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Wang Y, Yang X, Harkes P, van Steenbrugge JJM, Xu M, Geissen V. Soil microeukaryotic communities and phosphorus-cycling microorganisms respond to chloropicrin fumigation and azoxystrobin application. Sci Total Environ 2024; 933:172871. [PMID: 38697530 DOI: 10.1016/j.scitotenv.2024.172871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/23/2024] [Accepted: 04/27/2024] [Indexed: 05/05/2024]
Abstract
Fumigants and fungicides are effective at controlling soil-borne pathogens but might also adversely affect soil beneficial microbes, such as soil phosphorus (P) solubilizing microbes, further altering nutrient cycling processes. Therefore, this study investigated the effects of the fumigant chloropicrin (CP) and the fungicide azoxystrobin (AZO) on soil microeukaryotes and P-cycling related soil bacteria through a greenhouse experiment. Soil microeukaryotic communities and bacterial communities containing two phosphomonoesterase encoding genes (phoC and phoD) were analysed using high-throughput sequencing methods. Results showed that, when applied at the field recommended application dosage, the fungicide AZO had no significant influence on the community structure of soil microeukaryotes and phoD-containing bacteria. However, in CP-fumigated soils, the soil microeukaryotic community composition changed from fungi-dominated to protist-dominated. CP fumigation significantly decreased the total phoC/phoD gene copy number but increased the relative abundance of some phoC/phoD-containing bacteria (such as Sinorhizobium and Streptomyces), which are significantly positively correlated to available P compositions in soil. The structural equation model (SEM) confirmed that CP fumigation could affect soil available P content directly by altering phoC-/phoD-containing bacteria, or indirectly by affecting phoC/phoD gene abundance and acid/alkaline phosphatases activity in soil. The inconsistent changes in phoC/phoD-containing bacteria, phoC/phoD gene number, and the phosphomonoesterase activities indicated that enzyme secretion may not be the only way for P solubilizing soil microorganisms to regulate P availability after soil fumigation. The outcome of this study can provide theoretical support for the design of soil beneficial microorganism recovery strategies and the regulation of phosphate fertilizer after soil fumigation.
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Affiliation(s)
- Yan Wang
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Soil Physics and Land Management Group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Xiaomei Yang
- Soil Physics and Land Management Group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands; College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Paula Harkes
- Soil Physics and Land Management Group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Joris J M van Steenbrugge
- Laboratory of Nematology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Minggang Xu
- Key Laboratory of Arable Land Quality Monitoring and Evaluation, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Eco-environment and Industrial Technology, Shanxi Agricultural University, Shanxi Province Key Laboratory of Soil Environment and Nutrient Resources, Taiyuan 030031, China.
| | - Violette Geissen
- Soil Physics and Land Management Group, Wageningen University, P.O. Box 47, 6700 AA Wageningen, the Netherlands
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Willig JJ, Sonneveld D, van Steenbrugge JJM, Deurhof L, van Schaik CC, Teklu MG, Goverse A, Lozano-Torres JL, Smant G, Sterken MG. From root to shoot: quantifying nematode tolerance in Arabidopsis thaliana by high-throughput phenotyping of plant development. J Exp Bot 2023; 74:5487-5499. [PMID: 37432651 PMCID: PMC10540735 DOI: 10.1093/jxb/erad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/10/2023] [Indexed: 07/12/2023]
Abstract
Nematode migration, feeding site formation, withdrawal of plant assimilates, and activation of plant defence responses have a significant impact on plant growth and development. Plants display intraspecific variation in tolerance limits for root-feeding nematodes. Although disease tolerance has been recognized as a distinct trait in biotic interactions of mainly crops, we lack mechanistic insights. Progress is hampered by difficulties in quantification and laborious screening methods. We turned to the model plant Arabidopsis thaliana, since it offers extensive resources to study the molecular and cellular mechanisms underlying nematode-plant interactions. Through imaging of tolerance-related parameters, the green canopy area was identified as an accessible and robust measure for assessing damage due to cyst nematode infection. Subsequently, a high-throughput phenotyping platform simultaneously measuring the green canopy area growth of 960 A. thaliana plants was developed. This platform can accurately measure cyst nematode and root-knot nematode tolerance limits in A. thaliana through classical modelling approaches. Furthermore, real-time monitoring provided data for a novel view of tolerance, identifying a compensatory growth response. These findings show that our phenotyping platform will enable a new mechanistic understanding of tolerance to below-ground biotic stress.
