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Gao J, Chen L, Wang J, Zhao W, Zhang J, Qin Z, Wang M, Chen X, Li M, Yang Q. Response of the Symbiotic Microbial Community of Dioscorea opposita Cultivar Tiegun to Root-Knot Nematode Infection. PLANT DISEASE 2024; 108:2472-2483. [PMID: 38549276 DOI: 10.1094/pdis-01-24-0169-re] [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: 08/03/2024]
Abstract
Yam is an important medicinal and edible dual-purpose plant with high economic value. However, nematode damage severely affects its yield and quality. One of the major effects of nematode infestations is the secondary infection of pathogenic bacteria or fungi through entry wounds made by the nematodes. Understanding the response of the symbiotic microbial community of yam plants to nematodes is crucial for controlling such a disease. In this study, we investigated the rhizosphere and how endophytic microbiomes shift after nematode infection during the tuber expansion stage in the Dioscorea opposita Thunb. cultivar Tiegun. Our results revealed that soil depth affected the abundance of nematodes, and the relative number of Meloidogyne incognita was higher in the diseased soil at a depth of 16 to 40 cm than those at a depth of 0 to 15 and 41 to 70 cm. The abundance of and interactions among soil microbiota members were significantly correlated with root-knot nematode (RKN) parasitism at various soil depths. However, the comparison of the microbial α-diversity and composition between healthy and diseased rhizosphere soil showed no difference. Compared with healthy soils, the co-occurrence networks of M. incognita-infested soils included a higher ratio of positive correlations linked to plant health. In addition, we detected a higher abundance of certain taxonomic groups belonging to Chitinophagaceae and Xanthobacteraceae in the rhizosphere of RKN-infested plants. The nematodes, besides causing direct damage to plants, also possess the ability to act synergistically with other pathogens, especially Ramicandelaber and Fusarium, leading to the development of disease complexes. In contrast to soil samples, RKN parasitism specifically had a significant effect on the composition and assembly of the root endophytic microbiota. The RKN colonization impacted a wide variety of endophytic microbiomes, including Pseudomonas, Sphingomonas, Rhizobium, Neocosmospora, and Fusarium. This study revealed the relationship between RKN disease and changes in the rhizosphere and endophytic microbial community, which may provide novel insights that help improve biological management of yam RKNs.
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Affiliation(s)
- Jin Gao
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Liting Chen
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Jingjing Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Weichao Zhao
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Jiangli Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Zhao Qin
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Mingzhu Wang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
| | - Xia Chen
- Cell Biology and Plant Biochemistry, University of Regensburg, Regensburg 93053, Germany
| | - Mingjun Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Qingxiang Yang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
- Henan International Joint Laboratory of Agricultural Microbial Ecology and Technology, Henan Normal University, Xinxiang 453007, China
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Liu R, Chen M, Liu B, Huang K, Mao Z, Li H, Zhao J. A root-knot nematode effector manipulates the rhizosphere microbiome for establishing parasitism relationship with hosts. Front Microbiol 2023; 14:1217863. [PMID: 37538840 PMCID: PMC10395084 DOI: 10.3389/fmicb.2023.1217863] [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: 05/06/2023] [Accepted: 06/28/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction Root-knot nematode (RKN; Meloidogyne spp.) is one of the most infamous soilborne plant diseases, causing severe crop losses every year. Effector proteins secreted by RKNs play crucial roles during plant-nematode interaction. However, less is known about whether RKN effector proteins can impact the rhizosphere microbial environment. Methods In this study, we investigated the rhizosphere microbiome community of MiMIF-2 (a plant immunity-modulating effector) transgenic Arabidopsis thaliana with or without nematode infection using the Illumina high-throughput sequencing analysis. Results and discussion The results showed that the bacterial species richness index increased, while the fungi species richness index decreased in M. incognita-infected MiMIF-2 transgenic A. thaliana plants. The relative abundance of genera such as Clitopilus, Komagataeibacter, Lactobacillus, Prevotella, Moritella, Vibrio, Escherichia-Shigella, and Pseudomonas was reduced in MiMIF-2 transgenic A. thaliana plants compared to wild type, but was significantly increased after inoculation with M. incognita. The Cluster of Orthologous Genes (COG) function classification analysis revealed a decrease in the relative abundance of defense mechanisms, secondary metabolite biosynthesis, transport, and nematode infection catabolism-related functions in MiMIF-2 lines compared to the wild type. These differences may be the reason for the increased susceptibility of MiMIF-2 transgenic A. thaliana to nematode infection. Our results provide a new insight into RKN effector proteins and their association with the microbial community, host, and plant pathogens, which will lead to the exploration of new innovative ideas for future biological control of RKNs.
