization of genetic resistance, cultural techniques, and since the 1950's the use of nematicides. Although nematicides have been hugely successful in controlling nematodes, their toxicity to humans, domestic animals, beneficial organisms, and the environment has raised concerns regarding their use. Alternatives are therefore being sought. The Pasteuria group of bacteria that form endospores has generated much interest among companies wanting to develop microbial biocontrol products. A major challenge in developing these bacteria as biocontrol agents is their host-specificity; one population of the bacterium can attach to and infect one population of plant-parasitic nematode but not another of the same species. Here we will review the mechanism by which infection is initiated with the adhesion of endospores to the nematode cuticle. To understand the genetics of the molecular processes between Pasteuria endospores and the nematode cuticle, the review focuses on the nature of the bacterial adhesins and how they interact with the nematode cuticle receptors by exploiting new insights gained from studies of bacterial infections of Carnorhabditis elegans. A new Velcro-like multiple adhesin model is proposed in which the cuticle surface coat, which has an important role in endospore adhesion, is a complex extracellular matrix containing glycans originating in seam cells. The genes associated with these seam cells appear to have a dual role by retaining some characteristics of stem cells.
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Affiliation(s)
- Keith G. Davies
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Sharad Mohan
- Division of Nematology, Indian Agricultural Research Institute, New Delhi, India
| | - Victor Phani
- Department of Agricultural Entomology, College of Agriculture, Uttar Banga Krishi Viswavidyalaya, Dakshin Dinajpur, West Bengal, India
| | - Arohi Srivastava
- Dr. D. Y Patil Biotechnology & Bioinformatics Institute, Dr. D. Y. Patil Vidyapeeth, Pune, India
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3
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Maciag T, Kozieł E, Rusin P, Otulak-Kozieł K, Jafra S, Czajkowski R. Microbial Consortia for Plant Protection against Diseases: More than the Sum of Its Parts. Int J Mol Sci 2023; 24:12227. [PMID: 37569603 PMCID: PMC10418420 DOI: 10.3390/ijms241512227] [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: 07/12/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Biological plant protection presents a promising and exciting alternative to chemical methods for safeguarding plants against the increasing threats posed by plant diseases. This approach revolves around the utilization of biological control agents (BCAs) to suppress the activity of significant plant pathogens. Microbial BCAs have the potential to effectively manage crop disease development by interacting with pathogens or plant hosts, thereby increasing their resistance. However, the current efficacy of biological methods remains unsatisfactory, creating new research opportunities for sustainable plant cultivation management. In this context, microbial consortia, comprising multiple microorganisms with diverse mechanisms of action, hold promise in terms of augmenting the magnitude and stability of the overall antipathogen effect. Despite scientific efforts to identify or construct microbial consortia that can aid in safeguarding vital crops, only a limited number of microbial consortia-based biocontrol formulations are currently available. Therefore, this article aims to present a complex analysis of the microbial consortia-based biocontrol status and explore potential future directions for biological plant protection research with new technological advancements.
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Affiliation(s)
- Tomasz Maciag
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Edmund Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Piotr Rusin
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Katarzyna Otulak-Kozieł
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences—SGGW, Nowoursynowska Street 159, 02-776 Warsaw, Poland
| | - Sylwia Jafra
- Division of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Antoniego Abrahama Street 58, 80-307 Gdansk, Poland
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Price-Christenson G, Yannarell A. Use of Ecological Theory to Understand the Efficacy and Mechanisms of Multistrain Biological Control. PHYTOPATHOLOGY 2023; 113:381-389. [PMID: 36656290 DOI: 10.1094/phyto-04-22-0115-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Since the 1970s, over 6,500 articles have been published about microbial biocontrols and over 200 microbial isolates have been registered for commercial use. However, many of these solutions have seen limited use due to limitations with their in-field efficacy. Even when multiple biocontrol agents are combined to create multistrain biocontrols, the resulting combinations can be less effective than the individual agents. One likely contributor is due to how multistrain microbial biocontrols are created. Multistrain microbial biocontrols are generally produced under controlled settings that are divorced from the ecological conditions they will need to function under. Traditionally, researchers culture, identify, and screen isolates for pathogen suppression traits. Then these researchers will combine the most promising isolates in an attempt to create more effective solutions. This approach, while effective for identifying suppressive isolates and determining the mechanisms of pathogen suppression, does not take into consideration the variability of natural environments, nor the complex ecological interactions that occur between plant hosts, pathogens, and component biocontrol agents, thus limiting the range of circumstances that these multistrain solutions can reliably succeed. To address these limitations, we suggest the application of relevant ecological theory to determine which isolates should be combined to create more reliable multistrain biocontrols. In this synthesis, we build on prior work focused on addressing plant pathogens through the use of multistrain microbial biocontrols, but we argue that viewing this work through the lens of ecology reveals key "design principles" from natural communities that are stable, functioning, and comprise multiple species.
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Affiliation(s)
- Gabriel Price-Christenson
- Department of Agricultural Microbiology, Earnest Agriculture, Rantoul, IL 61866
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Anthony Yannarell
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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5
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Comparative genomic analysis of Echinococcus multilocularis with other tapeworms. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01120-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Srivastava A, Mohan S, Davies KG. Exploring Bacillus thuringiensis as a model for endospore adhesion and its potential to investigate adhesins in Pasteuria penetrans. J Appl Microbiol 2022; 132:4371-4387. [PMID: 35286009 PMCID: PMC9311801 DOI: 10.1111/jam.15522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/30/2022]
Abstract
Aims Phytonematodes are a constraint on crop production and have been controlled using nematicides; these are highly toxic and legislation in Europe and elsewhere is prohibiting their use and alternatives are being sought. Pasteuria penetrans is a hyperparasitic bacterium that form endospores and have potential to control root‐knot nematodes (Meloidogyne spp.), but their attachment to the nematode cuticle is host‐specific. Understanding host specificity has relied upon endospore inhibition bioassays using immunological and biochemical approaches. Phylogenetic analysis of survey sequences has shown P. penetrans to be closely related to Bacillus and to have a diverse range of collagen‐like fibres which we hypothesise to be involved in the endospore adhesion. However, due to the obligately hyperparasitic nature of Pasteuria species, identifying and characterizing these collagenous‐like proteins through gain of function has proved difficult and new approaches are required. Methods and Results Using antibodies raised to synthetic peptides based on Pasteuria collagen‐like genes we show similarities between P. penetrans and the more easily cultured bacterium Bacillus thuringiensis and suggest it be used as a gain of function platform/model. Using immunological approaches similar proteins between P. penetrans and B. thuringiensis are identified and characterized, one >250 kDa and another ~72 kDa are glycosylated with N‐acetylglucosamine and both of which are digested if treated with collagenase. These treatments also affected endospore attachment and suggest these proteins are involved in adhesion of endospores to nematode cuticle. Conclusion There are conserved similarities in the collagen‐like proteins present on the surface of endospores of both P. penetrans and B. thuringiensis. Significance and Impact of Study As B. thuringiensis is relatively easy to culture and can be transformed, it could be developed as a platform for studying the role of the collagen‐like adhesins from Pasteuria in endospore adhesion.
