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Gómez-Govea MA, Peña-Carillo KI, Ruiz-Ayma G, Guzmán-Velasco A, Flores AE, Ramírez-Ahuja MDL, Rodríguez-Sánchez IP. Unveiling the Microbiome Diversity in Telenomus (Hymenoptera: Scelionidae) Parasitoid Wasps. INSECTS 2024; 15:468. [PMID: 39057201 PMCID: PMC11277331 DOI: 10.3390/insects15070468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/28/2024]
Abstract
Bacterial symbionts in insects constitute a key factor for the survival of the host due to the benefits they provide. Parasitoid wasps are closely associated with viruses, bacteria, and fungi. However, the primary symbionts and their functions are not yet known. This study was undertaken to determine the gut microbiota of six species of the Telenomus genus: T. alecto (Crawford), T. sulculus Johnson, T. fariai Costa Lima, T. remus Nixon, T. podisi Ashmead, and T. lobatus Johnson & Bin. Wasp parasitoids were collected from their hosts in different locations in Mexico. DNA was extracted from gut collection, and sequencing of bacterial 16S rRNA was carried out in Illumina® MiSeq™. Among the six species of wasps, results showed that the most abundant phylum were Proteobacteria (82.3%), Actinobacteria (8.1%), and Firmicutes (7.8%). The most important genera were Delftia and Enterobacter. Seventeen bacteria species were found to be shared among the six species of wasps. The associate microbiota will help to understand the physiology of Telenomus to promote the use of these wasp parasitoids in the management of insect pests and as potential biomarkers to target new strategies to control pests.
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Affiliation(s)
- Mayra A. Gómez-Govea
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
| | - Kenzy I. Peña-Carillo
- Campo Experimental General Terán, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Km 31 Carretera Montemorelos-China, General Terán 67400, Mexico;
| | - Gabriel Ruiz-Ayma
- Laboratorio de Conservación de Vida Silvestre y Desarrollo Sustentable, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico; (G.R.-A.); (A.G.-V.)
| | - Antonio Guzmán-Velasco
- Laboratorio de Conservación de Vida Silvestre y Desarrollo Sustentable, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico; (G.R.-A.); (A.G.-V.)
| | - Adriana E. Flores
- Laboratorio de Entomología Médica, Departamento de Zoología de Invertebrados, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - María de Lourdes Ramírez-Ahuja
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
| | - Iram Pablo Rodríguez-Sánchez
- Laboratorio de Fisiología Molecular y Estructural, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 64460, Mexico;
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Luo C, Belghazi M, Schmitz A, Lemauf S, Desneux N, Simon JC, Poirié M, Gatti JL. Hosting certain facultative symbionts modulates the phenoloxidase activity and immune response of the pea aphid Acyrthosiphon pisum. INSECT SCIENCE 2021; 28:1780-1799. [PMID: 33200579 DOI: 10.1111/1744-7917.12888] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/08/2020] [Accepted: 11/01/2020] [Indexed: 06/11/2023]
Abstract
The pea aphid Acyrthosiphon pisum hosts different facultative symbionts (FS) which provide it with various benefits, such as tolerance to heat or protection against natural enemies (e.g., fungi, parasitoid wasps). Here, we investigated whether and how the presence of certain FS could affect phenoloxidase (PO) activity, a key component of insect innate immunity, under normal and stressed conditions. For this, we used clones of A. pisum of different genetic backgrounds (LL01, YR2 and T3-8V1) lacking FS or harboring one or two (Regiella insecticola, Hamiltonella defensa, Serratia symbiotica + Rickettsiella viridis). Gene expression and proteomics analyses of the aphid hemolymph indicated that the two A. pisum POs, PPO1 and PPO2, are expressed and translated into proteins. The level of PPO genes expression as well as the amount of PPO proteins and phenoloxidase activity in the hemolymph depended on both the aphid genotype and FS species. In particular, H. defensa and R. insecticola, but not S. symbiotica + R. viridis, caused a sharp decrease in PO activity by interfering with both transcription and translation. The microinjection of different types of stressors (yeast, Escherichia coli, latex beads) in the YR2 lines hosting different symbionts affected the survival rate of aphids and, in most cases, also decreased the expression of PPO genes after 24 h. The amount and activity of PPO proteins varied according to the type of FS and stressor, without clear corresponding changes in gene expression. These data demonstrate that the presence of certain FS influences an important component of pea aphid immunity.