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Affiliation(s)
- Rui Liu
- College of Plant Protection, Gansu Agricultural University/Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Lanzhou, Gansu, China
| | - Mengfei Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Boliang Liu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaiwei Huang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenchuan Mao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huixia Li
- College of Plant Protection, Gansu Agricultural University/Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Lanzhou, Gansu, China
| | - Jianlong Zhao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Lu P, Shi H, Tao J, Jin J, Wang S, Zheng Q, Liu P, Xiang B, Chen Q, Xu Y, Li Z, Tan J, Cao P. Metagenomic insights into the changes in the rhizosphere microbial community caused by the root-knot nematode Meloidogyne incognita in tobacco. ENVIRONMENTAL RESEARCH 2023; 216:114848. [PMID: 36403441 DOI: 10.1016/j.envres.2022.114848] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Root-knot nematode (RKN) disease is a destructive soil disease that affects crop health and causes huge losses in crop production. To explore the relationships between soil environments, rhizobacterial communities, and plant health, rhizosphere bacterial communities were analyzed using metagenomic sequencing in tobacco samples with different grades of RKN disease. The results showed that the community structure and function of the plant rhizosphere were significantly correlated to the RKN disease. RKN density and urease content were key factors affecting the rhizosphere bacterial community. Urease accelerated the catabolism of urea and led to the production of high concentrations of ammonia, which directly suppressed the development of RKNs or by improving the nutritional and growth status of microorganisms that were antagonistic to RKNs. Further experiments showed that the suppression role of ammonia should be attributed to the direct inhibition of NH3. The bacterial members that were positively correlated with RKN density, contained many plant cell wall degrading enzymes, which might destroy plant cell walls and promote the colonization of RKN in tobacco roots. The analysis of metatranscriptome and metabolism demonstrated the role of these cell wall degrading enzymes. This study offers a comprehensive insight into the relationships between RKNs, bacteria, and soil environmental factors and provides new ideas for the biological control of RKNs.
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Affiliation(s)
- Peng Lu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Heli Shi
- Enshi Tobacco Company of Hubei Province, Enshi, Hubei, China
| | - Jiemeng Tao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Sujie Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Qingxia Zheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Pingping Liu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Bikun Xiang
- Enshi Tobacco Company of Hubei Province, Enshi, Hubei, China
| | - Qiansi Chen
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Jun Tan
- Enshi Tobacco Company of Hubei Province, Enshi, Hubei, China.
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China.
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Lamelas A, Desgarennes D, López-Lima D, Villain L, Alonso-Sánchez A, Artacho A, Latorre A, Moya A, Carrión G. The Bacterial Microbiome of Meloidogyne-Based Disease Complex in Coffee and Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:136. [PMID: 32174936 PMCID: PMC7056832 DOI: 10.3389/fpls.2020.00136] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/29/2020] [Indexed: 02/05/2023]
Abstract
The Meloidogyne-based disease complexes (MDCs) are caused by the interaction of different root-knot nematode species and phytopathogenic fungi. These complexes are devastating several important crops worldwide including tomato and coffee. Despite their relevance, little is known about the role of the bacterial communities in the MDCs. In this study 16s rDNA gene sequencing was used to analyze the bacterial microbiome associated with healthy and infested roots, as well with females and eggs of Meloidogyne enterolobii and M. paranaensis, the causal agents of MDC in tomato and coffee, respectively. Each MDC pathosystems displayed a specific taxonomic diversity and relative abundances constituting a very complex system. The main bacterial drivers of the MDC infection process were identified for both crops at order level. While corky-root coffee samples presented an enrichment of Bacillales and Burkholderiales, the corcky-root tomato samples presented an enrichment on Saprospirales, Chthoniobacterales, Alteromonadales, and Xanthomonadales. At genus level, Nocardia was common to both systems, and it could be related to the development of tumor symptoms by altering both nematode and plant systems. Furthermore, we predicted the healthy metabolic profile of the roots microbiome and a shift that may result in an increment of activity of central metabolism and the presence of pathogenic genes in both crops.