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Affiliation(s)
- Arohi Srivastava
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Sharad Mohan
- Division of Nematology, Indian Agricultural Research Institute, Pusa Campus, New Delhi110012, India
| | - Keith G Davies
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
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Fredericksen M, Ameline C, Krebs M, Hüssy B, Fields PD, Andras JP, Ebert D. Infection phenotypes of a coevolving parasite are highly diverse, structured, and specific. Evolution 2021; 75:2540-2554. [PMID: 34431523 PMCID: PMC9290032 DOI: 10.1111/evo.14323] [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: 03/13/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/27/2022]
Abstract
Understanding how diversity is maintained in natural populations is a major goal of evolutionary biology. In coevolving hosts and parasites, negative frequency-dependent selection is one mechanism predicted to maintain genetic variation. While much is known about host diversity, parasite diversity remains understudied in coevolutionary research. Here, we survey natural diversity in a bacterial parasite by characterizing infection phenotypes for over 50 isolates in relation to 12 genotypes of their host, Daphnia magna. We find striking phenotypic variation among parasite isolates, and we discover the parasite can infect its host through at least five different attachment sites. Variation in attachment success at each site is explained to varying degrees by host and parasite genotypes. A spatial correlation analysis showed that infectivity of different isolates does not correlate with geographic distance, meaning isolates from widespread populations are equally able to infect the host. Overall, our results reveal that infection phenotypes of this parasite are highly diverse. Our results are consistent with the prediction that under Red Queen coevolutionary dynamics both the host and the parasite should show high genetic diversity for traits of functional importance in their interactions.
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Affiliation(s)
- Maridel Fredericksen
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Camille Ameline
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Michelle Krebs
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Benjamin Hüssy
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
| | - Jason P Andras
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland.,Department of Biological Sciences, Clapp Laboratory, Mount Holyoke College, South Hadley, Massachusetts
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, CH-4051, Switzerland
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Topalović O, Vestergård M. Can microorganisms assist the survival and parasitism of plant-parasitic nematodes? Trends Parasitol 2021; 37:947-958. [PMID: 34162521 DOI: 10.1016/j.pt.2021.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/19/2021] [Accepted: 05/20/2021] [Indexed: 12/14/2022]
Abstract
Plant-parasitic nematodes (PPNs) remain a hardly treatable problem in many crops worldwide. Low efficacy of many biocontrol agents may be due to negligence of the native microbiota that is naturally associated with nematodes in soil, and which may protect nematodes against microbial antagonists. This phenomenon is more extensively studied for other nematode parasites, so we compiled these studies and drew parallels to the existing knowledge on PPN. We describe how microbial-mediated modulation of host immune responses facilitate nematode parasitism and discuss the role of Caenorhabditis elegans-protective microbiota to get an insight into the microbial protection of PPNs in soil. Molecular mechanisms of PPN-microbial interactions are also discussed. An understanding of microbial-aided PPN performance is thus pivotal for efficient management of PPNs.
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Affiliation(s)
- Olivera Topalović
- Aarhus University, Institute for Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark.
| | - Mette Vestergård
- Aarhus University, Institute for Agroecology, Faculty of Technical Sciences, Aarhus University, 4200, Slagelse, Denmark.
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9
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Andras JP, Fields PD, Du Pasquier L, Fredericksen M, Ebert D. Genome-Wide Association Analysis Identifies a Genetic Basis of Infectivity in a Model Bacterial Pathogen. Mol Biol Evol 2021; 37:3439-3452. [PMID: 32658956 PMCID: PMC7743900 DOI: 10.1093/molbev/msaa173] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/22/2020] [Accepted: 07/08/2020] [Indexed: 12/22/2022] Open
Abstract
Knowledge of the genetic architecture of pathogen infectivity and host resistance is essential for a mechanistic understanding of coevolutionary processes, yet the genetic basis of these interacting traits remains unknown for most host-pathogen systems. We used a comparative genomic approach to explore the genetic basis of infectivity in Pasteuria ramosa, a Gram-positive bacterial pathogen of planktonic crustaceans that has been established as a model for studies of Red Queen host-pathogen coevolution. We sequenced the genomes of a geographically, phenotypically, and genetically diverse collection of P. ramosa strains and performed a genome-wide association study to identify genetic correlates of infection phenotype. We found multiple polymorphisms within a single gene, Pcl7, that correlate perfectly with one common and widespread infection phenotype. We then confirmed this perfect association via Sanger sequencing in a large and diverse sample set of P. ramosa clones. Pcl7 codes for a collagen-like protein, a class of adhesion proteins known or suspected to be involved in the infection mechanisms of a number of important bacterial pathogens. Consistent with expectations under Red Queen coevolution, sequence variation of Pcl7 shows evidence of balancing selection, including extraordinarily high diversity and absence of geographic structure. Based on structural homology with a collagen-like protein of Bacillus anthracis, we propose a hypothesis for the structure of Pcl7 and the physical location of the phenotype-associated polymorphisms. Our results offer strong evidence for a gene governing infectivity and provide a molecular basis for further study of Red Queen dynamics in this model host-pathogen system.
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Affiliation(s)
- Jason P Andras
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA
| | - Peter D Fields
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Louis Du Pasquier
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Maridel Fredericksen
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Dieter Ebert
- Division of Zoology, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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10
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Biological control: a novel strategy for the control of the plant parasitic nematodes. Antonie van Leeuwenhoek 2021; 114:885-912. [PMID: 33893903 DOI: 10.1007/s10482-021-01577-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 11/25/2022]
Abstract
Plant parasitic nematodes (Root-knot nematodes, Meloidogyne spp.) are rounded worms, microscopic, and cause many agricultural economic losses. Their attacks have a direct impact on the productivity of cultivated crops by reducing their fruit quantity. Chemical control is widespread all over the world, but biological control is the most effective way to reduce the number of pests that infect crops, particularly by the use of microorganisms like fungi and bacteria. Biological control is rapidly evolving, and more products are being sold worldwide over time. They can be produced by fungi, bacteria, or actinomycetes that can destruct plant parasite nematodes and feed on them. Nematophagous microorganisms as the natural enemies of nematodes have a promising way of controlling nematodes. Some of them create net-like substances and traps to take the worms from outside and finally kill them. Other parasites serve as internal parasites in order to produce toxins and to produce virulence to kill nematodes. Comprehension of the molecular basis for microbial nematode interactions gives important insights into how successful biological nematode control agents can be created. We discuss recent advances in our understanding of nematodes and nematophagous microorganisms, with an emphasis on molecular mechanisms that infect nematodes with nematophagous microorganisms and on nematode safety from pathogenic attacks. Finally, we addressed numerous key areas for future research and development, including possible approaches to the application of our recent expertise in the development of successful biocontrol strategies.
