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Manentzos AN, Pahl AMC, Melloh P, Martin EA, Leybourne DJ. Low prevalence of secondary endosymbionts in aphids sampled from rapeseed crops in Germany. BULLETIN OF ENTOMOLOGICAL RESEARCH 2024:1-6. [PMID: 38444236 DOI: 10.1017/s0007485324000063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Peach-potato aphids, Myzus persicae Sulzer (Hemiptera:Aphididae), and cabbage aphids, Brevicoryne brassicae Linnaeus (Hemiptera:Aphididae), are herbivorous insects of significant agricultural importance. Aphids can harbour a range of non-essential (facultative) endosymbiotic bacteria that confer multiple costs and benefits to the host aphid. A key endosymbiont-derived phenotype is protection against parasitoid wasps, and this protective phenotype has been associated with several defensive enodsymbionts. In recent years greater emphasis has been placed on developing alternative pest management strategies, including the increased use of natural enemies such as parasitoids wasps. For the success of aphid control strategies to be estimated the presence of defensive endosymbionts that can potentially disrupt the success of biocontrol agents needs to be determined in natural aphid populations. Here, we sampled aphids and mummies (parasitised aphids) from an important rapeseed production region in Germany and used multiplex PCR assays to characterise the endosymbiont communities. We found that aphids rarely harboured facultative endosymbionts, with 3.6% of M. persicae and 0% of B. brassicae populations forming facultative endosymbiont associations. This is comparable with endosymbiont prevalence described for M. persicae populations surveyed in Australia, Europe, Chile, and USA where endosymbiont infection frequencies range form 0-2%, but is in contrast with observations from China where M. persicae populations have more abundant and diverse endosymbiotic communities (endosymbionts present in over 50% of aphid populations).
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Affiliation(s)
- A N Manentzos
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - A M C Pahl
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - P Melloh
- Zoological Biodiversity, Institute of Geobotany, Gottfried Wilhelm Leibniz University Hannover, Hannover, Germany
| | - E A Martin
- Animal Ecology, Institute of Animal Ecology and Systematics, Justus Liebig University of Gießen, Gießen, Germany
| | - D J Leybourne
- Department of Evolution, Ecology, and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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2
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Kloth KJ, Shah P, Broekgaarden C, Ström C, Albrectsen BR, Dicke M. SLI1 confers broad-spectrum resistance to phloem-feeding insects. PLANT, CELL & ENVIRONMENT 2021; 44:2765-2776. [PMID: 33837973 PMCID: PMC8360143 DOI: 10.1111/pce.14064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 05/13/2023]
Abstract
Resistance (R) genes usually compete in a coevolutionary arms race with reciprocal effectors to confer strain-specific resistance to pathogens or herbivorous insects. Here, we investigate the specificity of SLI1, a recently identified R gene in Arabidopsis that encodes a small heat shock-like protein involved in resistance to Myzus persicae aphids. In a panel with several aphid and whitefly species, SLI1 compromised reproductive rates of three species: the tobacco aphid M. persicae nicotianae, the cabbage aphid Brevicoryne brassicae and the cabbage whitefly Aleyrodes proletella. Electrical penetration graph recording of aphid behaviour, revealed shorter salivations and a 3-to-5-fold increase in phloem feeding on sli1 loss-of-function plants. The mustard aphid Lipaphis erysimi and Bemisia tabaci whitefly were not affected by SLI1. Unlike the other two aphid species, L. erysimi exhibited repetitive salivations preceding successful phloem feeding, indicating a role of salivary effectors in overcoming SLI1-mediated resistance. Microscopic characterization showed that SLI1 proteins localize in the sieve tubes of virtually all above- and below-ground tissues and co-localize with the aphid stylet tip after penetration of the sieve element plasma membrane. These observations reveal an unconventional R gene that escapes the paradigm of strain specificity and confers broad-spectrum quantitative resistance to phloem-feeding insects.