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Affiliation(s)
- Chen Luo
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
- Present address: State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi Province, 712100, China
| | - Maya Belghazi
- INP, UMR7051, CNRS, Aix Marseille Université, Marseille, 13015, France
| | - Antonin Schmitz
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
| | - Séverine Lemauf
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
| | - Nicolas Desneux
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), 06000 Nice, France
| | | | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
| | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, UMR Institut Sophia Agrobiotech (ISA), Sophia Antipolis, France
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O'Brien PA, Andreakis N, Tan S, Miller DJ, Webster NS, Zhang G, Bourne DG. Testing cophylogeny between coral reef invertebrates and their bacterial and archaeal symbionts. Mol Ecol 2021; 30:3768-3782. [PMID: 34060182 DOI: 10.1111/mec.16006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 05/16/2021] [Accepted: 05/24/2021] [Indexed: 12/25/2022]
Abstract
Marine invertebrates harbour a complex suite of bacterial and archaeal symbionts, a subset of which are probably linked to host health and homeostasis. Within a complex microbiome it can be difficult to tease apart beneficial or parasitic symbionts from nonessential commensal or transient microorganisms; however, one approach is to detect strong cophylogenetic patterns between microbial lineages and their respective hosts. We employed the Procrustean approach to cophylogeny (PACo) on 16S rRNA gene derived microbial community profiles paired with COI, 18S rRNA and ITS1 host phylogenies. Second, we undertook a network analysis to identify groups of microbes that were co-occurring within our host species. Across 12 coral, 10 octocoral and five sponge species, each host group and their core microbiota (50% prevalence within host species replicates) had a significant fit to the cophylogenetic model. Independent assessment of each microbial genus and family found that bacteria and archaea affiliated to Endozoicomonadaceae, Spirochaetaceae and Nitrosopumilaceae have the strongest cophylogenetic signals. Further, local Moran's I measure of spatial autocorrelation identified 14 ASVs, including Endozoicomonadaceae and Spirochaetaceae, whose distributions were significantly clustered by host phylogeny. Four co-occurring subnetworks were identified, each of which was dominant in a different host group. Endozoicomonadaceae and Spirochaetaceae ASVs were abundant among the subnetworks, particularly one subnetwork that was exclusively comprised of these two bacterial families and dominated the octocoral microbiota. Our results disentangle key microbial interactions that occur within complex microbiomes and reveal long-standing, essential microbial symbioses in coral reef invertebrates.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Nikos Andreakis
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia
| | - Shangjin Tan
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Qld, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Qld, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia.,Australian Centre for Ecogenomics, University of Queensland, Brisbane, Qld, Australia
| | - Guojie Zhang
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China.,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, Qld, Australia.,Australian Institute of Marine Science, Townsville, Qld, Australia.,AIMS@JCU, Townsville, Qld, Australia
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Xu T, Chen J, Jiang L, Qiao G. Diversity of bacteria associated with Hormaphidinae aphids (Hemiptera: Aphididae). INSECT SCIENCE 2021; 28:165-179. [PMID: 31840419 PMCID: PMC7818174 DOI: 10.1111/1744-7917.12746] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 10/07/2019] [Accepted: 12/01/2019] [Indexed: 05/29/2023]
Abstract
Bacteria are ubiquitous inhabitants of animals. Hormaphidinae is a particular aphid group exhibiting very diverse life history traits. However, the microbiota in this group is poorly known. In the present study, using high-throughput sequencing of bacterial 16S ribosomal RNA gene amplicons, we surveyed the bacterial flora in hormaphidine aphids and explored whether the aphid tribe, host plant and geographical distribution are associated with the distribution of secondary symbionts. The most dominant bacteria detected in hormaphidine species are heritable symbionts. As expected, the primary endosymbiont Buchnera aphidicola is the most abundant symbiont across all species and has cospeciated with its host aphids. Six secondary symbionts were detected in Hormaphidinae. Arsenophonus is widespread in Hormaphidinae species, suggesting the possibility of ancient acquisition of this symbiont. Ordination analyses and statistical tests show that the symbiont composition does not seem to relate to any of the aphid tribes, host plants or geographical distributions, which indicate that horizontal transfers might occur for these symbionts in Hormaphidinae. Correlation analysis exhibits negative interference between Buchnera and coexisting secondary symbionts, while the interactions between different secondary symbionts are complicated. These findings display a comprehensive picture of the microbiota in Hormaphidinae and may be helpful in understanding the symbiont diversity within a group of aphids.
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Affiliation(s)
- Ting‐Ting Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Li‐Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
| | - Ge‐Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of ZoologyChinese Academy of SciencesBeijingChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
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Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota and a potential to switch between hosts. Sci Rep 2021; 11:396. [PMID: 33431987 PMCID: PMC7801462 DOI: 10.1038/s41598-020-79842-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023] Open
Abstract
Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate and uninucleate cells, and sporogonial plasmodia that form uninucleate spores. Nephridiophagids are poor in morphological characteristics, and although they have been tentatively identified as early-branching fungi based on the SSU rRNA gene sequences of three species, their exact position within the fungal tree of live remained unclear. In this study, we describe two new species of nephridiophagids (Nephridiophaga postici and Nephridiophaga javanicae) from cockroaches. Using long-read sequencing of the nearly complete rDNA operon of numerous further species obtained from cockroaches and earwigs to improve the resolution of the phylogenetic analysis, we found a robust affiliation of nephridiophagids with the Chytridiomycota-a group of zoosporic fungi that comprises parasites of diverse host taxa, such as microphytes, plants, and amphibians. The presence of the same nephridiophagid species in two only distantly related cockroaches indicates that their host specificity is not as strict as generally assumed.