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Qiu Y, Zhai C, Chen L, Liu X, Yeo J. Current Insights on the Diverse Structures and Functions in Bacterial Collagen-like Proteins. ACS Biomater Sci Eng 2021. [PMID: 33871954 DOI: 10.1021/acsbiomaterials.1c00018] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The dearth of knowledge on the diverse structures and functions in bacterial collagen-like proteins is in stark contrast to the deep grasp of structures and functions in mammalian collagen, the ubiquitous triple-helical scleroprotein that plays a central role in tissue architecture, extracellular matrix organization, and signal transduction. To fill and highlight existing gaps due to the general paucity of data on bacterial CLPs, we comprehensively reviewed the latest insight into their functional and structural diversity from multiple perspectives of biology, computational simulations, and materials engineering. The origins and discovery of bacterial CLPs were explored. Their genetic distribution and molecular architecture were analyzed, and their structural and functional diversity in various bacterial genera was examined. The principal roles of computational techniques in understanding bacterial CLPs' structural stability, mechanical properties, and biological functions were also considered. This review serves to drive further interest and development of bacterial CLPs, not only for addressing fundamental biological problems in collagen but also for engineering novel biomaterials. Hence, both biology and materials communities will greatly benefit from intensified research into the diverse structures and functions in bacterial collagen-like proteins.
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Affiliation(s)
- Yimin Qiu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China.,State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, PR China
| | - Chenxi Zhai
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
| | - Ling Chen
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Xiaoyan Liu
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, PR China
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials, Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York 14850, United States
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Topalović O, Hussain M, Heuer H. Plants and Associated Soil Microbiota Cooperatively Suppress Plant-Parasitic Nematodes. Front Microbiol 2020; 11:313. [PMID: 32184773 PMCID: PMC7058703 DOI: 10.3389/fmicb.2020.00313] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 02/12/2020] [Indexed: 12/27/2022] Open
Abstract
Disease suppressive soils with specific suppression of soil-borne pathogens and parasites have been long studied and are most often of microbiological origin. As for the plant-parasitic nematodes (PPN), which represent a huge threat to agricultural crops and which successfully defy many conventional control methods, soil progression from conducive to suppressive state is accompanied by the enrichment of specific antagonistic microbial consortia. However, a few microbial groups have come to the fore in diminishing PPN in disease suppressive soils using culture-dependent methods. Studies with cultured strains resulted in understanding the mechanisms by which nematodes are antagonized by microorganisms. Recent culture-independent studies on the microbiome associated with soil, plant roots, and PPN contributed to a better understanding of the functional potential of disease suppressive microbial cohort. Plant root exudation is an important pathway determining host-microbe communication and plays a key role in selection and enrichment of a specific set of microbial antagonists in the rhizosphere as first line of defense against crop pathogens or parasites. Root exudates comprising primary metabolites such as amino acids, sugars, organic acids, and secondary metabolites can also cause modifications in the nematode surface and subsequently affect microbial attachment. A positive interaction between hosts and their beneficial root microbiota is correlated with a low nematode performance on the host. In this review, we first summarized the historical records of nematode-suppressive soils and then focused on more recent studies in this aspect, emphasizing the advances in studying nematode-microbe interactions over time. We highlighted nematode biocontrol mechanisms, especially parasitism, induced systemic resistance, and volatile organic compounds using microbial consortia, or bacterial strains of the genera Pasteuria, Bacillus, Pseudomonas, Rhizobium, Streptomyces, Arthrobacter, and Variovorax, or fungal isolates of Pochonia, Dactylella, Nematophthora, Purpureocillium, Trichoderma, Hirsutella, Arthrobotrys, and Mortierella. We discussed the importance of root exudates in plant communication with PPN and soil microorganisms, emphasizing their role in microbial attachment to the nematode surface and subsequent events of nematode parasitism. Comprehensive understanding of the plant-beneficial microbial consortia and the mechanisms underlying disease suppression may help to develop synthetic microbial communities for biocontrol of PPN, thereby reducing nematicides and fertilizers inputs.
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Affiliation(s)
- Olivera Topalović
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang, China
| | - Holger Heuer
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany
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13
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Mohan S, Kiran Kumar K, Sutar V, Saha S, Rowe J, Davies KG. Plant Root-Exudates Recruit Hyperparasitic Bacteria of Phytonematodes by Altered Cuticle Aging: Implications for Biological Control Strategies. FRONTIERS IN PLANT SCIENCE 2020; 11:763. [PMID: 32582268 PMCID: PMC7296116 DOI: 10.3389/fpls.2020.00763] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/13/2020] [Indexed: 05/21/2023]
Abstract
Phytonematodes are globally important functional components of the belowground ecology in both natural and agricultural soils; they are a diverse group of which some species are economically important pests, and environmentally benign control strategies are being sought to control them. Using eco-evolutionary theory, we test the hypothesis that root-exudates of host plants will increase the ability of a hyperparasitic bacteria, Pasteuria penetrans and other closely related bacteria, to infect their homologous pest nematodes, whereas non-host root exudates will not. Plant root-exudates from good hosts, poor hosts and non-hosts were characterized by gas chromatography-mass spectrometry (GC/MS) and we explore their interaction on the attachment of the hyperparasitic bacterial endospores to homologous and heterologous pest nematode cuticles. Although GC/MS did not identify any individual compounds as responsible for changes in cuticle susceptibility to endospore adhesion, standardized spore binding assays showed that Pasteuria endospore adhesion decreased with nematode age, and that infective juveniles pre-treated with homologous host root-exudates reduced the aging process and increased attachment of endospores to the nematode cuticle, whereas non-host root-exudates did not. We develop a working model in which plant root exudates manipulate the nematode cuticle aging process, and thereby, through increased bacterial endospore attachment, increase bacterial infection of pest nematodes. This we suggest would lead to a reduction of plant-parasitic nematode burden on the roots and increases plant fitness. Therefore, by the judicious manipulation of environmental factors produced by the plant root and by careful crop rotation this knowledge can help in the development of environmentally benign control strategies.