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Affiliation(s)
- Karen J. Kloth
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
| | - Parth Shah
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
| | | | - Cecilia Ström
- Department of Plant Physiology, Umeå Plant Science CentreUmeå UniversityUmeåSweden
| | | | - Marcel Dicke
- Laboratory of EntomologyWageningen University & ResearchWageningenThe Netherlands
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3
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Bacterial communities of Aphis gossypii and Myzus persicae (Hemiptera: Aphididae) from pepper crops (Capsicum sp.). Sci Rep 2019; 9:5766. [PMID: 30962510 PMCID: PMC6453963 DOI: 10.1038/s41598-019-42232-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/21/2019] [Indexed: 11/09/2022] Open
Abstract
Insects harbor a wide variety of microorganisms that form complex and changing communities and play an important role in the biology and evolution of their hosts. Aphids have been used as model organisms to study microorganism-insect interactions. Almost all aphids are infected with the obligate endosymbiont Buchnera aphidicola and can host different bacteria that allow them to acquire traits of agronomic importance, such as resistance to high temperatures and/or defense against natural enemies. However, the bacterial communities of most aphid species remain poorly characterized. In this study, we used high-throughput DNA sequencing to characterize the bacterial communities of Aphis gossypii and Myzus persicae from two cultivable pepper species, Capsicum frutescens (Tabasco variety) and C. annuum (Cayenne variety), in four localities of southwestern Colombia. In addition, we evaluated the dynamics of A. gossypii-associated microorganisms on a seasonal basis. Our results show that the bacterial communities of A. gossypii and M. persicae are dominated by the primary endosymbiont B. aphidicola, while the presence of the facultative symbiont Arsenophonus sp. was only detected in one A. gossypii population from cayenne pepper. In addition to these two known symbionts, eight bacterial OTUs were identified that presented a frequency of 1% or more in at least one of the analyzed populations. The results show that the bacterial communities of aphids associated with pepper crops appears to be structured according to the host aphid species and the geographical location, while no differences were observed in the diversity of bacteria between host plants. Finally, the diversity and abundance of the A. gossypii bacterial community was variable among the four sampling points evaluated over the year and showed a relation with the aphid’s population dynamics. This study represents the first approach to the knowledge of the bacterial community present in chili pepper aphids from Colombia. Nevertheless, more in-depth studies, including replicates, are required to confirm the patterns observed in the microbial communities of aphids from pepper crops.
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Grigorescu AS, Renoz F, Sabri A, Foray V, Hance T, Thonart P. Accessing the Hidden Microbial Diversity of Aphids: an Illustration of How Culture-Dependent Methods Can Be Used to Decipher the Insect Microbiota. MICROBIAL ECOLOGY 2018; 75:1035-1048. [PMID: 29119316 DOI: 10.1007/s00248-017-1092-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
Microorganism communities that live inside insects can play critical roles in host development, nutrition, immunity, physiology, and behavior. Over the past decade, high-throughput sequencing reveals the extraordinary microbial diversity associated with various insect species and provides information independent of our ability to culture these microbes. However, their cultivation in the laboratory remains crucial for a deep understanding of their physiology and the roles they play in host insects. Aphids are insects that received specific attention because of their ability to form symbiotic associations with a wide range of endosymbionts that are considered as the core microbiome of these sap-feeding insects. But, if the functional diversity of obligate and facultative endosymbionts has been extensively studied in aphids, the diversity of gut symbionts and other associated microorganisms received limited consideration. Herein, we present a culture-dependent method that allowed us to successfully isolate microorganisms from several aphid species. The isolated microorganisms were assigned to 24 bacterial genera from the Actinobacteria, Firmicutes, and Proteobacteria phyla and three fungal genera from the Ascomycota and Basidiomycota phyla. In our study, we succeeded in isolating already described bacteria found associated to aphids (e.g., the facultative symbiont Serratia symbiotica), as well as microorganisms that have never been described in aphids before. By unraveling a microbial community that so far has been ignored, our study expands our current knowledge on the microbial diversity associated with aphids and illustrates how fast and simple culture-dependent approaches can be applied to insects in order to capture their diverse microbiota members.
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Affiliation(s)
- Alina S Grigorescu
- Walloon Center of Industrial Biology, Université de Liège, Sart-Tilman, B40, 4000, Liège, Belgium.
| | - François Renoz
- Earth and Life Institute, Biodiversity Research Center, Université Catholique de Louvain, Croix de Sud 4-5, bte L7.07.04, 1348, Louvain-la-Neuve, Belgium.