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Affiliation(s)
- Araceli Lamelas
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Damaris Desgarennes
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Daniel López-Lima
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | | | - Alexandro Alonso-Sánchez
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
| | - Alejandro Artacho
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
| | - Amparo Latorre
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Andrés Moya
- Joint Unit of Research in Genomics and Health, Foundation for the Promotion of Health and Biomedical Research in the Valencian Community (FISABIO) and Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Gloria Carrión
- Red de Estudios Moleculares Avanzados and Red de Biodiversidad y Sistemática, Instituto de Ecología A. C., Xalapa, Mexico
- *Correspondence: Gloria Carrión,
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Tayyrov A, Stanley CE, Azevedo S, Künzler M. Combining microfluidics and RNA-sequencing to assess the inducible defensome of a mushroom against nematodes. BMC Genomics 2019; 20:243. [PMID: 30909884 PMCID: PMC6434838 DOI: 10.1186/s12864-019-5607-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Fungi are an attractive source of nutrients for predators. As part of their defense, some fungi are able to induce the production of anti-predator protein toxins in response to predation. A previous study on the interaction of the model mushroom Coprinopsis cinerea by the fungivorous nematode Aphelenchus avenae on agar plates has shown that the this fungal defense response is most pronounced in the part of the mycelium that is in direct contact with the nematode. Hence, we hypothesized that, for a comprehensive characterization of this defense response, an experimental setup that maximizes the zone of direct interaction between the fungal mycelium and the nematode, was needed. RESULTS In this study, we conducted a transcriptome analysis of C. cinerea vegetative mycelium upon challenge with A. avenae using a tailor-made microfluidic device. The device was designed such that the interaction between the fungus and the nematode was confined to a specific area and that the mycelium could be retrieved from this area for analysis. We took samples from the confrontation area after different time periods and extracted and sequenced the poly(A)+ RNA thereof. The identification of 1229 differentially expressed genes (DEGs) shows that this setup profoundly improved sensitivity over co-cultivation on agar plates where only 37 DEGs had been identified. The product of one of the most highly upregulated genes shows structural homology to bacterial pore-forming toxins, and revealed strong toxicity to various bacterivorous nematodes. In addition, bacteria associated with the fungivorous nematode A. avenae were profiled with 16S rRNA deep sequencing. Similar to the bacterivorous and plant-feeding nematodes, Proteobacteria and Bacteroidetes were the most dominant phyla in A. avenae. CONCLUSIONS The use of a novel experimental setup for the investigation of the defense response of a fungal mycelium to predation by fungivorous nematodes resulted in the identification of a comprehensive set of DEGs and the discovery of a novel type of fungal defense protein against nematodes. The bacteria found to be associated with the fungivorous nematode are a possible explanation for the induction of some antibacterial defense proteins upon nematode challenge.
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Affiliation(s)
- Annageldi Tayyrov
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Claire E. Stanley
- Agroecology and Environment Research Division, Agroscope, Reckenholzstrasse 191, CH-8046 Zürich, Switzerland
| | - Sophie Azevedo
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland
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Toju H, Tanaka Y. Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes. ROYAL SOCIETY OPEN SCIENCE 2019; 6:181693. [PMID: 31032023 PMCID: PMC6458363 DOI: 10.1098/rsos.181693] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/21/2019] [Indexed: 06/01/2023]
Abstract
Cyst and root-knot nematodes are major risk factors of agroecosystem management, often causing devastating impacts on crop production. The use of microbes that parasitize or prey on nematodes has been considered as a promising approach for suppressing phytopathogenic nematode populations. However, effects and persistence of those biological control agents often vary substantially depending on regions, soil characteristics and agricultural practices: more insights into microbial community processes are required to develop reproducible control of nematode populations. By performing high-throughput sequencing profiling of bacteria and fungi, we examined how root and soil microbiomes differ between benign and nematode-infected plant individuals in a soybean field in Japan. Results indicated that various taxonomic groups of bacteria and fungi occurred preferentially on the soybean individuals infected by root-knot nematodes or those uninfected by nematodes. Based on a network analysis of potential microbe-microbe associations, we further found that several fungal taxa potentially preying on nematodes (Dactylellina (Orbiliales), Rhizophydium (Rhizophydiales), Clonostachys (Hypocreales), Pochonia (Hypocreales) and Purpureocillium (Hypocreales)) co-occurred in the soybean rhizosphere at a small spatial scale. This study suggests how 'consortia' of anti-nematode microbes can derive from indigenous (resident) microbiomes, providing basic information for managing anti-nematode microbial communities in agroecosystems.
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Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2133, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Yu Tanaka
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo, Kyoto 606-8502, Japan
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Bahram M, Vanderpool D, Pent M, Hiltunen M, Ryberg M. The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:155-166. [PMID: 29327481 DOI: 10.1111/1758-2229.12612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 12/19/2017] [Accepted: 01/04/2018] [Indexed: 06/07/2023]
Abstract
Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.