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Affiliation(s)
- Sharad Mohan
- Division of Nematology, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Sharad Mohan,
| | - K. Kiran Kumar
- Indian Council of Agricultural Research, Central Citrus Research Institute, Nagpur, India
| | - Vivek Sutar
- Division of Nematology, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi, India
| | - Supradip Saha
- Division of Agricultural Chemicals, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi, India
| | - Janet Rowe
- Plant Pathology and Microbiology, Rothamsted Research, Harpenden, United Kingdom
| | - Keith G. Davies
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, United Kingdom
- Norwegian Institute of Bioeconomy Research, Ås, Norway
- Keith G. Davies,
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Srivastava A, Mohan S, Mauchline TH, Davies KG. Evidence for diversifying selection of genetic regions of encoding putative collagen-like host-adhesive fibers in Pasteuria penetrans. FEMS Microbiol Ecol 2019; 95:5149496. [PMID: 30380051 PMCID: PMC6238073 DOI: 10.1093/femsec/fiy217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/29/2018] [Indexed: 11/16/2022] Open
Abstract
Pasteuria spp. belong to a group of genetically diverse endospore-forming bacteria (phylum: Firmicutes) that are known to parasitize plant-parasitic nematodes and water fleas (Daphnia spp.). Collagen-like fibres form the nap on the surface of endospores and the genes encoding these sequences have been hypothesised to be involved in the adhesion of the endospores of Pasteuria spp. to their hosts. We report a group of 17 unique collagen-like genes putatively encoded by Pasteuria penetrans (strain: Res148) that formed five different phylogenetic clusters and suggest that collagen-like proteins are an important source of genetic diversity in animal pathogenic Firmicutes including Pasteuria. Additionally, and unexpectedly, we identified a putative collagen-like sequence which had a very different sequence structure to the other collagen-like proteins but was similar to the protein sequences in Megaviruses that are involved in host-parasite interactions. We, therefore, suggest that these diverse endospore surface proteins in Pasteuria are involved in biological functions, such as cellular adhesion; however, they are not of monophyletic origin and were possibly obtained de novo by mutation or possibly through selection acting upon several historic horizontal gene transfer events.
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Affiliation(s)
- Arohi Srivastava
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Sharad Mohan
- Division of Nematology, Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Tim H Mauchline
- Department of AgroEcology, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Keith G Davies
- Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Postboks 115, Ås-1431, Norway
- Corresponding author: Keith G Davies, Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK. E-mail:
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15
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Dyrdahl-Young R, Hu W, DiGennaro P. Temporal expression patterns of Pasteuria spp. sporulation genes. J Nematol 2019; 51:e2019-39. [PMID: 34179813 PMCID: PMC6916136 DOI: 10.21307/jofnem-2019-039] [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: 12/12/2018] [Indexed: 11/11/2022] Open
Abstract
Endospore-forming bacterium in the genus Pasteuria spp. infect multiple agriculturally significant plant parasitic nematodes and has potential as a potent biological control. Success as a biological control requires not only spore attachment to the cuticle, but sporulation and reproduction within the nematode host. Tracking and identifying Pasteuria spp. development is then critical to demonstrating efficacy as a biocontrol. Microscopic observations suggest Pasteuria spp. follows the model bacterium, Bacillus subtilis, sporulation. Here, we identified B. subtilis homologs of sporulation regulators in Pasteuria spp. and characterized the temporal expression of these genes throughout the bacterium's ∼30-d lifecycle in Meloidogyne arenaria as a means of tracking sporulation development. Detectable levels of transcripts of Spo0F were present as early as 5 d after the nematodes were exposes to Pasteuria spp. and were relatively constant throughout the 30-d lifecycle. Transcripts to Sigma-F were significantly higher in the middle of the lifecycle, while the transcripts of Sigma-G were detectable between 15 and 25 d, nearing the end of the lifecycle. These three markers can be used to track the process of sporulation in the nematode and augment microscopic observations. Tracking sporulation of Pasteuria spp. is important to fully realize its potential as a biological control method as it can more readily identify successful parasitism, define host ranges, and inform in vitro growth progress.
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Affiliation(s)
| | - Weiming Hu
- Department of Entomology and Nematology, University of Florida, Gainesville, FL32611
| | - Peter DiGennaro
- Department of Entomology and Nematology, University of Florida, Gainesville, FL32611
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16
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Ben-Ami F. Host Age Effects in Invertebrates: Epidemiological, Ecological, and Evolutionary Implications. Trends Parasitol 2019; 35:466-480. [PMID: 31003758 DOI: 10.1016/j.pt.2019.03.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/19/2019] [Accepted: 03/21/2019] [Indexed: 12/26/2022]
Abstract
In most species, variation in age among individuals is the strongest and most visible form of phenotypic variation. Individual-level age effects on disease traits, caused by differences in the age at exposure of the host or its parents, have been widely documented in invertebrates. They can influence diverse traits, such as host susceptibility, virulence, parasite reproduction and further transmission, and may cascade to the population level, influencing disease prevalence and within-host competition. Here, I summarize what is known about the relationship between individual-level age/stage effects and infectious disease in invertebrates. I also attempt to link age effects to the theory of aging (senescence), and highlight the importance of population age structure to disease epidemiology and evolution. I conclude by identifying gaps in our understanding of individual- and population-level age effects in invertebrates. As the age structure of populations varies across space and time, age effects have strong epidemiological, ecological, and evolutionary implications for explaining variation in infectious diseases of invertebrates.
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Affiliation(s)
- Frida Ben-Ami
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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17
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Liu C, Gibson AK, Timper P, Morran LT, Tubbs RS. Rapid change in host specificity in a field population of the biological control organism Pasteuria penetrans. Evol Appl 2019; 12:744-756. [PMID: 30976307 PMCID: PMC6439493 DOI: 10.1111/eva.12750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 11/21/2018] [Accepted: 11/28/2018] [Indexed: 12/29/2022] Open
Abstract
In biological control, populations of both the biological control agent and the pest have the potential to evolve and even to coevolve. This feature marks the most powerful and unpredictable aspect of biological control strategies. In particular, evolutionary change in host specificity of the biological control agent could increase or decrease its efficacy. Here, we tested for change in host specificity in a field population of the biological control organism Pasteuria penetrans. Pasteuria penetrans is an obligate parasite of the plant parasitic nematodes Meloidogyne spp., which are major agricultural pests. From 2013 through 2016, we collected yearly samples of P. penetrans from eight plots in a field infested with M. arenaria. Plots were planted either with peanut (Arachis hypogaea) or with a rotation of peanut and soybean (Glycine max). To detect temporal change in host specificity, we tested P. penetrans samples annually for their ability to attach to (and thereby infect) four clonal lines of M. arenaria. After controlling for temporal variation in parasite abundance, we found that P. penetrans from each of the eight plots showed temporal variation in their attachment specificity to the clonal host lines. The trajectories of change in host specificity were largely unique to each plot. This result suggests that local forces, at the level of individual plots, drive change in specificity. We hypothesize that coevolution with local M. arenaria hosts may be one such force. Lastly, we observed an overall reduction in attachment rate with samples from rotation plots relative to samples from peanut plots. This result may reflect lower abundance of P. penetrans under crop rotation, potentially due to suppressed density of host nematodes. As a whole, the results show local change in specificity on a yearly basis, consistent with evolution of a biological control organism in its ability to infect and suppress its target pest.