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Bourguignon T, Kinjo Y, Villa-Martín P, Coleman NV, Tang Q, Arab DA, Wang Z, Tokuda G, Hongoh Y, Ohkuma M, Ho SY, Pigolotti S, Lo N. Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes. Curr Biol 2020; 30:3848-3855.e4. [DOI: 10.1016/j.cub.2020.07.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/27/2020] [Accepted: 07/09/2020] [Indexed: 01/08/2023]
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Xu S, Jiang L, Qiao G, Chen J. The Bacterial Flora Associated with the Polyphagous Aphid Aphis gossypii Glover (Hemiptera: Aphididae) Is Strongly Affected by Host Plants. MICROBIAL ECOLOGY 2020; 79:971-984. [PMID: 31802184 PMCID: PMC7198476 DOI: 10.1007/s00248-019-01435-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 08/28/2019] [Indexed: 06/10/2023]
Abstract
Aphids live in symbiosis with a variety of bacteria, including the obligate symbiont Buchnera aphidicola and diverse facultative symbionts. The symbiotic associations for one aphid species, especially for polyphagous species, often differ across populations. In the present study, by using high-throughput 16S rRNA sequencing, we surveyed in detail the microbiota in natural populations of the cotton aphid Aphis gossypii in China and assessed differences in bacterial diversity with respect to host plant and geography. The microbial community of A. gossypii was dominated by a few heritable symbionts. Arsenophonus was the most dominant secondary symbiont, and Spiroplasma was detected for the first time. Statistical tests and ordination analyses showed that host plants rather than geography seemed to have shaped the associated symbiont composition. Special symbiont communities inhabited the Cucurbitaceae-feeding populations, which supported the ecological specialization of A. gossypii on cucurbits from the viewpoint of symbiotic bacteria. Correlation analysis suggested antagonistic interactions between Buchnera and coexisting secondary symbionts and more complicated interactions between different secondary symbionts. Our findings lend further support to an important role of the host plant in structuring symbiont communities of polyphagous aphids and will improve our understanding of the interactions among phytophagous insects, symbionts, and environments.
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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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8
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Xu TT, Jiang LY, Chen J, Qiao GX. Host Plants Influence the Symbiont Diversity of Eriosomatinae (Hemiptera: Aphididae). INSECTS 2020; 11:E217. [PMID: 32244698 PMCID: PMC7240687 DOI: 10.3390/insects11040217] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/16/2020] [Accepted: 03/28/2020] [Indexed: 01/13/2023]
Abstract
Eriosomatinae is a particular aphid group with typically heteroecious holocyclic life cycle, exhibiting strong primary host plant specialization and inducing galls on primary host plants. Aphids are frequently associated with bacterial symbionts, which can play fundamental roles in the ecology and evolution of their host aphids. However, the bacterial communities in Eriosomatinae are poorly known. In the present study, using high-throughput sequencing of the bacterial 16S ribosomal RNA gene, we surveyed the bacterial flora of eriosomatines and explored the associations between symbiont diversity and aphid relatedness, aphid host plant and geographical distribution. The microbiota of Eriosomatinae is dominated by the heritable primary endosymbiont Buchnera and several facultative symbionts. The primary endosymbiont Buchnera is expectedly the most abundant symbiont across all species. Six facultative symbionts were identified. Regiella was the most commonly identified facultative symbiont, and multiple infections of facultative symbionts were detected in the majority of the samples. Ordination analyses and statistical tests show that the symbiont community of aphids feeding on plants from the family Ulmaceae were distinguishable from aphids feeding on other host plants. Species in Eriosomatinae feeding on different plants are likely to carry different symbiont compositions. The symbiont distributions seem to be not related to taxonomic distance and geographical distance. Our findings suggest that host plants can affect symbiont maintenance, and will improve our understanding of the interactions between aphids, their symbionts and ecological conditions.
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Affiliation(s)
- Ting-Ting Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (T.-T.X.); (L.-Y.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (T.-T.X.); (L.-Y.J.)
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (T.-T.X.); (L.-Y.J.)
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; (T.-T.X.); (L.-Y.J.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Huot C, Clerissi C, Gourbal B, Galinier R, Duval D, Toulza E. Schistosomiasis Vector Snails and Their Microbiota Display a Phylosymbiosis Pattern. Front Microbiol 2020; 10:3092. [PMID: 32082267 PMCID: PMC7006369 DOI: 10.3389/fmicb.2019.03092] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/20/2019] [Indexed: 01/05/2023] Open
Abstract
Planorbidae snails are the intermediate host for the trematode parasite of the Schistosoma genus, which is responsible for schistosomiasis, a disease that affects both humans and cattle. The microbiota for Schistosoma has already been described as having an effect on host/parasite interactions, specifically through immunological interactions. Here, we sought to characterize the microbiota composition of seven Planorbidae species and strains. Individual snail microbiota was determined using 16S ribosomal DNA amplicon sequencing. The bacterial composition was highly specific to the host strain with limited interindividual variation. In addition, it displayed complete congruence with host phylogeny, revealing a phylosymbiosis pattern. These results were confirmed in a common garden, suggesting that the host highly constrains microbial composition. This study presents the first comparison of bacterial communities between several intermediate snail hosts of Schistosoma parasites, paving the way for further studies on the understanding of this tripartite interaction.