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Affiliation(s)
- Mohammad Bahram
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Dan Vanderpool
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Mari Pent
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, 51005 Estonia
| | - Markus Hiltunen
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
| | - Martin Ryberg
- Department of Organismal Biology, Evolutionary Biology Centre Uppsala University, Norbyvägen 18D, Uppsala, 75236 Sweden
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Chen D, Wang D, Xu C, Chen C, Li J, Wu W, Huang X, Xie H. Nematicidal protease genes screened from a soil metagenomic library to control Radopholus similis mediated by Pseudomonas fluorescens pf36. Appl Microbiol Biotechnol 2018; 102:3301-3314. [DOI: 10.1007/s00253-018-8869-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/25/2018] [Accepted: 02/10/2018] [Indexed: 12/01/2022]
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Sinnathamby G, Henderson G, Umair S, Janssen P, Bland R, Simpson H. The bacterial community associated with the sheep gastrointestinal nematode parasite Haemonchus contortus. PLoS One 2018; 13:e0192164. [PMID: 29420571 PMCID: PMC5805237 DOI: 10.1371/journal.pone.0192164] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/17/2018] [Indexed: 11/23/2022] Open
Abstract
Culture-independent methods were used to study the microbiota of adult worms, third-stage larvae and eggs, both in faeces and laid in vitro, of Haemonchus contortus, a nematode parasite of the abomasa of ruminants which is a major cause of production losses and ill-health. Bacteria were identified in eggs, the female reproductive tract and the gut of adult and third-stage larvae (L3). PCR amplification of 16S rRNA sequences, denaturing gradient gel electrophoresis (DGGE) and clone libraries were used to compare the composition of the microbial communities of the different life-cycle stages of the parasites, as well as parasites and their natural environments. The microbiomes of adult worms and L3 were different from those in the abomasum or faeces respectively. The H. contortus microbiota was mainly comprised of members of the phyla Proteobacteria, Firmicutes and Bacteroidetes. Bacteria were localised in the gut, inside eggs and within the uterus of adult female worms using the universal FISH Eub338 probe, which targets most bacteria, and were also seen in these tissues by light and transmission electron microscopy. Streptococcus/Lactococcus sp. were identified within the distal uterus with the probe Strc493. Sequences from the genera Weissella and Leuconostoc were found in all life-cycle stages, except eggs collected from faeces, in which most sequences belonged to Clostridium sp. Bacteria affiliated with Weissella/Leuconostoc were identified in both PCR-DGGE short sequences and clone libraries of nearly full length 16S rRNA bacterial sequences in all life-cycle stages and subsequently visualised in eggs by fluorescent in situ hybridisation (FISH) with group-specific probes. This strongly suggests they are vertically transmitted endosymbionts. As this study was carried out on a parasite strain which has been maintained in the laboratory, other field isolates will need to be examined to establish whether these bacteria are more widely dispersed and have potential as targets to control H. contortus infections.
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Affiliation(s)
- Gajenathirin Sinnathamby
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | | | - Saleh Umair
- AgResearch Ltd, Palmerston North, New Zealand
| | | | - Ross Bland
- AgResearch Ltd, Palmerston North, New Zealand
| | - Heather Simpson
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
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Thomas L, Ram H, Singh VP. Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya. J Comput Biol 2017; 24:1029-1042. [PMID: 28177649 DOI: 10.1089/cmb.2016.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The cellulases from different cellulolytic organisms have evolutionary relationships, which range from single-celled prokaryotes to the complex eukaryotes of the living world. This in silico analysis revealed the presence of a conserved cellulase domain along with evolutionary relationships among cellulases from several species of Archaea, Bacteria, and Eukarya. The amino acid sequences of cellulases from Archaea and Bacteria showed closer identity with their domain or phylum members that provided insights into convergent and divergent evolution of cellulases from other enzymes with different substrate specificities. Evolutionary relatedness was also observed in phylogenetic trees among a number of cellulase sequences of diverse taxa. In cellulases, propensity for alanine, glycine, leucine, serine, and threonine was high, but low for cysteine, histidine, and methionine. Catalytic aspartic acid had a higher propensity than glutamic acid, and both were involved in regular expression patterns. Characteristic group and multigroup-specific conserved signature indels located in the catalytic domains of cellulases were observed that further clarified evolutionary relationships. These indels can be distinctive molecular tools for understanding phylogeny and identification of unknown cellulolytic species of common evolutionary descent in different environments.
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Affiliation(s)
- Lebin Thomas
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Hari Ram
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
| | - Ved Pal Singh
- Applied Microbiology and Biotechnology Laboratory, Department of Botany, University of Delhi , Delhi, India
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Son JA, Jung CS, Han HR. Migration and Attacking Ability of Bursaphelenchus mucronatus in Pinus thunbergii Stem Cuttings. THE PLANT PATHOLOGY JOURNAL 2016; 32:340-6. [PMID: 27493609 PMCID: PMC4968644 DOI: 10.5423/ppj.oa.01.2016.0025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/20/2016] [Accepted: 03/23/2016] [Indexed: 06/06/2023]
Abstract
To understand how Bursaphelenchus xylophilus kills pine trees, the differences between the effects of B. xylophilus and B. mucronatus on pine trees are usually compared. In this study, the migration and attacking ability of a non-pathogenic B. mucronatus in Pinus thunbergii were investigated. The distribution of B. mucronatus and the number of dead epithelial cells resulting from inoculation were compared with those of the pathogenic B. xylophilus. Although B. mucronatus is non-pathogenic in pines, its distribution pattern in P. thunbergii was the same as that of B. xylophilus. We therefore concluded that the non-pathogenicity of B. mucronatus could not be attributed to its migration ability. The sparse and sporadic attacking pattern of B. mucronatus was also the same as that of B. xylophilus. However, the number and area of the dead epithelial cells in pine cuttings inoculated with B. mucronatus were smaller than in those cuttings inoculated with B. xylophilus, meaning that the attacking ability of B. mucronatus is weaker than that of B. xylophilus. Therefore, we concluded that the weaker attacking ability of B. mucronatus might be the factor responsible for the non-pathogenicity.