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Affiliation(s)
- Chang Liu
- Department of Plant PathologyUniversity of GeorgiaTiftonGeorgia
| | | | | | | | - R. Scott Tubbs
- Crop and Soil Sciences, College of Agricultural and Environmental SciencesUniversity of GeorgiaTiftonGeorgia
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18
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Phani V, Shivakumara TN, Davies KG, Rao U. Knockdown of a mucin-like gene in Meloidogyne incognita (Nematoda) decreases attachment of endospores of Pasteuria penetrans to the infective juveniles and reduces nematode fecundity. MOLECULAR PLANT PATHOLOGY 2018; 19:2370-2383. [PMID: 30011135 PMCID: PMC6638177 DOI: 10.1111/mpp.12704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/14/2018] [Accepted: 06/08/2018] [Indexed: 05/30/2023]
Abstract
Mucins are highly glycosylated polypeptides involved in many host-parasite interactions, but their function in plant-parasitic nematodes is still unknown. In this study, a mucin-like gene was cloned from Meloidogyne incognita (Mi-muc-1, 1125 bp) and characterized. The protein was found to be rich in serine and threonine with numerous O-glycosylation sites in the sequence. Quantitative real-time polymerase chain reaction (qRT-PCR) showed the highest expression in the adult female and in situ hybridization revealed the localization of Mi-muc-1 mRNA expression in the tail area in the region of the phasmid. Knockdown of Mi-muc-1 revealed a dual role: (1) immunologically, there was a significant decrease in attachment of Pasteuria penetrans endospores and a reduction in binding assays with human red blood cells (RBCs), suggesting that Mi-MUC-1 is a glycoprotein present on the surface coat of infective second-stage juveniles (J2s) and is involved in cellular adhesion to the cuticle of infective J2s; pretreatment of J2s with different carbohydrates indicated that the RBCs bind to J2 cuticle receptors different from those involved in the interaction of Pasteuria endospores with Mi-MUC-1; (2) the long-term effect of RNA interference (RNAi)-mediated knockdown of Mi-muc-1 led to a significant reduction in nematode fecundity, suggesting a possible function for this mucin as a mediator in the interaction between the nematode and the host plant.
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Affiliation(s)
- Victor Phani
- Division of NematologyICAR‐Indian Agricultural Research InstituteNew Delhi110012India
| | | | - Keith G Davies
- Department of Biological and Environmental SciencesUniversity of HertfordshireHatfieldAL10 9ABUnited Kingdom
- Norwegian Institute of Bioeconomy ResearchÅs115, 1431Norway
| | - Uma Rao
- Division of NematologyICAR‐Indian Agricultural Research InstituteNew Delhi110012India
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19
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Phani V, Somvanshi VS, Rao U. Silencing of a Meloidogyne incognita selenium-binding protein alters the cuticular adhesion of Pasteuria penetrans endospores. Gene 2018; 677:289-298. [PMID: 30125659 DOI: 10.1016/j.gene.2018.08.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/30/2018] [Accepted: 08/16/2018] [Indexed: 11/30/2022]
Abstract
Pasteuria penetrans is an endospore forming hyperparasitic bacterium of the plant-pathogenic root-knot nematode, Meloidogyne incognita. For successful parasitization, the first step is adherence of bacterial endospores onto the cuticle surface of nematode juveniles. The knowledge of molecular intricacies involved during this adherence is sparse. Here, we identified a M. incognita selenium-binding protein (Mi-SeBP-1) differentially expressed during the initial interaction of M. incognita and P. penetrans, and show that it is involved in modulating parasitic adhesion of bacterial endospores onto nematode cuticle. Selenium-binding proteins (SeBPs) are selenium associated proteins important for growth regulation, tumor prevention and modulation of oxidation/reduction in cells. Although reported to be present in several nematodes, the function of SeBPs is not known in Phylum Nematoda. In situ hybridization assay localized the Mi-SeBP-1 mRNA to the hypodermal cells. RNAi-mediated silencing of Mi-SeBP-1 significantly increased the adherence of P. penetrans endospores to the nematode juvenile cuticle. Silencing of Mi-SeBP-1 did not change the nematode's ability to parasitize plants and reproduction potential within the host. These results suggest that M. incognita Mi-SeBP-1 might be involved in altering the attachment of microbial pathogens on the nematode cuticle, but is not involved in nematode-host plant interaction. This is the first report for a function of SeBP in Phylum Nematoda.
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Affiliation(s)
- Victor Phani
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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20
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Phani V, Shivakumara TN, Davies KG, Rao U. Meloidogyne incognita Fatty Acid- and Retinol- Binding Protein (Mi-FAR-1) Affects Nematode Infection of Plant Roots and the Attachment of Pasteuria penetrans Endospores. Front Microbiol 2017; 8:2122. [PMID: 29209280 PMCID: PMC5701614 DOI: 10.3389/fmicb.2017.02122] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/18/2017] [Indexed: 11/13/2022] Open
Abstract
Root-knot nematode (RKN) Meloidogyne incognita is an economically important pest of crops. Pasteuria penetrans, is a nematode hyperparasitic bacterium capable of suppressing the reproduction of RKN and thereby useful for its management. Secreted fatty acid and retinol-binding proteins are unique in nematodes and are engaged in nutrient acquisition, development and reproduction; they are also a component of the nematode cuticle and thought to be involved in the interface between hosts and parasites. Attachment of endospores to the cuticle of second stage juveniles of RKN is the primary step of infection and several factors have been identified to facilitate attachment. In this study, the full length of Mi-far-1 (573 bp) was cloned from M. incognita and characterized. Analysis revealed that the Mi-far-1 was rich in α-helix structure, contained a predicted consensus casein kinase II phosphorylation site and a glycosylation site. Quantitative PCR showed the highest expression in the fourth stage juveniles and in situ hybridization revealed the presence of Mi-far-1 mRNA in the hypodermis below the cuticle. Single copy insertion pattern of Mi-far-1 in M. incognita genome was detected by Southern blotting. Knockdown of Mi-far-1 showed significantly increased attachment of P. penetrans’ endospores on juvenile cuticle surface and also affected host finding, root infection and nematode fecundity.
