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Půža V, Machado RAR. Systematics and phylogeny of the entomopathogenic nematobacterial complexes Steinernema-Xenorhabdus and Heterorhabditis-Photorhabdus. ZOOLOGICAL LETTERS 2024; 10:13. [PMID: 39020388 PMCID: PMC11256433 DOI: 10.1186/s40851-024-00235-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 06/08/2024] [Indexed: 07/19/2024]
Abstract
Entomopathogenic nematodes of the genera Steinernema and Heterorhabditis, along with their bacterial symbionts from the genera Xenorhabdus and Photorhabdus, respectively, are important biological control agents against agricultural pests. Rapid progress in the development of genomic tools has catalyzed a transformation of the systematics of these organisms, reshaping our understanding of their phylogenetic and cophlylogenetic relationships. In this review, we discuss the major historical events in the taxonomy and systematics of this group of organisms, highlighting the latest advancements in these fields. Additionally, we synthesize information on nematode-bacteria associations and assess the existing evidence regarding their cophylogenetic relationships.
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Affiliation(s)
- Vladimír Půža
- Institute of Entomology, Biology centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic.
- Faculty of Agriculture and Technology, University of South Bohemia, Studentská 1668, České Budějovice, 37005, Czech Republic.
| | - Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchâtel, Neuchâtel, 2000, Switzerland.
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Abd-Elgawad MMM. Reproduction of Entomopathogenic Nematodes for Use in Pest Control. Methods Mol Biol 2024; 2756:351-382. [PMID: 38427305 DOI: 10.1007/978-1-0716-3638-1_14] [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
The growing interest in the use of entomopathogenic nematodes and their symbiotic bacteria as promising biocontrol agents of many arthropod pests and pathogens has created running technologies to expand their use globally. The related laboratory procedures and tests on these nematodes such as their isolation, count, culture, identification, pathogenicity, virulence, and environmental tolerance should form the solid basis for such an expansion with reliable uses. Extensive practical details of such procedures and tests as well as how to identify and overcome the problems associated with these aspects are addressed in this chapter.
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Machado RAR, Bhat AH, Castaneda-Alvarez C, Askary TH, Půža V, Pagès S, Abolafia J. Xenorhabdus aichiensis sp. nov., Xenorhabdus anantnagensis sp. nov., and Xenorhabdus yunnanensis sp. nov., Isolated from Steinernema Entomopathogenic Nematodes. Curr Microbiol 2023; 80:300. [PMID: 37493817 PMCID: PMC10371910 DOI: 10.1007/s00284-023-03373-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/12/2023] [Indexed: 07/27/2023]
Abstract
Three bacterial strains, XENO-2T, XENO-7T, and XENO-10T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel Xenorhabdus species. In this study, we describe these new species by whole-genome and whole-proteome phylogenomic reconstructions, by calculating sequence identity scores using core genome sequences, and by phenotypic characterization. Phylogenomic reconstructions using ribosomal and house-keeping genes, and whole-genome and whole-proteome sequences show that XENO-2T and XENO-10T are closely related to Xenorhabdus japonica DSM 16522T and that XENO-7T is closely related to Xenorhabdus bovienii subsp. africana XENO-1T and to X. bovienii subsp. bovienii T228T. The dDDH values between XENO-2T and XENO-10T and between XENO-2T and X. japonica DSM 16522T are 56.4 and 51.8%, respectively. The dDDH value between XENO-10T and X. japonica DSM 16522T is 53.4%. The dDDH values between XENO-7T and X. bovienii subsp. africana XENO-1T and between XENO-7T and X. bovienii subsp. bovienii T228T are 63.6 and 69.4%, respectively. These dDDH values are below the 70% divergence threshold for prokaryotic species delineation. The newly described species are highly pathogenic to G. mellonella larvae, grow at pH between 5 and 9 (optimum 5-7), at salt concentrations of 1-3% (optimum 1-2%), and temperatures between 20 and 37 °C (optimum 28-30 °C). Biochemical tests such as lysine decarboxylase, ornithine decarboxylase, urease, gelatinase, citrate utilization, indole and acetoin production, and cytochrome oxidase tests allow to differentiate the novel species from their more closely related species. Considering these genetic and phenotypic divergencies, we propose the following new species: Xenorhabdus aichiensis sp. nov. with XENO-7T (= CCM 9233T = CCOS 2024T) as the type strain, Xenorhabdus anantnagensis sp. nov., with XENO-2T (= CCM 9237T = CCOS 2023T) as the type strain, and Xenorhabdus yunnanensis sp. nov., with XENO-10T (= CCM 9322T = CCOS 2071T) as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.
