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Badger JH, Giordano R, Zimin A, Wappel R, Eskipehlivan SM, Muller S, Donthu R, Soto-Adames F, Vieira P, Zasada I, Goodwin S. Direct sequencing of insect symbionts via nanopore adaptive sampling. CURRENT OPINION IN INSECT SCIENCE 2024; 61:101135. [PMID: 37926187 DOI: 10.1016/j.cois.2023.101135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/07/2023]
Abstract
Insect symbionts can alter their host phenotype and their effects can range from beneficial to pathogenic. Moreover, many insects exhibit co-infections, making their study more challenging. Less than 1% of insect species have high-quality referenced genomes available and fewer still also have their symbionts sequenced. Two methods are commonly used to sequence symbionts: whole-genome sequencing to concomitantly capture the host and bacterial genomes, or isolation of the symbiont's genome before sequencing. These methods are limited when dealing with rare or poorly characterized symbionts. Long-read technology is an important tool to generate high-quality genomes as they can overcome high levels of heterozygosity, repeat content, and transposable elements that confound short-read methods. Oxford Nanopore (ONT) adaptive sampling allows a sequencing instrument to select or reject sequences in real time. We describe a method based on ONT adaptive sampling (subtractive) approach that readily permitted the sequencing of the complete genomes of mitochondria, Buchnera and its plasmids (pLeu, pTrp), and Wolbachia genomes in two aphid species, Aphis glycines and Pentalonia nigronervosa. Adaptive sampling is able to retrieve organelles such as mitochondria and symbionts that have high representation in their hosts such as Buchnera and Wolbachia, but is less successful at retrieving symbionts in low concentrations.
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Affiliation(s)
- Jonathan H Badger
- Genetics and Microbiome Core, Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosanna Giordano
- Institute of Environment, Florida International University, Miami, FL, USA
| | - Aleksey Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Ravikiran Donthu
- Centre for Life Sciences, Mahindra University, Bahadurpally, Hyderabad 500043, India
| | - Felipe Soto-Adames
- Florida Department of Agriculture and Consumer Services, Department of Plant Industry, Gainesville, FL 32614, USA
| | - Paulo Vieira
- USDA-ARS Agricultural Research Center, Mycology & Nematology Genetic Diversity & Biology Laboratory, Beltsville, MD, USA
| | - Inga Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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Safari Murhububa I, Tougeron K, Bragard C, Fauconnier ML, Mugisho Bugeme D, Bisimwa Basengere E, Walangululu Masamba J, Hance T. The aphid Pentalonia nigronervosa (Hemiptera: Aphididae) takes advantage from the quality change in banana plant associated with Banana bunchy top virus infection. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:1481-1489. [PMID: 37467484 DOI: 10.1093/jee/toad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/01/2023] [Accepted: 06/23/2023] [Indexed: 07/21/2023]
Abstract
Viral diseases can change plant metabolism, with potential impacts on the quality of the plant's food supply for insect pests, including virus vectors. The banana aphid, Pentalonia nigronervosa Coquerel, is the vector of the Banana bunchy top virus (BBTV), the causal agent of Banana bunchy top disease (BBTD), the most devastating viral disease of bananas in the world. The effect of BBTV on the life-history traits and population dynamics of P. nigronervosa remains poorly understood. We therefore studied the survival rate, longevity, daily fecundity per aphid, tibia length, population growth, and winged morph production of a P. nigronervosa clone grown on healthy or infected, dessert, or plantain banana plants. We found that daily fecundity was higher on infected banana than on healthy banana plants (plantain and dessert), and on plantain than on dessert banana plants (healthy and infected). Survival and longevity were lower on infected dessert bananas than on other types of bananas. In addition, virus infection resulted in a decrease in aphid hind tibia length on both plant genotypes. The survival and fecundity table revealed that the aphid net reproduction rate (Ro) was highest on plantains (especially infected plantain), and the intrinsic growth rate (r) was highest on infected plants. Finally, the increase of aphids and alate production was faster first on infected plantain, then on healthy plantain, and lower on dessert banana (infected and uninfected). Our results reinforce the idea of indirect and plant genotype-dependent manipulation of P. nigronervosa by the BBTV.