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Affiliation(s)
- Joung A Son
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul 02455,
Korea
| | - Chan Sik Jung
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul 02455,
Korea
| | - Hye Rim Han
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul 02455,
Korea
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Arbuzova EN, Kulinich OA, Mazurin ES, Ryss AY, Kozyreva NI, Zinovieva SV. Pine wilt disease and possible causes of its incidence in Russia. BIOL BULL+ 2016. [DOI: 10.1134/s1062359016040026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Kielak AM, Scheublin TR, Mendes LW, van Veen JA, Kuramae EE. Bacterial Community Succession in Pine-Wood Decomposition. Front Microbiol 2016; 7:231. [PMID: 26973611 PMCID: PMC4771932 DOI: 10.3389/fmicb.2016.00231] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/15/2016] [Indexed: 11/17/2022] Open
Abstract
Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.
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Affiliation(s)
- Anna M Kielak
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Tanja R Scheublin
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Lucas W Mendes
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology Wageningen, Netherlands
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Xiang Y, Wu XQ, Zhou AD. Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA. PLoS One 2015; 10:e0137386. [PMID: 26372013 PMCID: PMC4570786 DOI: 10.1371/journal.pone.0137386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 08/17/2015] [Indexed: 01/01/2023] Open
Abstract
Bursaphelenchus xylophilus is the pathogen of pine wilt disease. Bursaphelenchus mucronatus is similar to B. xylophilus in morphology. Both species share a common niche, but they are quite different in pathogenicity. Presently, the role of bacteria in pine wilt disease development has been widely speculated. The diversity of bacteria associated with B. xylophilus and B. mucronatus with different virulence remains unclear. In this study, virulence of four B. xylophilus and four B. mucronatus strains were evaluated by inoculating Pinus thunbergii. High-throughput sequencing targeted 16S rDNA of different virulence nematode strains was carried out. The associated bacterial community structures of the eight strains were analyzed. The results showed that 634,051 high-quality sequences were obtained from the eight nematode strains. The number of OTUs of bacteria associated with B. mucronatus was generally greater than those of B. xylophilus. The richness of the community of bacteria associated with high virulent B. xylophilus ZL1 and AmA3 was higher than moderately virulent B. xylophilus AA3, HE2, and all B. mucronatus strains. While the diversity of bacteria associated with B. mucronatus was higher than B. xylophilus. Stenotrophomonas, Pseudomonadaceae_Unclassified or Rhizobiaceae_Unclassified were predominant in the nematode strains with different virulence. Oxalobacteraceae and Achromobacter were found more abundant in the low virulent B. xylophilus and non-virulent B. mucronatus strains.
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Affiliation(s)
- Yang Xiang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Xiao-Qin Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
- * E-mail:
| | - Ai-Dong Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu, China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
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15
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Cao Y, Tian B, Ji X, Shang S, Lu C, Zhang K. Associated bacteria of different life stages of Meloidogyne incognita using pyrosequencing-based analysis. J Basic Microbiol 2015; 55:950-60. [PMID: 25809195 DOI: 10.1002/jobm.201400816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/30/2015] [Indexed: 11/09/2022]
Abstract
The root knot nematode (RKN), Meloidogyne incognita, belongs to the most damaging plant pathogens worldwide, and is able to infect almost all cultivated plants, like tomato. Recent research supports the hypothesis that bacteria often associated with plant-parasitic nematodes, function as nematode parasites, symbionts, or commensal organisms etc. In this study, we explored the bacterial consortia associated with M. incognita at different developmental stages, including egg mass, adult female and second-stage juvenile using the pyrosequencing approach. The results showed that Proteobacteria, with a proportion of 71-84%, is the most abundant phylum associated with M. incognita in infected tomato roots, followed by Actinobacteria, Bacteroidetes, Firmicutes etc. Egg mass, female and second-stage juvenile of M. incognita harbored a core microbiome with minor difference in communities and diversities. Several bacteria genera identified in M. incognita are recognized cellulosic microorganisms, pathogenic bacteria, nitrogen-fixing bacteria and antagonists to M. incognita. Some genera previously identified in other plant-parasitic nematodes were also found in tomato RKNs. The potential biological control microorganisms, including the known bacterial pathogens and nematode antagonists, such as Actinomycetes and Pseudomonas, showed the largest diversity and proportion in egg mass, and dramatically decreased in second-stage juvenile and female of M. incognita. This is the first comprehensive report of bacterial flora associated with the RKN identified by pyrosequencing-based analysis. The results provide valuable information for understanding nematode-microbiota interactions and may be helpful in the development of novel nematode-control strategies.