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Affiliation(s)
| | | | | | | | | | - Eve Toulza
- IHPE, Univ. Montpellier, CNRS, Ifremer, Univ. Perpignan Via Domitia, Perpignan, France
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Abstract
Bumble bee queens undergo a number of biological changes as they transition through adult emergence, mating, overwintering, foraging, and colony initiation including egg laying. Therefore, they represent an important system to understand the link between physiological, behavioral, and environmental changes and host-associated microbiota. It is plausible that the bumble bee queen gut bacteria play a role in shaping the ability of the queen to survive environmental extremes and reproduce, due to long-established coevolutionary relationships between the host and microbiome members. Bumble bees are important pollinators in natural and agricultural ecosystems. Their social colonies are founded by individual queens, which, as the predominant reproductive females of colonies, contribute to colony function through worker production and fitness through male and new queen production. Therefore, queen health is paramount, but even though there has been an increasing emphasis on the role of gut microbiota for animal health, there is limited information on the gut microbial dynamics of bumble bee queens. Employing 16S rRNA amplicon sequencing and quantitative PCR, we investigate how the adult life stage and physiological state influence a queen’s gut bacterial community diversity and composition in unmated, mated, and ovipositing queens of Bombus lantschouensis. We found significant shifts in total gut microbe abundance and microbiota composition across queen states. There are specific compositional signatures associated with different stages, with unmated and ovipositing queens showing the greatest similarity in composition and mated queens being distinct. The bacterial genera Gilliamella, Snodgrassella, and Lactobacillus were relatively dominant in unmated and ovipositing queens, with Bifidobacterium dominant in ovipositing queens only. Bacillus, Lactococcus, and Pseudomonas increased following queen mating. Intriguingly, however, further analysis of unmated queens matching the mated queens in age showed that changes are independent of the act of mating. Our study is the first to explore the gut microbiome of bumble bee queens across key life stages from adult eclosion to egg laying and provides useful information for future studies of the function of gut bacteria in queen development and colony performance. IMPORTANCE Bumble bee queens undergo a number of biological changes as they transition through adult emergence, mating, overwintering, foraging, and colony initiation including egg laying. Therefore, they represent an important system to understand the link between physiological, behavioral, and environmental changes and host-associated microbiota. It is plausible that the bumble bee queen gut bacteria play a role in shaping the ability of the queen to survive environmental extremes and reproduce, due to long-established coevolutionary relationships between the host and microbiome members.
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Cooke I, Mead O, Whalen C, Boote C, Moya A, Ying H, Robbins S, Strugnell JM, Darling A, Miller D, Voolstra CR, Adamska M. Molecular techniques and their limitations shape our view of the holobiont. ZOOLOGY 2019; 137:125695. [PMID: 31759226 DOI: 10.1016/j.zool.2019.125695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/08/2019] [Accepted: 07/12/2019] [Indexed: 11/26/2022]
Abstract
It is now recognised that the biology of almost any organism cannot be fully understood without recognising the existence and potential functional importance of associated microbes. Arguably, the emergence of this holistic viewpoint may never have occurred without the development of a crucial molecular technique, 16S rDNA amplicon sequencing, which allowed microbial communities to be easily profiled across a broad range of contexts. A diverse array of molecular techniques are now used to profile microbial communities, infer their evolutionary histories, visualise them in host tissues, and measure their molecular activity. In this review, we examine each of these categories of measurement and inference with a focus on the questions they make tractable, and the degree to which their capabilities and limitations shape our view of the holobiont.
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Affiliation(s)
- Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia.
| | - Oliver Mead
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Casey Whalen
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Chloë Boote
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Aurelie Moya
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
| | - Steven Robbins
- Australian Center for Ecogenomics, University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Jan M Strugnell
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre of Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, 4810, QLD, Australia; Department of Ecology, Environment and Evolution, School of Life Sciences, La Trobe University, Melbourne, 3083, Australia
| | - Aaron Darling
- The ithree institute, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - David Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia; Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia; ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | | | - Maja Adamska
- ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, 2601, Australia; Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
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O'Brien PA, Webster NS, Miller DJ, Bourne DG. Host-Microbe Coevolution: Applying Evidence from Model Systems to Complex Marine Invertebrate Holobionts. mBio 2019; 10:e02241-18. [PMID: 30723123 PMCID: PMC6428750 DOI: 10.1128/mbio.02241-18] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Marine invertebrates often host diverse microbial communities, making it difficult to identify important symbionts and to understand how these communities are structured. This complexity has also made it challenging to assign microbial functions and to unravel the myriad of interactions among the microbiota. Here we propose to address these issues by applying evidence from model systems of host-microbe coevolution to complex marine invertebrate microbiomes. Coevolution is the reciprocal adaptation of one lineage in response to another and can occur through the interaction of a host and its beneficial symbiont. A classic indicator of coevolution is codivergence of host and microbe, and evidence of this is found in both corals and sponges. Metabolic collaboration between host and microbe is often linked to codivergence and appears likely in complex holobionts, where microbial symbionts can interact with host cells through production and degradation of metabolic compounds. Neutral models are also useful to distinguish selected microbes against a background population consisting predominately of random associates. Enhanced understanding of the interactions between marine invertebrates and their microbial communities is urgently required as coral reefs face unprecedented local and global pressures and as active restoration approaches, including manipulation of the microbiome, are proposed to improve the health and tolerance of reef species. On the basis of a detailed review of the literature, we propose three research criteria for examining coevolution in marine invertebrates: (i) identifying stochastic and deterministic components of the microbiome, (ii) assessing codivergence of host and microbe, and (iii) confirming the intimate association based on shared metabolic function.