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Affiliation(s)
- Victor Phani
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Keith G Davies
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom.,Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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21
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Bourgeois Y, Roulin AC, Müller K, Ebert D. Parasitism drives host genome evolution: Insights from thePasteuria ramosa-Daphnia magnasystem. Evolution 2017; 71:1106-1113. [DOI: 10.1111/evo.13209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/16/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Yann Bourgeois
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
| | - Anne C. Roulin
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
- Institute of Plant and Microbial Biology; Zollikerstrasse 107 8008 Zürich Switzerland
| | - Kristina Müller
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
| | - Dieter Ebert
- Zoological Institute; Basel University; Vesalgasse 1 4051 Basel Switzerland
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22
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Bell NL, Adam KH, Jones RJ, Johnson RD, Mtandavari YF, Burch G, Cave V, Cameron C, Maclean P, Popay AJ, Fleetwood D. Detection of Invertebrate Suppressive Soils, and Identification of a Possible Biological Control Agent for Meloidogyne Nematodes Using High Resolution Rhizosphere Microbial Community Analysis. FRONTIERS IN PLANT SCIENCE 2016; 7:1946. [PMID: 28082997 PMCID: PMC5183635 DOI: 10.3389/fpls.2016.01946] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/07/2016] [Indexed: 05/29/2023]
Abstract
White clover (Trifolium repens) is the key legume component of New Zealand pastoral agriculture due to the high quality feed and nitrogen inputs it provides. Invertebrate pests constrain white clover growth and this study investigated rhizosphere-associated fungal controls for two of these pests and attempts to disentangle the underpinning mechanisms. The degree of suppressiveness of 10 soils, in a latitudinal gradient down New Zealand, to added Meloidogyne hapla and Costelytra zealandica scarab larvae was measured in untreated soil. Most of the soils showed no suppressive activity against these pests but two showed activity against M. hapla and two against C. zealandica. Rhizosphere fungi responsible for pest suppressive responses were elucidated via next-generation sequencing. In the M. hapla-suppressive soils nematode-trapping Orbiliomycetes fungi were present in significantly greater abundance than non-suppressive soils and their abundance increased further with addition of M. hapla. A comparison of plant growth and the rhizosphere fungal community between untreated and irradiated soil was carried out on 5 of the 10 soils using Pyronota as the scarab larvae. Soil irradiation either: reduced (by 60-70%); increased (16×) or made no difference to white clover growth across the five soils tested, illustrating the range of microbial impacts on plant production. In one of the M. hapla suppressive soils irradiation resulted in a significant increase in nematode galling suggesting that Orbiliomycetes fungi were indeed responsible for the suppressive effect. Lack of consistent changes in soil macronutrients and pH post-irradiation suggest these were not responsible for plant or invertebrate responses. The use of next generation sequencing in controlled pot trials has allowed identification of a potential biological control organism and bioindicator for M. hapla suppression.
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Affiliation(s)
- Nigel L. Bell
- Soil Biology Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Katharine H. Adam
- Soil Biology Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Rhys J. Jones
- Soil Biology Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Richard D. Johnson
- Plant/Fungal Interactions Team, AgResearch Ltd, Grasslands Research CentrePalmerston North, New Zealand
| | | | - Gabriela Burch
- Soil Biology Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Vanessa Cave
- Bioinformatics and Statistics Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Catherine Cameron
- Bioinformatics and Statistics Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Paul Maclean
- Bioinformatics and Statistics Team, AgResearch Ltd, Lincoln Research CentreChristchurch, New Zealand
| | - Alison J. Popay
- Soil Biology Team, AgResearch Ltd, Ruakura Research CentreHamilton, New Zealand
| | - Damien Fleetwood
- Biotelliga Ltd, Institute for Innovation in BiotechnologyAuckland, New Zealand
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23
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Joseph S, Schmidt LM, Danquah WB, Timper P, Mekete T. Genotyping of single spore isolates of a Pasteuria penetrans population occurring in Florida using SNP-based markers. J Appl Microbiol 2016; 122:389-401. [PMID: 27862724 DOI: 10.1111/jam.13345] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/16/2016] [Accepted: 11/03/2016] [Indexed: 11/26/2022]
Abstract
AIMS To generate single spore lines of a population of bacterial parasite of root-knot nematode (RKN), Pasteuria penetrans, isolated from Florida and examine genotypic variation and virulence characteristics exist within the population. METHODS AND RESULTS Six single spore lines (SSP), 16SSP, 17SSP, 18SSP, 25SSP, 26SSP and 30SSP were generated. Genetic variability was evaluated by comparing single-nucleotide polymorphisms (SNPs) in six protein-coding genes and the 16S rRNA gene. An average of one SNP was observed for every 69 bp in the 16S rRNA, whereas no SNPs were observed in the protein-coding sequences. Hierarchical cluster analysis of 16S rRNA sequences placed the clones into three distinct clades. Bio-efficacy analysis revealed significant heterogeneity in the level virulence and host specificity between the individual clones. CONCLUSIONS The SNP markers developed to the 5' hypervariable region of the 16S rRNA gene may be useful in biotype differentiation within a population of P. penetrans. SIGNIFICANCE AND IMPACT OF THE STUDY This study demonstrates an efficient method for generating single spore lines of P. penetrans and gives a deep insight into genetic heterogeneity and varying level of virulence exists within a population parasitizing a specific Meloidogyne sp. host. The results also suggest that the application of generalist spore lines in nematode management may achieve broad RKN control.