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Affiliation(s)
- Ignace Safari Murhububa
- Earth and Life Institute, Ecology and Biodiversity, UCLouvain, Louvain-la-Neuve, Belgium
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, Bukavu, Democratic Republic of the Congo
- Institut Supérieur d'Etudes Agronomiques et Vétérinaires (ISEAV/Walungu), Walungu, Democratic Republic of the Congo
| | - Kévin Tougeron
- Earth and Life Institute, Ecology and Biodiversity, UCLouvain, Louvain-la-Neuve, Belgium
- UMR CNRS 7058 EDYSAN (Écologie et Dynamique des Systèmes Anthropisés), Université de Picardie Jules Verne, Amiens, France
- EIGC laboratory, Research Institute for Biosciences, Université de Mons, Mons, Belgium
| | - Claude Bragard
- Earth and Life Institute, Applied Microbiology, UCLouvain, Louvain-la-Neuve, Belgium
| | - Marie-Laure Fauconnier
- Laboratory of Chemistry of Natural Molecules, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - David Mugisho Bugeme
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Espoir Bisimwa Basengere
- Faculté des Sciences Agronomiques, Université Catholique de Bukavu, Bukavu, Democratic Republic of the Congo
| | - Jean Walangululu Masamba
- Institut Supérieur d'Etudes Agronomiques et Vétérinaires (ISEAV/Walungu), Walungu, Democratic Republic of the Congo
| | - Thierry Hance
- Earth and Life Institute, Ecology and Biodiversity, UCLouvain, Louvain-la-Neuve, Belgium
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Rodrigues J, Lefoulon E, Gavotte L, Perillat-Sanguinet M, Makepeace B, Martin C, D'Haese CA. Wolbachia springs eternal: symbiosis in Collembola is associated with host ecology. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230288. [PMID: 37266040 PMCID: PMC10230187 DOI: 10.1098/rsos.230288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
Wolbachia are endosymbiotic alpha-proteobacteria infecting a wide range of arthropods and nematode hosts with diverse interactions, from reproductive parasites to obligate mutualists. Their taxonomy is defined by lineages called supergroups (labelled by letters of the alphabet), while their evolutionary history is complex, with multiple horizontal transfers and secondary losses. One of the least recently derived, supergroup E, infects springtails (Collembola), widely distributed hexapods, with sexual and/or parthenogenetic populations depending on species. To better characterize the diversity of Wolbachia infecting springtails, the presence of Wolbachia was screened in 58 species. Eleven (20%) species were found to be positive, with three Wolbachia genotypes identified for the first time in supergroup A. The novel genotypes infect springtails ecologically and biologically different from those infected by supergroup E. To root the Wolbachia phylogeny, rather than distant other Rickettsiales, supergroup L infecting plant-parasitic nematodes was used here. We hypothesize that the ancestor of Wolbachia was consumed by soil-dwelling nematodes, and was transferred horizontally via plants into aphids, which then infected edaphic arthropods (e.g. springtails and oribatid mites) before expanding into most clades of terrestrial arthropods and filarial nematodes.
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Affiliation(s)
- Jules Rodrigues
- UMR7245, MCAM, Museum national d'Histoire naturelle, Paris, France
| | - Emilie Lefoulon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | | | | | - Benjamin Makepeace
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Coralie Martin
- UMR7245, MCAM, Museum national d'Histoire naturelle, Paris, France
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Weyandt N, Aghdam SA, Brown AMV. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes. Front Microbiol 2022; 13:867392. [PMID: 35547116 PMCID: PMC9084900 DOI: 10.3389/fmicb.2022.867392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.
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Affiliation(s)
- Nicholas Weyandt
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Shiva A Aghdam
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
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Insight into the bacterial communities of the subterranean aphid Anoecia corni. PLoS One 2021; 16:e0256019. [PMID: 34379678 PMCID: PMC8357138 DOI: 10.1371/journal.pone.0256019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/28/2021] [Indexed: 11/23/2022] Open
Abstract
Many insect species are associated with bacterial partners that can significantly influence their evolutionary ecology. Compared to other insect groups, aphids harbor a bacterial microbiota that has the reputation of being poorly diversified, generally limited to the presence of the obligate nutritional symbiont Buchnera aphidicola and some facultative symbionts. In this study, we analyzed the bacterial diversity associated with the dogwood-grass aphid Anoecia corni, an aphid species that spends much of its life cycle in a subterranean environment. Little is known about the bacterial diversity associated with aphids displaying such a lifestyle, and one hypothesis is that close contact with the vast microbial community of the rhizosphere could promote the acquisition of a richer bacterial diversity compared to other aphid species. Using 16S rRNA amplicon Illumina sequencing on specimens collected on wheat roots in Morocco, we identified 10 bacterial operational taxonomic units (OTUs) corresponding to five bacterial genera. In addition to the obligate symbiont Buchnera, we identified the facultative symbionts Serratia symbiotica and Wolbachia in certain aphid colonies. The detection of Wolbachia is unexpected as it is considered rare in aphids. Moreover, its biological significance remains unknown in these insects. Besides, we also detected Arsenophonus and Dactylopiibacterium carminicum. These results suggest that, despite its subterranean lifestyle, A. corni shelter a bacterial diversity mainly limited to bacterial endosymbionts.
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Xu S, Jiang L, Qiao G, Chen J. Diversity of bacterial symbionts associated with Myzus persicae (Sulzer) (Hemiptera: Aphididae: Aphidinae) revealed by 16S rRNA Illumina sequencing. MICROBIAL ECOLOGY 2021; 81:784-794. [PMID: 33070212 PMCID: PMC7982390 DOI: 10.1007/s00248-020-01622-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Aphids are known to be associated with a variety of symbiotic bacteria. To improve our knowledge of the bacterial diversity of polyphagous aphids, in the present study, we investigated the microbiota of the cosmopolitan agricultural pest Myzus persicae (Sulzer). Ninety-two aphid samples collected from different host plants in various regions of China were examined using high-throughput amplicon sequencing. We comprehensively characterized the symbiont diversity of M. persicae and assessed the variations in aphid-associated symbiont communities. We detected a higher diversity of symbionts than has been previously observed. M. persicae hosted the primary endosymbiont Buchnera aphidicola and seven secondary symbionts, among which Wolbachia was the most prevalent and Rickettsia, Arsenophonus, and Spiroplasma were reported for the first time. Ordination analyses and statistical tests revealed that the symbiont flora associated with M. persicae did not change with respect to host plant or geography, which may be due to frequent migrations between different aphid populations. These findings will advance our knowledge of the microbiota of polyphagous insects and will enrich our understanding of assembly of host-microbiome systems.
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Affiliation(s)
- Shifen Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liyun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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