| | - Ahmed Sabri
- Artechno SA, Rue Herman Meganck 21, 5032, Isnes, Belgium
| | - Vincent Foray
- Centre de Recherches de Biochimie Macromoléculaire (UMR-CNRS 5237), 1919, Route de Mende, 34293, Montpellier Cedex 05, France
| | - Thierry Hance
- Earth and Life Institute, Biodiversity Research Center, Université Catholique de Louvain, Croix de Sud 4-5, bte L7.07.04, 1348, Louvain-la-Neuve, Belgium
| | - Philippe Thonart
- Walloon Center of Industrial Biology, Université de Liège, Sart-Tilman, B40, 4000, Liège, Belgium
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Ivens ABF, Gadau A, Kiers ET, Kronauer DJC. Can social partnerships influence the microbiome? Insights from ant farmers and their trophobiont mutualists. Mol Ecol 2018; 27:1898-1914. [PMID: 29411455 PMCID: PMC5935579 DOI: 10.1111/mec.14506] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/21/2017] [Accepted: 11/28/2017] [Indexed: 01/02/2023]
Abstract
Mutualistic interactions with microbes have played a crucial role in the evolution and ecology of animal hosts. However, it is unclear what factors are most important in influencing particular host–microbe associations. While closely related animal species may have more similar microbiota than distantly related species due to phylogenetic contingencies, social partnerships with other organisms, such as those in which one animal farms another, may also influence an organism's symbiotic microbiome. We studied a mutualistic network of Brachymyrmex and Lasius ants farming several honeydew‐producing Prociphilus aphids and Rhizoecus mealybugs to test whether the mutualistic microbiomes of these interacting insects are primarily correlated with their phylogeny or with their shared social partnerships. Our results confirm a phylogenetic signal in the microbiomes of aphid and mealybug trophobionts, with each species harbouring species‐specific endosymbiont strains of Buchnera (aphids), Tremblaya and Sodalis (mealybugs), and Serratia (both mealybugs and aphids) despite being farmed by the same ants. This is likely explained by strict vertical transmission of trophobiont endosymbionts between generations. In contrast, our results show the ants’ microbiome is possibly shaped by their social partnerships, with ants that farm the same trophobionts also sharing strains of sugar‐processing Acetobacteraceae bacteria, known from other honeydew‐feeding ants and which likely reside extracellularly in the ants’ guts. These ant–microbe associations are arguably more “open” and subject to horizontal transmission or social transmission within ant colonies. These findings suggest that the role of social partnerships in shaping a host's symbiotic microbiome can be variable and is likely dependent on how the microbes are transmitted across generations.
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Affiliation(s)
- Aniek B F Ivens
- Animal Ecology Section, Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands.,Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Alice Gadau
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - E Toby Kiers
- Animal Ecology Section, Department of Ecological Science, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
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6
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Fromont C, Riegler M, Cook JM. Relative Abundance and Strain Diversity in the Bacterial Endosymbiont Community of a Sap-Feeding Insect Across Its Native and Introduced Geographic Range. MICROBIAL ECOLOGY 2017; 74:722-734. [PMID: 28386769 DOI: 10.1007/s00248-017-0971-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 03/20/2017] [Indexed: 06/07/2023]
Abstract
Most insects are associated with bacterial symbionts. The bacterial diversity and community composition within hosts may play an important role in shaping insect population biology, ecology and evolution. We focussed on the bacterial microbiome of the Australian fig homotomid Mycopsylla fici (Hemiptera: Psylloidea), which can cause defoliation of its only host tree, Ficus macrophylla. This sap-feeding insect is native to mainland Australia and Lord Howe Island (LHI) but also occurs where its host has been planted, notably in New Zealand. By using a high-throughput 16S rDNA amplicon sequencing approach, we compared the bacterial diversity and community composition in individual adult males of four host populations, Sydney, Brisbane, LHI and Auckland. We also compared males, females and nymphs of the Sydney population. The microbiome of M. fici was simple and consisted mostly of the following three maternally inherited endosymbiont species: the primary endosymbiont Carsonella, a secondary (S-) endosymbiont and Wolbachia. However, the relative abundance of their sequence reads varied between host populations, except for similarities between Sydney and Auckland. In addition, insects from Sydney and Auckland had identical bacterial strains supporting the hypothesis that Sydney is the source population for Auckland. In contrast, mainland and LHI populations harboured the same S-endosymbiont, co-diverged Carsonella but different Wolbachia strains. Besides detecting endosymbiont-specific patterns of either co-evolution or horizontal acquisition, our study highlights that relative abundance of maternally inherited endosymbionts should also be taken into account when studying bacterial communities across host populations, as variations in bacterial density may impact host biology and ecology.
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Affiliation(s)
- Caroline Fromont
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia.