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Affiliation(s)
- S Joseph
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
| | - L M Schmidt
- Syngenta Crop Protection, LLC, Gainesville, FL, USA
| | - W B Danquah
- Department of Plant Pathology, University of California, Davis, CA, USA
| | | | - T Mekete
- Entomology and Nematology Department, University of Florida, Gainesville, FL, USA
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24
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Parnell JJ, Berka R, Young HA, Sturino JM, Kang Y, Barnhart DM, DiLeo MV. From the Lab to the Farm: An Industrial Perspective of Plant Beneficial Microorganisms. FRONTIERS IN PLANT SCIENCE 2016; 7:1110. [PMID: 27540383 PMCID: PMC4973397 DOI: 10.3389/fpls.2016.01110] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/12/2016] [Indexed: 05/18/2023]
Abstract
Any successful strategy aimed at enhancing crop productivity with microbial products ultimately relies on the ability to scale at regional to global levels. Microorganisms that show promise in the lab may lack key characteristics for widespread adoption in sustainable and productive agricultural systems. This paper provides an overview of critical considerations involved with taking a strain from discovery to the farmer's field. In addition, we review some of the most effective microbial products on the market today, explore the reasons for their success and outline some of the major challenges involved in industrial production and commercialization of beneficial strains for widespread agricultural application. General processes associated with commercializing viable microbial products are discussed in two broad categories, biofertility inoculants and biocontrol products. Specifically, we address what farmers desire in potential microbial products, how mode of action informs decisions on product applications, the influence of variation in laboratory and field study data, challenges with scaling for mass production, and the importance of consistent efficacy, product stability and quality. In order to make a significant impact on global sustainable agriculture, the implementation of plant beneficial microorganisms will require a more seamless transition between laboratory and farm application. Early attention to the challenges presented here will improve the likelihood of developing effective microbial products to improve crop yields, decrease disease severity, and help to feed an increasingly hungry planet.
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25
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The Exosporium Layer of Bacterial Spores: a Connection to the Environment and the Infected Host. Microbiol Mol Biol Rev 2016; 79:437-57. [PMID: 26512126 DOI: 10.1128/mmbr.00050-15] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Much of what we know regarding bacterial spore structure and function has been learned from studies of the genetically well-characterized bacterium Bacillus subtilis. Molecular aspects of spore structure, assembly, and function are well defined. However, certain bacteria produce spores with an outer spore layer, the exosporium, which is not present on B. subtilis spores. Our understanding of the composition and biological functions of the exosporium layer is much more limited than that of other aspects of the spore. Because the bacterial spore surface is important for the spore's interactions with the environment, as well as being the site of interaction of the spore with the host's innate immune system in the case of spore-forming bacterial pathogens, the exosporium is worthy of continued investigation. Recent exosporium studies have focused largely on members of the Bacillus cereus family, principally Bacillus anthracis and Bacillus cereus. Our understanding of the composition of the exosporium, the pathway of its assembly, and its role in spore biology is now coming into sharper focus. This review expands on a 2007 review of spore surface layers which provided an excellent conceptual framework of exosporium structure and function (A. O. Henriques and C. P. Moran, Jr., Annu Rev Microbiol 61:555-588, 2007, http://dx.doi.org/10.1146/annurev.micro.61.080706.093224). That review began a process of considering outer spore layers as an integrated, multilayered structure rather than simply regarding the outer spore components as independent parts.
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26
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Ebert D, Duneau D, Hall MD, Luijckx P, Andras JP, Du Pasquier L, Ben-Ami F. A Population Biology Perspective on the Stepwise Infection Process of the Bacterial Pathogen Pasteuria ramosa in Daphnia. ADVANCES IN PARASITOLOGY 2015; 91:265-310. [PMID: 27015951 DOI: 10.1016/bs.apar.2015.10.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The infection process of many diseases can be divided into series of steps, each one required to successfully complete the parasite's life and transmission cycle. This approach often reveals that the complex phenomenon of infection is composed of a series of more simple mechanisms. Here we demonstrate that a population biology approach, which takes into consideration the natural genetic and environmental variation at each step, can greatly aid our understanding of the evolutionary processes shaping disease traits. We focus in this review on the biology of the bacterial parasite Pasteuria ramosa and its aquatic crustacean host Daphnia, a model system for the evolutionary ecology of infectious disease. Our analysis reveals tremendous differences in the degree to which the environment, host genetics, parasite genetics and their interactions contribute to the expression of disease traits at each of seven different steps. This allows us to predict which steps may respond most readily to selection and which steps are evolutionarily constrained by an absence of variation. We show that the ability of Pasteuria to attach to the host's cuticle (attachment step) stands out as being strongly influenced by the interaction of host and parasite genotypes, but not by environmental factors, making it the prime candidate for coevolutionary interactions. Furthermore, the stepwise approach helps us understanding the evolution of resistance, virulence and host ranges. The population biological approach introduced here is a versatile tool that can be easily transferred to other systems of infectious disease.
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Affiliation(s)
- Dieter Ebert
- Zoological Institute, University of Basel, Basel, Switzerland
| | - David Duneau
- Zoological Institute, University of Basel, Basel, Switzerland; Department Ecologie et Diversité Biologique, University Paul Sabatier-Toulouse III, Toulouse, France
| | - Matthew D Hall
- Zoological Institute, University of Basel, Basel, Switzerland; Monash University, School of Biological Sciences, Clayton Campus, Melbourne, VIC, Australia
| | - Pepijn Luijckx
- Zoological Institute, University of Basel, Basel, Switzerland; Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason P Andras
- Zoological Institute, University of Basel, Basel, Switzerland; Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | | | - Frida Ben-Ami
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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27
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Li J, Zou C, Xu J, Ji X, Niu X, Yang J, Huang X, Zhang KQ. Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2015; 53:67-95. [PMID: 25938277 DOI: 10.1146/annurev-phyto-080614-120336] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.
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Affiliation(s)
- Juan Li
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, 650091, China;
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Zou X, Xiao J, Huang H, Zhang X, Zhang F, Sun Q, Liu M, Bao S. Population diversity of Pasteuria penetrans from pepper fields and its genetic variation from single root-knot nematodes. NEMATOLOGY 2015. [DOI: 10.1163/15685411-00002912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pasteuria penetrans is an obligate parasite of root-knot nematodes. Pepper (Piper nigrum) is one of the main economic crops in Hainan Island, China, and the incidence of root-knot diseases is high. The Pasteuria samples from 20 pepper fields of seven counties in Hainan Island were identified, and the results suggested that there were various P. penetrans populations in the same field but no obvious specificity among different regions. However, five strains appeared to be potentially novel species of the genus Pasteuria by 16S rRNA gene sequence analysis. Additionally, further study showed that a single nematode of Meloidogyne incognita and of M. javanica could be infected by different strains of P. penetrans, and the genetic diversities of P. penetrans between two different host species were found only in gyrB rather than 16S rRNA and sigE gene sequences. These findings will provide some theoretical underpinning for the research of obligate parasitism mechanism between root-knot nematodes and P. penetrans.