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Affiliation(s)
- Yi Cao
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China.,Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Baoyu Tian
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xinglai Ji
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Shenghua Shang
- Key Laboratory of Molecular Genetics, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Chaojun Lu
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
| | - Keqin Zhang
- Key Laboratory for Conservation and Utilization of Bio-resource, and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming, China
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Nascimento FX, Hasegawa K, Mota M, Vicente CSL. Bacterial role in pine wilt disease development - review and future perspectives. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:51-63. [PMID: 25139220 DOI: 10.1111/1758-2229.12202] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 08/14/2014] [Indexed: 05/02/2023]
Abstract
Mutualistic and beneficial relationships between nematodes and bacteria are highly present in nature, mostly occurring because of nutritional dependence and pathogen protection, and intrinsically related with the environment, the ecological conditions and the nematode life stages. Thirty-four years have passed since the first hypothesis suggesting a bacterial role in pine wilt disease (PWD), associated with the pinewood nematode (PWN), Bursaphelenchus xylophilus. In 1980, researchers reported that bacteria associated with the PWN could produce toxins that lead to PWD development in pine seedlings. It was also suggested a double vector system for PWD, where bacteria were vectored by the PWN and the PWN vectored by an insect from the Monochamus genus. Presently, the specific involvement of bacteria in such complex disease is still controversial, even though the increased number of studies focused on the potential bacteria role has increased considerably. This review is an up-to-date comprehensive perspective and brings new insights on the role of PWN-associated bacteria in PWD.
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Affiliation(s)
- Francisco X Nascimento
- ICAAM - Instituto de Ciências Agrárias e Ambientais Mediterrânicas, Departamento de Biologia, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal
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17
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Specific microbial attachment to root knot nematodes in suppressive soil. Appl Environ Microbiol 2014; 80:2679-86. [PMID: 24532076 DOI: 10.1128/aem.03905-13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Understanding the interactions of plant-parasitic nematodes with antagonistic soil microbes could provide opportunities for novel crop protection strategies. Three arable soils were investigated for their suppressiveness against the root knot nematode Meloidogyne hapla. For all three soils, M. hapla developed significantly fewer galls, egg masses, and eggs on tomato plants in unsterilized than in sterilized infested soil. Egg numbers were reduced by up to 93%. This suggested suppression by soil microbial communities. The soils significantly differed in the composition of microbial communities and in the suppressiveness to M. hapla. To identify microorganisms interacting with M. hapla in soil, second-stage juveniles (J2) baited in the test soil were cultivation independently analyzed for attached microbes. PCR-denaturing gradient gel electrophoresis of fungal ITS or 16S rRNA genes of bacteria and bacterial groups from nematode and soil samples was performed, and DNA sequences from J2-associated bands were determined. The fingerprints showed many species that were abundant on J2 but not in the surrounding soil, especially in fungal profiles. Fungi associated with J2 from all three soils were related to the genera Davidiella and Rhizophydium, while the genera Eurotium, Ganoderma, and Cylindrocarpon were specific for the most suppressive soil. Among the 20 highly abundant operational taxonomic units of bacteria specific for J2 in suppressive soil, six were closely related to infectious species such as Shigella spp., whereas the most abundant were Malikia spinosa and Rothia amarae, as determined by 16S rRNA amplicon pyrosequencing. In conclusion, a diverse microflora specifically adhered to J2 of M. hapla in soil and presumably affected female fecundity.
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Cheng XY, Tian XL, Wang YS, Lin RM, Mao ZC, Chen N, Xie BY. Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation. Sci Rep 2013; 3:1869. [PMID: 23694939 PMCID: PMC3660777 DOI: 10.1038/srep01869] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 04/30/2013] [Indexed: 11/09/2022] Open
Abstract
Our recent research revealed that pinewood nematode (PWN) possesses few genes encoding enzymes for degrading α-pinene, which is the main compound in pine resin. In this study, we examined the role of PWN microbiome in xenobiotics detoxification by metagenomic and bacteria culture analyses. Functional annotation of metagenomes illustrated that benzoate degradation and its related metabolisms may provide the main metabolic pathways for xenobiotics detoxification in the microbiome, which is obviously different from that in PWN that uses cytochrome P450 metabolism as the main pathway for detoxification. The metabolic pathway of degrading α-pinene is complete in microbiome, but incomplete in PWN genome. Experimental analysis demonstrated that most of tested cultivable bacteria can not only survive the stress of 0.4% α-pinene, but also utilize α-pinene as carbon source for their growth. Our results indicate that PWN and its microbiome have established a potentially mutualistic symbiotic relationship with complementary pathways in detoxification metabolism.