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Affiliation(s)
- Ricardo A R Machado
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
| | - Aashaq Hussain Bhat
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Department of Biosciences, University Center for Research and Development, Chandigarh University, Mohali, Punjab, India
| | - Carlos Castaneda-Alvarez
- Experimental Biology Research Group, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Departamento de Sanidad Vegetal, Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Tarique Hassan Askary
- Division of Entomology, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology, Wadura Campus, Jammu, Jammu and Kashmir, India
| | - Vladimir Půža
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Sylvie Pagès
- INRAe, Université de Montpellier, Montpellier, France
| | - Joaquín Abolafia
- Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Campus 'Las Lagunillas', Jaén, Spain
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Awori RM, Waturu CN, Pidot SJ, Amugune NO, Bode HB. Draft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya. Access Microbiol 2023; 5:acmi000531.v4. [PMID: 37323942 PMCID: PMC10267655 DOI: 10.1099/acmi.0.000531.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/27/2023] [Indexed: 06/17/2023] Open
Abstract
As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae . The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.
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Affiliation(s)
- Ryan Musumba Awori
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Elakistos Biosciences, PO Box 19301-00100, Nairobi, Kenya
| | - Charles N. Waturu
- Horticulture Research Institute, Kenya Agricultural and Livestock Research Organisation, PO Box 220 Thika
| | - Sacha J. Pidot
- Department of Microbiology and Immunology at the Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Nelson O. Amugune
- Department of Biology, University of Nairobi, PO Box 30197-00100, Nairobi, Kenya
| | - Helge B. Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
- Department of Natural Products in Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Chemical Biology, Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt am Main, Germany
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Awori RM. Nematophilic bacteria associated with entomopathogenic nematodes and drug development of their biomolecules. Front Microbiol 2022; 13:993688. [PMID: 36187939 PMCID: PMC9520725 DOI: 10.3389/fmicb.2022.993688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022] Open
Abstract
The importance of Xenorhabdus and Photorhabdus symbionts to their respective Steinernema and Heterorhabditis nematode hosts is that they not only contribute to their entomopathogenicity but also to their fecundity through the production of small molecules. Thus, this mini-review gives a brief introductory overview of these nematophilic bacteria. Specifically, their type species, nematode hosts, and geographic region of isolations are tabulated. The use of nucleotide sequence-based techniques for their species delineation and how pangenomes can improve this are highlighted. Using the Steinernema–Xenorhabdus association as an example, the bacterium-nematode lifecycle is visualized with an emphasis on the role of bacterial biomolecules. Those currently in drug development are discussed, and two potential antimalarial lead compounds are highlighted. Thus, this mini-review tabulates forty-eight significant nematophilic bacteria and visualizes the ecological importance of their biomolecules. It further discusses three of these biomolecules that are currently in drug development. Through it, one is introduced to Xenorhabdus and Photorhabdus bacteria, their natural production of biomolecules in the nematode-bacterium lifecycle, and how these molecules are useful in developing novel therapies.
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Affiliation(s)
- Ryan Musumba Awori
- Department of Biology, University of Nairobi, Nairobi, Kenya
- Elakistos Biosciences, Nairobi, Kenya
- *Correspondence: Ryan Musumba Awori,
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Xenorhabdus spp.: An Overview of the Useful Facets of Mutualistic Bacteria of Entomopathogenic Nematodes. Life (Basel) 2022; 12:life12091360. [PMID: 36143397 PMCID: PMC9503066 DOI: 10.3390/life12091360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/17/2022] Open
Abstract
Mounting concern over the misuse of chemical pesticides has sparked broad interest for safe and effective alternatives to control plant pests and pathogens. Xenorhabdus bacteria, as pesticidal symbionts of the entomopathogenic nematodes Steinernema species, can contribute to this solution with a treasure trove of insecticidal compounds and an ability to suppress a variety of plant pathogens. As many challenges face sound exploitation of plant–phytonematode interactions, a full useful spectrum of such interactions should address nematicidal activity of Xenorhabdus. Steinernema–Xenorhabdus complex or Xenorhabdus individually should be involved in mechanisms underlying the favorable side of plant–nematode interactions in emerging cropping systems. Using Xenorhabdus bacteria should earnestly be harnessed to control not only phytonematodes, but also other plant pests and pathogens within integrated pest management plans. This review highlights the significance of fitting Xenorhabdus-obtained insecticidal, nematicidal, fungicidal, acaricidal, pharmaceutical, antimicrobial, and toxic compounds into existing, or arising, holistic strategies, for controlling many pests/pathogens. The widespread utilization of Xenorhabdus bacteria, however, has been slow-going, due to costs and some issues with their commercial processing. Yet, advances have been ongoing via further mastering of genome sequencing, discovering more of the beneficial Xenorhabdus species/strains, and their successful experimentations for pest control. Their documented pathogenicity to a broad range of arthropods and pathogens and versatility bode well for useful industrial products. The numerous beneficial traits of Xenorhabdus bacteria can facilitate their integration with other tactics for better pest/disease management programs.