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Affiliation(s)
- Jaap-Jan Willig
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Devon Sonneveld
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | | | - Laurens Deurhof
- Laboratory of Phytopathology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Casper C van Schaik
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Misghina G Teklu
- Agrosystems Research, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Jose L Lozano-Torres
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, 6708PB Wageningen, The Netherlands
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Verhoeven A, Finkers-Tomczak A, Prins P, Valkenburg-van Raaij DR, van Schaik CC, Overmars H, van Steenbrugge JJM, Tacken W, Varossieau K, Slootweg EJ, Kappers IF, Quentin M, Goverse A, Sterken MG, Smant G. The root-knot nematode effector MiMSP32 targets host 12-oxophytodienoate reductase 2 to regulate plant susceptibility. New Phytol 2023; 237:2360-2374. [PMID: 36457296 DOI: 10.1111/nph.18653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
To establish persistent infections in host plants, herbivorous invaders, such as root-knot nematodes, must rely on effectors for suppressing damage-induced jasmonate-dependent host defenses. However, at present, the effector mechanisms targeting the biosynthesis of biologically active jasmonates to avoid adverse host responses are unknown. Using yeast two-hybrid, in planta co-immunoprecipitation, and mutant analyses, we identified 12-oxophytodienoate reductase 2 (OPR2) as an important host target of the stylet-secreted effector MiMSP32 of the root-knot nematode Meloidogyne incognita. MiMSP32 has no informative sequence similarities with other functionally annotated genes but was selected for the discovery of novel effector mechanisms based on evidence of positive, diversifying selection. OPR2 catalyzes the conversion of a derivative of 12-oxophytodienoate to jasmonic acid (JA) and operates parallel to 12-oxophytodienoate reductase 3 (OPR3), which controls the main pathway in the biosynthesis of jasmonates. We show that MiMSP32 targets OPR2 to promote parasitism of M. incognita in host plants independent of OPR3-mediated JA biosynthesis. Artificially manipulating the conversion of the 12-oxophytodienoate by OPRs increases susceptibility to multiple unrelated plant invaders. Our study is the first to shed light on a novel effector mechanism targeting this process to regulate the susceptibility of host plants.
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Affiliation(s)
- Ava Verhoeven
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
- Plant Stress Resilience, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
- Plant-Environment Signaling, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
| | - Anna Finkers-Tomczak
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Pjotr Prins
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Debbie R Valkenburg-van Raaij
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Casper C van Schaik
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Hein Overmars
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Joris J M van Steenbrugge
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Wannes Tacken
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Koen Varossieau
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Erik J Slootweg
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Iris F Kappers
- Laboratory of Plant Physiology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, ISA, F-06903, Sophia Antipolis, France
| | - Aska Goverse
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Geert Smant
- Laboratory of Nematology, Department of Plant Sciences, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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van Steenbrugge JJM, van den Elsen S, Holterman M, Lozano‐Torres J, Putker V, Thorpe P, Goverse A, Sterken M, Smant G, Helder J. Comparative genomics among cyst nematodes reveals distinct evolutionary histories among effector families and an irregular distribution of effector-associated promoter motifs. Mol Ecol 2023; 32:1515-1529. [PMID: 35560992 PMCID: PMC10946958 DOI: 10.1111/mec.16505] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/26/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022]
Abstract
Potato cyst nematodes (PCNs), an umbrella term used for two species, Globodera pallida and G. rostochiensis, belong worldwide to the most harmful pathogens of potato. Pathotype-specific host plant resistances are essential for PCN control. However, the poor delineation of G. pallida pathotypes has hampered the efficient use of available host plant resistances. Long-read sequencing technology allowed us to generate a new reference genome of G. pallida population D383 and, as compared to the current reference, the new genome assembly is 42 times less fragmented. For comparison of diversification patterns of six effector families between G. pallida and G. rostochiensis, an additional reference genome was generated for an outgroup, the beet cyst nematode Heterodera schachtii (IRS population). Large evolutionary contrasts in effector family topologies were observed. While VAPs (venom allergen-like proteins) diversified before the split between the three cyst nematode species, the families GLAND5 and GLAND13 only expanded in PCNs after their separation from the genus Heterodera. Although DNA motifs in the promoter regions thought to be involved in the orchestration of effector expression ("DOG boxes") were present in all three cyst nematode species, their presence is not a necessity for dorsal gland-produced effectors. Notably, DOG box dosage was only loosely correlated with the expression level of individual effector variants. Comparison of the G. pallida genome with those of two other cyst nematodes underlined the fundamental differences in evolutionary history between effector families. Resequencing of PCN populations with different virulence characteristics will allow for the linking of these characteristics to the composition of the effector repertoire as well as for the mapping of PCN diversification patterns resulting from extreme anthropogenic range expansion.