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Affiliation(s)
- Paul A O'Brien
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, Australia
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
- AIMS@JCU, Townsville, QLD, Australia
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Paniagua Voirol LR, Frago E, Kaltenpoth M, Hilker M, Fatouros NE. Bacterial Symbionts in Lepidoptera: Their Diversity, Transmission, and Impact on the Host. Front Microbiol 2018; 9:556. [PMID: 29636736 PMCID: PMC5881003 DOI: 10.3389/fmicb.2018.00556] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/12/2018] [Indexed: 01/05/2023] Open
Abstract
The insect’s microbiota is well acknowledged as a “hidden” player influencing essential insect traits. The gut microbiome of butterflies and moths (Lepidoptera) has been shown to be highly variable between and within species, resulting in a controversy on the functional relevance of gut microbes in this insect order. Here, we aim to (i) review current knowledge on the composition of gut microbial communities across Lepidoptera and (ii) elucidate the drivers of the variability in the lepidopteran gut microbiome and provide an overview on (iii) routes of transfer and (iv) the putative functions of microbes in Lepidoptera. To find out whether Lepidopterans possess a core gut microbiome, we compared studies of the microbiome from 30 lepidopteran species. Gut bacteria of the Enterobacteriaceae, Bacillaceae, and Pseudomonadaceae families were the most widespread across species, with Pseudomonas, Bacillus, Staphylococcus, Enterobacter, and Enterococcus being the most common genera. Several studies indicate that habitat, food plant, and age of the host insect can greatly impact the gut microbiome, which contributes to digestion, detoxification, or defense against natural enemies. We mainly focus on the gut microbiome, but we also include some examples of intracellular endosymbionts. These symbionts are present across a broad range of insect taxa and are known to exert different effects on their host, mostly including nutrition and reproductive manipulation. Only two intracellular bacteria genera (Wolbachia and Spiroplasma) have been reported to colonize reproductive tissues of Lepidoptera, affecting their host’s reproduction. We explore routes of transmission of both gut microbiota and intracellular symbionts and have found that these microbes may be horizontally transmitted through the host plant, but also vertically via the egg stage. More detailed knowledge about the functions and plasticity of the microbiome in Lepidoptera may provide novel leads for the control of lepidopteran pest species.
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Affiliation(s)
| | - Enric Frago
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Saint-Pierre, La Réunion
| | - Martin Kaltenpoth
- Department for Evolutionary Ecology, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Monika Hilker
- Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
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Wang Y, Xu C, Tian M, Deng X, Cen Y, He Y. Genetic diversity of Diaphorina citri and its endosymbionts across east and south-east Asia. PEST MANAGEMENT SCIENCE 2017; 73:2090-2099. [PMID: 28374537 DOI: 10.1002/ps.4582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 03/15/2017] [Accepted: 03/28/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Diaphorina citri is the vector of 'Candidatus Liberibacter asiaticus', the most widespread pathogen associated huanglongbing, the most serious disease of citrus. To enhance our understanding of the distribution and origin of the psyllid, we investigated the genetic diversity and population structures of 24 populations in Asia and one from Florida based on the mtCOI gene. Simultaneously, genetic diversity and population structures of the primary endosymbiont (P-endosymbiont) 'Candidatus Carsonella ruddii' and secondary endosymbiont (S-endosymbiont) 'Candidatus Profftella armatura' of D. citri were determined with the housekeeping genes. RESULT AMOVA analysis indicated that populations of D. citri and its endosymbionts in east and south-east Asia were genetically distinct from populations in Pakistan and Florida. Furthermore, P-endosymbiont populations displayed a strong geographical structure across east and south-east Asia, while low genetic diversity indicated the absence of genetic structure among the populations of D. citri and its S-endosymbiont across these regions. CONCLUSION The 'Ca. C. ruddii' is more diverse and structured than the D. citri and the 'Ca. P. armatura' across east and south-east Asia. Multiple introductions of the psyllid have occurred in China. Management application for controlling the pest is proposed based on the genetic information of D. citri and its endosymbionts. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Yanjing Wang
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Changbao Xu
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Mingyi Tian
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Xiaoling Deng
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yijing Cen
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
| | - Yurong He
- Laboratory of Insect Ecology/Citrus Huanglongbing Research Laboratory, South China Agricultural University, Guangzhou, China
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15
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Xu TT, Chen J, Jiang LY, Qiao GX. Historical and cospeciating associations between Cerataphidini aphids (Hemiptera: Aphididae: Hormaphidinae) and their primary endosymbiont Buchnera aphidicola. Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ting-Ting Xu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
- College of Life Sciences, University of Chinese Academy of Sciences, Shijingshan District, Beijing, P.R. China