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - James M Cook
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
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7
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Guidolin AS, Cônsoli FL. Symbiont Diversity of Aphis (Toxoptera) citricidus (Hemiptera: Aphididae) as Influenced by Host Plants. MICROBIAL ECOLOGY 2017; 73:201-210. [PMID: 27872949 DOI: 10.1007/s00248-016-0892-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 10/31/2016] [Indexed: 06/06/2023]
Abstract
Aphids are well known for their association with endosymbiont bacteria. Almost all aphids harbor Buchnera aphidicola as an obligate symbiont and several other bacteria as facultative symbionts. Associations of facultative symbionts and aphids are quite variable in terms of diversity and prevalence across aphid species. Facultative symbionts can have a major impact on aphid bioecological traits. A number of factors shape the outcome of the facultative symbiont-aphid association, including aphid clone, bacterial genotype, geography, and host plant association. The effects of host plant on aphid-facultative symbiont associations are the least understood. We performed deep sequencing of the bacterial community associated with field populations of the oligophagous aphid Aphis (Toxoptera) citricidus collected from different host plants. We demonstrate that (i) A. citricidus has low symbiont diversity, (ii) symbiont diversity is affected by host plant, and (iii) host plants affect the relative abundance of the obligate symbiont Buchnera and an unknown genus of Enterobacteriaceae.
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Affiliation(s)
- Aline Sartori Guidolin
- Insect Interactions Lab., Department of Entomology and Acarology/ESALQ, University of São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, São Paulo, Brazil
| | - Fernando Luis Cônsoli
- Insect Interactions Lab., Department of Entomology and Acarology/ESALQ, University of São Paulo, Av. Pádua Dias 11, 13418-900, Piracicaba, São Paulo, Brazil.
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8
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Meseguer AS, Manzano-Marín A, Coeur d'Acier A, Clamens AL, Godefroid M, Jousselin E. Buchnerahas changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts. Mol Ecol 2016; 26:2363-2378. [DOI: 10.1111/mec.13910] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 09/30/2016] [Accepted: 10/27/2016] [Indexed: 02/02/2023]
Affiliation(s)
- A. S. Meseguer
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A. Manzano-Marín
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A. Coeur d'Acier
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - A.-L. Clamens
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - M. Godefroid
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
| | - E. Jousselin
- INRA; UMR 1062; Centre de Biologie pour la Gestion des Populations CBGP (INRA; IRD; CIRAD; Montpellier SupAgro); Montferrier-sur-Lez 34980 France
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9
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Campillo T, Luna E, Portier P, Fischer-Le Saux M, Lapitan N, Tisserat NA, Leach JE. Erwinia iniecta sp. nov., isolated from Russian wheat aphid (Diuraphis noxia). Int J Syst Evol Microbiol 2016. [PMID: 26198254 DOI: 10.1099/ijsem.0.000466] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Short, Gram-negative-staining, rod-shaped bacteria were isolated from crushed bodies of Russian wheat aphid [Diuraphis noxia (Kurdjumov)] and artificial diets after Russian wheat aphid feeding. Based on multilocus sequence analysis involving the 16S rRNA, atpD, infB, gyrB and rpoB genes, these bacterial isolates constitute a novel clade in the genus Erwinia, and were most closely related to Erwinia toletana. Representative distinct strains within this clade were used for comparisons with related species of Erwinia. Phenotypic comparisons using four distinct strains and average nucleotide identity (ANI) measurements using two distinct draft genomes revealed that these strains form a novel species within the genus Erwinia. The name Erwinia iniecta sp. nov. is proposed, and strain B120T ( = CFBP 8182T = NCCB 100485T) was designated the type strain. Erwinia iniecta sp. nov. was not pathogenic to plants. However, virulence to the Russian wheat aphid was observed.
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Affiliation(s)
- Tony Campillo
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA.,Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Emily Luna
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Perrine Portier
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France.,Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France.,Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
| | - Marion Fischer-Le Saux
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France.,Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, Angers, France.,Université d'Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
| | - Nora Lapitan
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1177, USA.,Bureau for Food Security, US Agency for International Development, 1300 Pennsylvania Ave NW, Washington, DC 20523, USA
| | - Ned A Tisserat
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA
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10
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Lazarova SS, Brown DJ, Oliveira CMG, Fenton B, MacKenzie K, Wright F, Malloch G, Neilson R. Diversity of endosymbiont bacteria associated with a non-filarial nematode group. NEMATOLOGY 2016. [DOI: 10.1163/15685411-00002982] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
There is a significant knowledge gap with regard to non-filarial nematodes and their relationships, if any, with intracellular bacteria, with only sporadic reports in the literature. An intracellular bacteriaXiphinematobacter, belonging to subdivision 2 of the Verrucomicrobia, was previously reported in the ovaries of three species of the non-filarialXiphinema americanum-group of nematodes. We explored the diversity ofXiphinematobacterin 22 populations ofX. americanumsourced from six continents and conservatively have identified nine phylotypes, six of which have not previously been reported. A geographic basis to the phylotypes was noted with phylotypes A and B only found in Europe, whereas phylotypes F, G, H and I were mainly found in North America. Phylotypes C, D and E showed greater geographical variation. Sequences ofXiphinematobacterfrom this study help to inform the taxonomy of Verrucomicrobia such that the status and composition of Verrucomicrobia subdivision 2 potentially requires reflection.