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Affiliation(s)
| | - Sven van den Elsen
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Martijn Holterman
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
- SolyntaWageningenThe Netherlands
| | | | - Vera Putker
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Peter Thorpe
- School of Medicine, Medical & Biological SciencesUniversity of St. AndrewsSt AndrewsUK
| | - Aska Goverse
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Mark G. Sterken
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Geert Smant
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
| | - Johannes Helder
- Laboratory of NematologyWageningen University & ResearchWageningenThe Netherlands
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Willig J, Guarneri N, van Steenbrugge JJM, de Jong W, Chen J, Goverse A, Lozano Torres JL, Sterken MG, Bakker J, Smant G. The Arabidopsis transcription factor TCP9 modulates root architectural plasticity, reactive oxygen species-mediated processes, and tolerance to cyst nematode infections. Plant J 2022; 112:1070-1083. [PMID: 36181710 PMCID: PMC9828446 DOI: 10.1111/tpj.15996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/06/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Infections by root-feeding nematodes have profound effects on root system architecture and consequently shoot growth of host plants. Plants harbor intraspecific variation in their growth responses to belowground biotic stresses by nematodes, but the underlying mechanisms are not well understood. Here, we show that the transcription factor TEOSINTE BRANCHED/CYCLOIDEA/PROLIFERATING CELL FACTOR-9 (TCP9) modulates root system architectural plasticity in Arabidopsis thaliana in response to infections by the endoparasitic cyst nematode Heterodera schachtii. Young seedlings of tcp9 knock-out mutants display a significantly weaker primary root growth inhibition response to cyst nematodes than wild-type Arabidopsis. In older plants, tcp9 reduces the impact of nematode infections on the emergence and growth of secondary roots. Importantly, the altered growth responses by tcp9 are most likely not caused by less biotic stress on the root system, because TCP9 does not affect the number of infections, nematode development, and size of the nematode-induced feeding structures. RNA-sequencing of nematode-infected roots of the tcp9 mutants revealed differential regulation of enzymes involved in reactive oxygen species (ROS) homeostasis and responses to oxidative stress. We also found that root and shoot growth of tcp9 mutants is less sensitive to exogenous hydrogen peroxide and that ROS accumulation in nematode infection sites in these mutants is reduced. Altogether, these observations demonstrate that TCP9 modulates the root system architectural plasticity to nematode infections via ROS-mediated processes. Our study further points at a novel regulatory mechanism contributing to the tolerance of plants to root-feeding nematodes by mitigating the impact of belowground biotic stresses.
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Affiliation(s)
- Jaap‐Jan Willig
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Nina Guarneri
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | | | - Willem de Jong
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Jingrong Chen
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Aska Goverse
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - José L. Lozano Torres
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Mark G. Sterken
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Jaap Bakker
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
| | - Geert Smant
- Laboratory of NematologyWageningen University & Research6708PBWageningenThe Netherlands
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van Steenbrugge JJM, van den Elsen S, Holterman M, Sterken MG, Thorpe P, Goverse A, Smant G, Helder J. Comparative genomics of two inbred lines of the potato cyst nematode Globodera rostochiensis reveals disparate effector family-specific diversification patterns. BMC Genomics 2021; 22:611. [PMID: 34380421 PMCID: PMC8359618 DOI: 10.1186/s12864-021-07914-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Potato cyst nematodes belong to the most harmful pathogens in potato, and durable management of these parasites largely depends on host-plant resistances. These resistances are pathotype specific. The current Globodera rostochiensis pathotype scheme that defines five pathotypes (Ro1 - Ro5) is both fundamentally and practically of limited value. Hence, resistant potato varieties are used worldwide in a poorly informed manner. RESULTS We generated two novel reference genomes of G. rostochiensis inbred lines derived from a Ro1 and a Ro5 population. These genome sequences comprise 173 and 189 scaffolds respectively, marking a ≈ 24-fold reduction in fragmentation as compared to the current reference genome. We provide copy number variations for 19 effector families. Four dorsal gland effector families were investigated in more detail. SPRYSECs, known to be implicated in plant defence suppression, constitute by far the most diversified family studied herein with 60 and 99 variants in Ro1 and Ro5 distributed over 18 and 26 scaffolds. In contrast, CLEs, effectors involved in feeding site induction, show strong physical clustering. The 10 and 16 variants cluster on respectively 2 and 1 scaffolds. Given that pathotypes are defined by their effectoromes, we pinpoint the disparate nature of the contributing effector families in terms of sequence diversification and loss and gain of variants. CONCLUSIONS Two novel reference genomes allow for nearly complete inventories of effector diversification and physical organisation within and between pathotypes. Combined with insights we provide on effector family-specific diversification patterns, this constitutes a basis for an effectorome-based virulence scheme for this notorious pathogen.
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Affiliation(s)
| | - Sven van den Elsen
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Martijn Holterman
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands.,Solynta, Dreijenlaan 2, 6703 HA, Wageningen, The Netherlands
| | - Mark G Sterken
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Peter Thorpe
- School of Medicine, Medical & Biological Sciences, University of St. Andrews, North Haugh, St Andrews, United Kingdom
| | - Aska Goverse
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Geert Smant
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
| | - Johannes Helder
- Laboratory of Nematology, Wageningen University & Research, Wageningen, The Netherlands
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