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Affiliation(s)
- XiaoXiao Zou
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - Jun Xiao
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - HuiQin Huang
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - XiaoLi Zhang
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - FuTe Zhang
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - QianGuang Sun
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - Min Liu
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
| | - ShiXiang Bao
- Institute of Tropical Biosciences and Biotechnology, Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, Hainan, P.R. China
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Gupta R, Vakhlu J. Bacterial biocontrol agents. Microb Biotechnol 2014. [DOI: 10.1201/b17587-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Costa SR, Kerry BR, Bardgett RD, Davies KG. Interactions between nematodes and their microbial enemies in coastal sand dunes. Oecologia 2012; 170:1053-66. [DOI: 10.1007/s00442-012-2359-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 05/02/2012] [Indexed: 11/24/2022]
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Mohan S, Mauchline TH, Rowe J, Hirsch PR, Davies KG. Pasteuria endospores from Heterodera cajani (Nematoda: Heteroderidae) exhibit inverted attachment and altered germination in cross-infection studies with Globodera pallida (Nematoda: Heteroderidae). FEMS Microbiol Ecol 2011; 79:675-84. [PMID: 22092805 DOI: 10.1111/j.1574-6941.2011.01249.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 10/18/2011] [Accepted: 11/02/2011] [Indexed: 11/30/2022] Open
Abstract
The Pasteuria group of Gram-positive, endospore-forming bacteria are parasites of invertebrates and exhibit differences in host specificity. We describe a cross-infection study between an isolate of Pasteuria from pigeon pea cyst nematode, Heterodera cajani, which also infects the potato cyst nematode, Globodera pallida, from the United Kingdom. A proportion of the attached endospores, 13% on H. cajani and 22% on G. pallida adhere to the cuticle in an inverted orientation. Inverted and conventionally attached endospores germinated and produced bacillus-like rods that completed their life cycle in < 15 weeks within females of G. pallida. This is the first example in which the life cycle of a Pasteuria population was systematically followed in two different nematode genera. A 1430-base pair fragment of the 16S rRNA gene sequence of the Pasteuria isolate from H. cajani revealed 98.6% similarity to the orthologous gene in Pasteuria nishizawae. Additionally, their respective endospore sizes were not significantly different, in contrast their host ranges are. Potential reasons for this remain unclear and are discussed.
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Affiliation(s)
- Sharad Mohan
- Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK
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McElroy K, Mouton L, Du Pasquier L, Qi W, Ebert D. Characterisation of a large family of polymorphic collagen-like proteins in the endospore-forming bacterium Pasteuria ramosa. Res Microbiol 2011; 162:701-14. [DOI: 10.1016/j.resmic.2011.06.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 05/04/2011] [Indexed: 11/26/2022]
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Identification of new single nucleotide polymorphism-based markers for inter- and intraspecies discrimination of obligate bacterial parasites (Pasteuria spp.) of invertebrates. Appl Environ Microbiol 2011; 77:6388-94. [PMID: 21803895 DOI: 10.1128/aem.05185-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein-encoding and 16S rRNA genes of Pasteuria penetrans populations from a wide range of geographic locations were examined. Most interpopulation single nucleotide polymorphisms (SNPs) were detected in the 16S rRNA gene. However, in order to fully resolve all populations, these were supplemented with SNPs from protein-encoding genes in a multilocus SNP typing approach. Examination of individual 16S rRNA gene sequences revealed the occurrence of "cryptic" SNPs which were not present in the consensus sequences of any P. penetrans population. Additionally, hierarchical cluster analysis separated P. penetrans 16S rRNA gene clones into four groups, and one of which contained sequences from the most highly passaged population, demonstrating that it is possible to manipulate the population structure of this fastidious bacterium. The other groups were made from representatives of the other populations in various proportions. Comparison of sequences among three Pasteuria species, namely, P. penetrans, P. hartismeri, and P. ramosa, showed that the protein-encoding genes provided greater discrimination than the 16S rRNA gene. From these findings, we have developed a toolbox for the discrimination of Pasteuria at both the inter- and intraspecies levels. We also provide a model to monitor genetic variation in other obligate hyperparasites and difficult-to-culture microorganisms.
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Abstract
The surface coat (SC) of the plant-parasitic nematode cuticle is an understudied area of current research, even though it likely plays key roles in both nematode-plant and nematode-microbe interactions. Although in several ways Caenorhabditis elegans is a poor model for plant-parasitic nematodes, it is a useful starting point for investigations of the cuticle and its SC, especially in the light of recent work using this species as a model for innate immunity and the generic biology underpinning much host-parasite biology. We review the research focused on the involvement of the SC of plant-parasitic nematodes. Using the insights gained from animal-parasitic nematodes and other sequenced nematodes, we discuss the key roles that the SC may play.
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Affiliation(s)
- Keith G Davies
- Plant Pathology and Microbiology, Rothamsted Research, Hertfordshire AL5 2JQ, United Kingdom
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Mauchline TH, Mohan S, Davies KG, Schaff JE, Opperman CH, Kerry BR, Hirsch PR. A method for release and multiple strand amplification of small quantities of DNA from endospores of the fastidious bacterium Pasteuria penetrans. Lett Appl Microbiol 2010; 50:515-21. [PMID: 20302597 DOI: 10.1111/j.1472-765x.2010.02830.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To establish a reliable protocol to extract DNA from Pasteuria penetrans endospores for use as template in multiple strand amplification, thus providing sufficient material for genetic analyses. To develop a highly sensitive PCR-based diagnostic tool for P. penetrans. METHODS AND RESULTS An optimized method to decontaminate endospores, release and purify DNA enabled multiple strand amplification. DNA purity was assessed by cloning and sequencing gyrB and 16S rRNA gene fragments obtained from PCR using generic primers. Samples indicated to be 100%P. penetrans by the gyrB assay were estimated at 46% using the 16S rRNA gene. No bias was detected on cloning and sequencing 12 housekeeping and sporulation gene fragments from amplified DNA. The detection limit by PCR with Pasteuria-specific 16S rRNA gene primers following multiple strand amplification of DNA extracted using the method was a single endospore. CONCLUSIONS Generation of large quantities DNA will facilitate genomic sequencing of P. penetrans. Apparent differences in sample purity are explained by variations in 16S rRNA gene copy number in Eubacteria leading to exaggerated estimations of sample contamination. Detection of single endospores will facilitate investigations of P. penetrans molecular ecology. SIGNIFICANCE AND IMPACT OF THE STUDY These methods will advance studies on P. penetrans and facilitate research on other obligate and fastidious micro-organisms where it is currently impractical to obtain DNA in sufficient quantity and quality.
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Affiliation(s)
- T H Mauchline
- Nematode Interactions Unit, Department of Plant Pathology and Microbiology, Rothamsted Research, Harpenden, Hertfordshire, UK.
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