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Li-Yun Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, P.R. China
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Hall AAG, Morrow JL, Fromont C, Steinbauer MJ, Taylor GS, Johnson SN, Cook JM, Riegler M. Codivergence of the primary bacterial endosymbiont of psyllids versus host switches and replacement of their secondary bacterial endosymbionts. Environ Microbiol 2016; 18:2591-603. [DOI: 10.1111/1462-2920.13351] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/20/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Aidan A. G. Hall
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
| | - Jennifer L. Morrow
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
| | - Caroline Fromont
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
| | - Martin J. Steinbauer
- Department of Ecology, Environment & Evolution; La Trobe University; Melbourne VIC 3084 Australia
| | - Gary S. Taylor
- Australian Centre for Evolutionary Biology and Biodiversity; The University of Adelaide; Adelaide SA 5005 Australia
| | - Scott N. Johnson
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
| | - James M. Cook
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
| | - Markus Riegler
- Hawkesbury Institute for the Environment, Western Sydney University; Penrith NSW 2751 Australia
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Sattar S, Thompson GA. Small RNA Regulators of Plant-Hemipteran Interactions: Micromanagers with Versatile Roles. FRONTIERS IN PLANT SCIENCE 2016; 7:1241. [PMID: 27625654 PMCID: PMC5003895 DOI: 10.3389/fpls.2016.01241] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/04/2016] [Indexed: 05/13/2023]
Abstract
Non-coding small RNAs (sRNAs) in plants have important roles in regulating biological processes, including development, reproduction, and stress responses. Recent research indicates significant roles for sRNA-mediated gene silencing during plant-hemipteran interactions that involve all three of these biological processes. Plant responses to hemipteran feeding are determined by changes in the host transcriptome that appear to be fine-tuned by sRNAs. The role of sRNA in plant defense responses is complex. Different forms of sRNAs, with specific modes of action, regulate changes in the host transcriptome primarily through post-transcriptional gene silencing and occasionally through translational repression. Plant genetic resistance against hemipterans provides a model to explore the regulatory roles of sRNAs in plant defense. Aphid-induced sRNA expression in resistance genotypes delivers a new paradigm in understanding the regulation of R gene-mediated resistance in host plants. Unique sRNA profiles, including changes in sRNA biogenesis and expression can also provide insights into susceptibility to insect herbivores. Activation of phytohormone-mediated defense responses against insect herbivory is another hallmark of this interaction, and recent studies have shown that regulation of phytohormone signaling is under the control of sRNAs. Hemipterans feeding on resistant plants also show changes in insect sRNA profiles, possibly influencing insect development and reproduction. Changes in insect traits such as fecundity, host range, and resistance to insecticides are impacted by sRNAs and can directly contribute to the success of certain insect biotypes. In addition to causing direct damage to the host plant, hemipteran insects are often vectors of viral pathogens. Insect anti-viral RNAi machinery is activated to limit virus accumulation, suggesting a role in insect immunity. Virus-derived long sRNAs strongly resemble insect piRNAs, leading to the speculation that the piRNA pathway is induced in response to viral infection. Evidence for robust insect RNAi machinery in several hemipteran species is of immense interest and is being actively pursued as a possible tool for insect control. RNAi-induced gene silencing following uptake of exogenous dsRNA was successfully demonstrated in several hemipterans and the presence of sid-1 like genes support the concept of a systemic response in some species.
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Alkhedir H, Karlovsky P, Mashaly AMA, Vidal S. Phylogenetic Relationships of the Symbiotic Bacteria in the Aphid Sitobion avenae (Hemiptera: Aphididae). ENVIRONMENTAL ENTOMOLOGY 2015; 44:1358-1366. [PMID: 26314016 DOI: 10.1093/ee/nvv114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/29/2015] [Indexed: 06/04/2023]
Abstract
Aphids have developed symbiotic associations with different bacterial species, and some morphological and molecular analyses have provided evidence of the host relationship between the primary symbiotic bacteria (Buchnera aphidicola) and the aphid while the contrary with the secondary symbiotic bacteria. In this study, we investigated the phylogenetic relationships of the bacterial endosymbionts in the aphid Sitobion avenae (F.). We characterized all bacterial endosymbionts in 10 genetically defined S. avenae clones by denaturing gradient gel electrophoresis and, from these clones, sequenced the 16S rRNA genes of both the primary endosymbiont, B. aphidicola (for the first time), and the secondary endosymbionts, Regiella insecticola and Hamiltonella defensa (for the first time). The phylogenetic analysis indicated that Buchnera from Sitobion related to those in Macrosiphoni. The analysis of the secondary endosymbionts indicated that there is no host relationship between H. defensa and R. insecticola from Sitobion and those from other aphid species. In this study, therefore, we identified further evidence for the relationship between Buchnera and its host and reported a relationship within the secondary endosymbionts of S. avenae from the same country, even though there were no relationships between the secondary bacteria and their host. We also discussed the diversity within the symbiotic bacteria in S. avenae clones.