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Affiliation(s)
- Xin-Yue Cheng
- College of Life Sciences, Beijing Normal University, Beijing, China
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19
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Culture-independent investigation of the microbiome associated with the nematode Acrobeloides maximus. PLoS One 2013; 8:e67425. [PMID: 23894287 PMCID: PMC3718782 DOI: 10.1371/journal.pone.0067425] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 05/20/2013] [Indexed: 02/01/2023] Open
Abstract
Background Symbioses between metazoans and microbes are widespread and vital to many ecosystems. Recent work with several nematode species has suggested that strong associations with microbial symbionts may also be common among members of this phylu. In this work we explore possible symbiosis between bacteria and the free living soil bacteriovorous nematode Acrobeloides maximus. Methodology We used a soil microcosm approach to expose A. maximus populations grown monoxenically on RFP labeled Escherichia coli in a soil slurry. Worms were recovered by density gradient separation and examined using both culture-independent and isolation methods. A 16S rRNA gene survey of the worm-associated bacteria was compared to the soil and to a similar analysis using Caenorhabditis elegans N2. Recovered A. maximus populations were maintained on cholesterol agar and sampled to examine the population dynamics of the microbiome. Results A consistent core microbiome was extracted from A. maximus that differed from those in the bulk soil or the C. elegans associated set. Three genera, Ochrobactrum, Pedobacter, and Chitinophaga, were identified at high levels only in the A. maximus populations, which were less diverse than the assemblage associated with C. elegans. Putative symbiont populations were maintained for at least 4 months post inoculation, although the levels decreased as the culture aged. Fluorescence in situ hybridization (FISH) using probes specific for Ochrobactrum and Pedobacter stained bacterial cells in formaldehyde fixed nematode guts. Conclusions Three microorganisms were repeatedly observed in association with Acrobeloides maximus when recovered from soil microcosms. We isolated several Ochrobactrum sp. and Pedobacter sp., and demonstrated that they inhabit the nematode gut by FISH. Although their role in A. maximus is not resolved, we propose possible mutualistic roles for these bacteria in protection of the host against pathogens and facilitating enzymatic digestion of other ingested bacteria.
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Charan SS, Pawar KD, Severson DW, Patole MS, Shouche YS. Comparative analysis of midgut bacterial communities of Aedes aegypti mosquito strains varying in vector competence to dengue virus. Parasitol Res 2013; 112:2627-37. [PMID: 23636307 DOI: 10.1007/s00436-013-3428-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 04/05/2013] [Indexed: 02/02/2023]
Abstract
Differences in midgut bacterial communities of Aedes aegypti, the primary mosquito vector of dengue viruses (DENV), might influence the susceptibility of these mosquitoes to infection by DENV. As a first step toward addressing this hypothesis, comparative analysis of bacterial communities from midguts of mosquito strains with differential genetic susceptibility to DENV was performed. 16S rRNA gene libraries and real-time PCR approaches were used to characterize midgut bacterial community composition and abundance in three Aedes aegypti strains: MOYO, MOYO-R, and MOYO-S. Although Pseudomonas spp.-related clones were predominant across all libraries, some interesting and potentially significant differences were found in midgut bacterial communities among the three strains. Pedobacter sp.- and Janthinobacterium sp.-related phylotypes were identified only in the MOYO-R strain libraries, while Bacillus sp. was detected only in the MOYO-S strain. Rahnella sp. was found in MOYO-R and MOYO strains libraries but was absent in MOYO-S libraries. Both 16S rRNA gene library and real-time PCR approaches confirmed the presence of Pedobacter sp. only in the MOYO-R strain. Further, real-time PCR-based quantification of 16S rRNA gene copies showed bacterial abundance in midguts of the MOYO-R strain mosquitoes to be at least 10-100-folds higher than in the MOYO-S and MOYO strain mosquitoes. Our study identified some putative bacteria with characteristic physiological properties that could affect the infectivity of dengue virus. This analysis represents the first report of comparisons of midgut bacterial communities with respect to refractoriness and susceptibility of Aedes aegypti mosquitoes to DENV and will guide future efforts to address the potential interactive role of midgut bacteria of Aedes aegypti mosquitoes in determining vectorial capacity for DENV.
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Affiliation(s)
- Shakti S Charan
- Molecular Biology Unit, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India.