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Fodor A, Gualtieri M, Zeller M, Tarasco E, Klein MG, Fodor AM, Haynes L, Lengyel K, Forst SA, Furgani GM, Karaffa L, Vellai T. Type Strains of Entomopathogenic Nematode-Symbiotic Bacterium Species, Xenorhabdus szentirmaii (EMC) and X. budapestensis (EMA), Are Exceptional Sources of Non-Ribosomal Templated, Large-Target-Spectral, Thermotolerant-Antimicrobial Peptides (by Both), and Iodinin (by EMC). Pathogens 2022; 11:pathogens11030342. [PMID: 35335666 PMCID: PMC8950435 DOI: 10.3390/pathogens11030342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 01/26/2023] Open
Abstract
Antimicrobial multidrug resistance (MDR) is a global challenge, not only for public health, but also for sustainable agriculture. Antibiotics used in humans should be ruled out for use in veterinary or agricultural settings. Applying antimicrobial peptide (AMP) molecules, produced by soil-born organisms for protecting (soil-born) plants, seems a preferable alternative. The natural role of peptide-antimicrobials, produced by the prokaryotic partner of entomopathogenic-nematode/bacterium (EPN/EPB) symbiotic associations, is to sustain monoxenic conditions for the EPB in the gut of the semi-anabiotic infective dauer juvenile (IJ) EPN. They keep pathobiome conditions balanced for the EPN/EPB complex in polyxenic (soil, vanquished insect cadaver) niches. Xenorhabdus szentirmaii DSM16338(T) (EMC), and X. budapestensis DSM16342(T) (EMA), are the respective natural symbionts of EPN species Steinernema rarum and S. bicornutum. We identified and characterized both of these 15 years ago. The functional annotation of the draft genome of EMC revealed 71 genes encoding non-ribosomal peptide synthases, and polyketide synthases. The large spatial Xenorhabdus AMP (fabclavine), was discovered in EMA, and its biosynthetic pathway in EMC. The AMPs produced by EMA and EMC are promising candidates for controlling MDR prokaryotic and eukaryotic pathogens (bacteria, oomycetes, fungi, protozoa). EMC releases large quantity of iodinin (1,6-dihydroxyphenazine 5,10-dioxide) in a water-soluble form into the media, where it condenses to form spectacular water-insoluble, macroscopic crystals. This review evaluates the scientific impact of international research on EMA and EMC.
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Affiliation(s)
- András Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Genetics, University of Szeged, Középfasor 52, H-6726 Szeged, Hungary
- Correspondence: ; Tel.: +36-(30)-490-9294
| | - Maxime Gualtieri
- Nosopharm, 110 Allée Charles Babbage, Espace Innovation 2, 30000 Nîmes, France;
| | - Matthias Zeller
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47906, USA;
| | - Eustachio Tarasco
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy;
- Institute for Sustainable Plant Protection of CNR, Via Amendola 122/D, 70126 Bari, Italy
| | - Michael G. Klein
- USDA-ARS & Department of Entomology, The Ohio State University, 13416 Claremont Ave, Cleveland, OH 44130, USA;
| | - Andrea M. Fodor
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
| | - Leroy Haynes
- Department of Chemistry, The College of Wooster, Wooster, OH 44691, USA;
| | - Katalin Lengyel
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- National Institute of Pharmacy and Nutrition (NIPN), Zrinyi utca 3, H-1051 Budapest, Hungary
| | - Steven A. Forst
- Department of Biological Sciences, University of Wisconsin-Milwaukee, P.O. Box 413, Milwaukee, WI 53201, USA;
| | - Ghazala M. Furgani
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- Department of Plant Protection, Faculty of Agriculture, University of Tripoli, Tripoli P.O. Box 13793, Libya
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem Tér 1, H-4032 Debrecen, Hungary;
- Institute of Metagenomics, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös University, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary; (A.M.F.); (K.L.); or (G.M.F.); or (T.V.)
- MTA-ELTE Genetics Research Group, Pázmány Péter Sétány 1/C, H-1117 Budapest, Hungary
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