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Affiliation(s)
- Hussein Alkhedir
- Agricultural Entomology, Georg-August-University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany. Molecular Phytopathology and Mycotoxin Research, Georg-August-University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany.
| | - Petr Karlovsky
- Molecular Phytopathology and Mycotoxin Research, Georg-August-University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
| | - Ashraf Mohamed Ali Mashaly
- Department of Zoology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Kingdom of Saudi Arabia. Department of Zoology, Faculty of Science, Minia University, 61519 El Minia, Egypt
| | - Stefan Vidal
- Agricultural Entomology, Georg-August-University Göttingen, Grisebachstrasse 6, 37077, Göttingen, Germany
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Chen R, Wang Z, Chen J, Qiao GX. Avoidance and Potential Remedy Solutions of Chimeras in Reconstructing the Phylogeny of Aphids Using the 16S rRNA Gene of Buchnera: A Case in Lachninae (Hemiptera). Int J Mol Sci 2015; 16:20152-67. [PMID: 26307984 PMCID: PMC4613194 DOI: 10.3390/ijms160920152] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/07/2015] [Accepted: 08/18/2015] [Indexed: 11/30/2022] Open
Abstract
It is known that PCR amplification of highly homologous genes from complex DNA mixtures can generate a significant proportion of chimeric sequences. The 16S rRNA gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions. In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae. These chimeras are hybrid products of multiple parent sequences from the dominant species of endosymbionts in each corresponding host. It is difficult to identify the chimeric sequences of a new or unidentified species due to the high variability of their main parent, Buchnera aphidicola, and because the chimeric sequences can confuse the phylogenetic analysis of 16S rRNA gene sequences. These chimeras present a challenge to Buchnera-based phylogenetic research in aphids. Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.
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Affiliation(s)
- Rui Chen
- 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.
| | - Zhe Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
- Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China.
| | - Jing Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ge-Xia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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20
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Alves JMP, Klein CC, da Silva FM, Costa-Martins AG, Serrano MG, Buck GA, Vasconcelos ATR, Sagot MF, Teixeira MMG, Motta MCM, Camargo EP. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol Biol 2013; 13:190. [PMID: 24015778 PMCID: PMC3846528 DOI: 10.1186/1471-2148-13-190] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont's contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. RESULTS Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. CONCLUSION We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.
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21
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Hackstein JHP. Anaerobic Ciliates and Their Methanogenic Endosymbionts. (ENDO)SYMBIOTIC METHANOGENIC ARCHAEA 2010. [DOI: 10.1007/978-3-642-13615-3_2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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22
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Desai MS, Strassert JFH, Meuser K, Hertel H, Ikeda-Ohtsubo W, Radek R, Brune A. Strict cospeciation of devescovinid flagellates and Bacteroidales ectosymbionts in the gut of dry-wood termites (Kalotermitidae). Environ Microbiol 2009; 12:2120-32. [PMID: 21966907 DOI: 10.1111/j.1462-2920.2009.02080.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The surface of many termite gut flagellates is colonized with a dense layer of bacteria, yet little is known about the evolutionary relationships of such ectosymbionts and their hosts. Here we investigated the molecular phylogenies of devescovinid flagellates (Devescovina spp.) and their symbionts from a wide range of dry-wood termites (Kalotermitidae). From species-pure flagellate suspensions isolated with micropipettes, we obtained SSU rRNA gene sequences of symbionts and host. Phylogenetic analysis showed that the Devescovina spp. present in many species of Kalotermitidae form a monophyletic group, which includes also the unique devescovinid flagellate Caduceia versatilis. All members of this group were consistently associated with a distinct lineage of Bacteroidales, whose location on the cell surface was confirmed by fluorescence in situ hybridization. The well-supported congruence of the phylogenies of devescovinids and their ectosymbionts documents a strict cospeciation. In contrast, the endosymbionts of the same flagellates ('Endomicrobia') were clearly polyphyletic and must have been acquired independently by horizontal transfer from other flagellate lineages. Also the Bacteroidales ectosymbionts of Oxymonas flagellates present in several Kalotermitidae belonged to several distantly related lines of descent, underscoring the general perception that the evolutionary history of flagellate-bacteria symbioses in the termite gut is complex.
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Affiliation(s)
- Mahesh S Desai
- Max Planck Institute for Terrestrial Microbiology, Department of Biogeochemistry, Karl-von-Frisch-Straße, 35043 Marburg, Germany
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Riegler M, O'Neill SL. Evolutionary dynamics of insect symbiont associations. Trends Ecol Evol 2007; 22:625-7. [PMID: 17981362 DOI: 10.1016/j.tree.2007.08.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Revised: 08/23/2007] [Accepted: 08/28/2007] [Indexed: 11/16/2022]
Abstract
Bacterial symbionts of insects are pervasive and influence several ecologically relevant traits of their hosts. Although there has been rapid progress in understanding the extent and phenotypic outcome of these associations, there is a paucity of empirical data on fine-scale evolutionary processes that operate between the genomes of host and symbiont. Recently published papers examining symbiont relationships of aphids, fruit flies and butterflies are starting to reveal that these associations might be more dynamic than was appreciated previously.