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Santos CS, Pinheiro M, Silva AI, Egas C, Vasconcelos MW. Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening. BMC Genomics 2012; 13:599. [PMID: 23134679 PMCID: PMC3542250 DOI: 10.1186/1471-2164-13-599] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/30/2012] [Indexed: 11/01/2022] Open
Abstract
BACKGROUND Pine wilt disease (PWD), caused by the pinewood nematode (PWN; Bursaphelenchus xylophilus), damages and kills pine trees and is causing serious economic damage worldwide. Although the ecological mechanism of infestation is well described, the plant's molecular response to the pathogen is not well known. This is due mainly to the lack of genomic information and the complexity of the disease. High throughput sequencing is now an efficient approach for detecting the expression of genes in non-model organisms, thus providing valuable information in spite of the lack of the genome sequence. In an attempt to unravel genes potentially involved in the pine defense against the pathogen, we hereby report the high throughput comparative sequence analysis of infested and non-infested stems of Pinus pinaster (very susceptible to PWN) and Pinus pinea (less susceptible to PWN). RESULTS Four cDNA libraries from infested and non-infested stems of P. pinaster and P. pinea were sequenced in a full 454 GS FLX run, producing a total of 2,083,698 reads. The putative amino acid sequences encoded by the assembled transcripts were annotated according to Gene Ontology, to assign Pinus contigs into Biological Processes, Cellular Components and Molecular Functions categories. Most of the annotated transcripts corresponded to Picea genes-25.4-39.7%, whereas a smaller percentage, matched Pinus genes, 1.8-12.8%, probably a consequence of more public genomic information available for Picea than for Pinus. The comparative transcriptome analysis showed that when P. pinaster was infested with PWN, the genes malate dehydrogenase, ABA, water deficit stress related genes and PAR1 were highly expressed, while in PWN-infested P. pinea, the highly expressed genes were ricin B-related lectin, and genes belonging to the SNARE and high mobility group families. Quantitative PCR experiments confirmed the differential gene expression between the two pine species. CONCLUSIONS Defense-related genes triggered by nematode infestation were detected in both P. pinaster and P. pinea transcriptomes utilizing 454 pyrosequencing technology. P. pinaster showed higher abundance of genes related to transcriptional regulation, terpenoid secondary metabolism (including some with nematicidal activity) and pathogen attack. P. pinea showed higher abundance of genes related to oxidative stress and higher levels of expression in general of stress responsive genes. This study provides essential information about the molecular defense mechanisms utilized by P. pinaster and P. pinea against PWN infestation and contributes to a better understanding of PWD.
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Affiliation(s)
- Carla S Santos
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
| | - Miguel Pinheiro
- Bioinformatics Unit, Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 03, Cantanhede, 3060-197, Portugal
| | - Ana I Silva
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
| | - Conceição Egas
- Advanced Services Unit, Biocant, Parque Tecnológico de Cantanhede, Núcleo 04, Lote 03, Cantanhede, 3060-197, Portugal
| | - Marta W Vasconcelos
- CBQF – Centro de Biotecnologia e Química Fina, Escola Superior de Biotecnologia, Centro Regional do Porto da Universidade Católica Portuguesa, Rua Dr. António Bernardino Almeida, Porto, 4200-072, Portugal
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Zhu LH, Ye J, Negi S, Xu XL, Wang ZL, Ji JY. Pathogenicity of aseptic Bursaphelenchus xylophilus. PLoS One 2012; 7:e38095. [PMID: 22662271 PMCID: PMC3360648 DOI: 10.1371/journal.pone.0038095] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/30/2012] [Indexed: 11/25/2022] Open
Abstract
Pine wilt is a disease of pine (Pinus spp.) caused by the pine wood nematode (PWN), Bursaphelenchus xylophilus. However, the pathogenic mechanism of pine wilt disease (PWD) remains unclear. Although the PWN was thought to be the only pathogenic agent associated with this disease, a potential role for bacterial symbionts in the disease process was recently proposed. Studies have indicated that aseptic PWNs do not cause PWD in aseptic pine trees, while PWNs associated with bacteria cause wilting symptoms. To investigate the pathogenicity of the PWN and its associated bacteria, 3-month-old microcuttings derived from certain clones of Pinus densiflora Siebold & Zucc. produced in vitro were inoculated under aseptic conditions with aseptic PWNs, non-aseptic PWNs and bacteria isolated from the nematodes. Six-month-old aseptic P. densiflora microcuttings and 7-month-old P. massoniana seedlings were also inoculated under aseptic conditions with aseptic PWNs and non-aseptic PWNs. The results showed that the aseptic microcuttings and seedlings inoculated with aseptic PWNs or non-aseptic PWNs wilted, while those inoculated with bacterial isolates did not wilt. Nematodes were recovered from wilted microcuttings and seedlings inoculated with aseptic PWNs and non-aseptic PWNs, and the asepsis of nematodes recovered from aseptic PWN-inoculated microcuttings and seedlings was reconfirmed by culturing them in NB liquid medium at 30°C for more than 7 days. Taken together, the results indicate that the asepsis of PWN did not cause the loss of pathogenicity.
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Affiliation(s)
- Li-hua Zhu
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
| | - Jianren Ye
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
- * E-mail:
| | - Sapna Negi
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
| | - Xu-ling Xu
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
| | - Zhang-li Wang
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
| | - Jin-yi Ji
- Institute of Forest Protection, College of Forest Resources and Environment, Nanjing Forestry University, Nanjing, People’s Republic of China
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing, People’s Republic of China
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