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Affiliation(s)
- Stela S. Lazarova
- Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | - Derek J.F. Brown
- Institute of Biodiversity and Ecosystem Research, 2 Gagarin Street, 1113 Sofia, Bulgaria
| | | | - Brian Fenton
- Scotland’s Rural College (SRUC), Peter Wilson Building, Kings Buildings, West Mains Road, Edinburgh EH9 3JG, Scotland, UK
| | - Katrin MacKenzie
- Biomathematics and Statistics Scotland, Dundee DD2 5DA, Scotland, UK
| | - Frank Wright
- Biomathematics and Statistics Scotland, Dundee DD2 5DA, Scotland, UK
| | - Gaynor Malloch
- The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Roy Neilson
- The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
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11
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Jousselin E, Clamens AL, Galan M, Bernard M, Maman S, Gschloessl B, Duport G, Meseguer AS, Calevro F, Coeur d'acier A. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. Mol Ecol Resour 2015; 16:628-40. [PMID: 26458227 DOI: 10.1111/1755-0998.12478] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023]
Abstract
The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.
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Affiliation(s)
- E Jousselin
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - A-L Clamens
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Galan
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Bernard
- INRA - UMR 1313 GABI-SIGENAE, INRA de Jouy en Josas, Domaine de Vilvert, 78352, Jouy en Josas, France
| | - S Maman
- INRA, GenPhySE, Sigenae, Chemin de Borde rouge -CS 52627, 31326, Castanet Tolosan, France
| | - B Gschloessl
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - G Duport
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A S Meseguer
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - F Calevro
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A Coeur d'acier
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
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Downie HF, Adu MO, Schmidt S, Otten W, Dupuy LX, White PJ, Valentine TA. Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis. PLANT, CELL & ENVIRONMENT 2015; 38:1213-32. [PMID: 25211059 DOI: 10.1111/pce.12448] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 08/02/2014] [Accepted: 08/25/2014] [Indexed: 05/19/2023]
Abstract
The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions.
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Affiliation(s)
- H F Downie
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - M O Adu
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Leicestershire, LE12 5RD, UK
| | - S Schmidt
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
| | - W Otten
- The SIMBIOS Centre, Abertay University, Dundee, DD1 1HG, UK
| | - L X Dupuy
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - P J White
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
- King Saud University, Riyadh, Saudi Arabia
| | - T A Valentine
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, UK
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13
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Gauthier JP, Outreman Y, Mieuzet L, Simon JC. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA. PLoS One 2015; 10:e0120664. [PMID: 25807173 PMCID: PMC4373712 DOI: 10.1371/journal.pone.0120664] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/05/2015] [Indexed: 02/01/2023] Open
Abstract
Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was underestimated due to the possible loss of environmental or transient taxa.
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Affiliation(s)
- Jean-Pierre Gauthier
- INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France
| | - Yannick Outreman
- Agrocampus Ouest, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35042, Rennes, France
| | - Lucie Mieuzet
- INRA, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35653, Le Rheu, France
| | - Jean-Christophe Simon
- Agrocampus Ouest, UMR 1349 IGEPP "Institut de Génétique, Environnement et Protection des Plantes", 35042, Rennes, France
- * E-mail:
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Jing X, Wong ACN, Chaston JM, Colvin J, McKenzie CL, Douglas AE. The bacterial communities in plant phloem-sap-feeding insects. Mol Ecol 2014; 23:1433-1444. [DOI: 10.1111/mec.12637] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 12/06/2013] [Accepted: 12/13/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Xiangfeng Jing
- Department of Entomology; Comstock Hall; Cornell University; Ithaca NY 14853 USA
| | - Adam C-N Wong
- Department of Entomology; Comstock Hall; Cornell University; Ithaca NY 14853 USA
| | - John M. Chaston
- Department of Entomology; Comstock Hall; Cornell University; Ithaca NY 14853 USA
| | - John Colvin
- Agriculture, Health and Environment Group; Natural Resources Institute; University of Greenwich; Kent UK
| | - Cindy L. McKenzie
- ASDA-ARS; U.S. Horticultural Research Laboratory; 2001 South Rock Road Fort Pierce FL 34945 USA
| | - Angela E. Douglas
- Department of Entomology; Comstock Hall; Cornell University; Ithaca NY 14853 USA
- Department of Molecular Biology and Genetics; 526 Campus Road; Cornell University; Ithaca NY 14853 USA
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