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Affiliation(s)
- Markus Riegler
- School of Integrative Biology, The University of Queensland, St Lucia, QLD 4072, Australia
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24
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Hypsa V, Krízek J. Molecular evidence for polyphyletic origin of the primary symbionts of sucking lice (phthiraptera, anoplura). MICROBIAL ECOLOGY 2007; 54:242-51. [PMID: 17345136 DOI: 10.1007/s00248-006-9194-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 11/21/2006] [Accepted: 11/28/2006] [Indexed: 05/14/2023]
Abstract
Based on 16S rDNA analyses, the primary symbionts of sucking lice were found to form a polyphyletic assemblage of several distant lineages that have arisen several times within Enterobacteriaceae and at least once within Legionellaceae. Another independent lineage of endosymbiotic enterobacteria inhabits a sister group of the sucking lice, Rhynchophthirina. The inspection of 16S rDNA supports the symbiotic nature of the investigated bacteria; they display a typical trait of degenerative processes, an increased AT content (Adenine-Thymine content) in comparison with free-living bacteria. The calculation of divergence time between the closest anopluran and rhynchophthirine symbionts further support their independent origin. The results shown here, together with evidence from other groups, indicate that the significance of primary symbionts for blood-feeding insects should be reconsidered.
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Affiliation(s)
- Václav Hypsa
- Faculty of Biological Sciences, Ceské Budejovice, Czech Republic.
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25
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Pettersson ME, Berg OG. Muller’s ratchet in symbiont populations. Genetica 2006; 130:199-211. [PMID: 16924405 DOI: 10.1007/s10709-006-9007-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 07/13/2006] [Indexed: 11/25/2022]
Abstract
Muller's ratchet, the inevitable accumulation of deleterious mutations in asexual populations, has been proposed as a major factor in genome degradation of obligate symbiont organisms. Essentially, if left unchecked the ratchet will with certainty cause extinction due to the ever increasing mutational load. This paper examines the evolutionary fate of insect symbionts, using mathematical modelling to simulate the accumulation of deleterious mutations. We investigate the effects of a hierarchical two level population structure. Since each host contains its own subpopulation of symbionts, there will be a large number of small symbiont populations linked indirectly via selection on the host level. We show that although the separate subpopulations will accumulate deleterious mutations quickly, the symbiont population as a whole will be protected from extinction by selection acting on the hosts. As a consequence, the extent of genome degradation observed in present day symbionts is more likely to represent loss of functions that were (near-) neutral to the host, rather than a snap shot of a decline towards complete genetic collapse.
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Affiliation(s)
- Mats E Pettersson
- Department of Molecular Evolution, Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.
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26
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Kaltenpoth M, Goettler W, Dale C, Stubblefield JW, Herzner G, Roeser-Mueller K, Strohm E. 'Candidatus Streptomyces philanthi', an endosymbiotic streptomycete in the antennae of Philanthus digger wasps. Int J Syst Evol Microbiol 2006; 56:1403-1411. [PMID: 16738121 DOI: 10.1099/ijs.0.64117-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Symbiotic interactions with bacteria are essential for the survival and reproduction of many insects. The European beewolf (Philanthus triangulum, Hymenoptera, Crabronidae) engages in a highly specific association with bacteria of the genus Streptomyces that appears to protect beewolf offspring against infection by pathogens. Using transmission and scanning electron microscopy, the bacteria were located in the antennal glands of female wasps, where they form dense cell clusters. Using genetic methods, closely related streptomycetes were found in the antennae of 27 Philanthus species (including two subspecies of P. triangulum from distant localities). In contrast, no endosymbionts could be detected in the antennae of other genera within the subfamily Philanthinae (Aphilanthops, Clypeadon and Cerceris). On the basis of morphological, genetic and ecological data, 'Candidatus Streptomyces philanthi' is proposed. 16S rRNA gene sequence data are provided for 28 ecotypes of 'Candidatus Streptomyces philanthi' that reside in different host species and subspecies of the genus Philanthus. Primers for the selective amplification of 'Candidatus Streptomyces philanthi' and an oligonucleotide probe for specific detection by fluorescence in situ hybridization (FISH) are described.
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Affiliation(s)
- Martin Kaltenpoth
- University of Würzburg, Department for Animal Ecology and Tropical Biology, Am Hubland, D-97074 Würzburg, Germany
| | - Wolfgang Goettler
- University of Regensburg, Department of Zoology, D-93040 Regensburg, Germany
- University of Würzburg, Department for Animal Ecology and Tropical Biology, Am Hubland, D-97074 Würzburg, Germany
| | - Colin Dale
- University of Utah, Department of Biology, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | | | - Gudrun Herzner
- University of Regensburg, Department of Zoology, D-93040 Regensburg, Germany
| | - Kerstin Roeser-Mueller
- University of Würzburg, Department for Animal Ecology and Tropical Biology, Am Hubland, D-97074 Würzburg, Germany
| | - Erhard Strohm
- University of Regensburg, Department of Zoology, D-93040 Regensburg, Germany
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Lo N, Beninati T, Sassera D, Bouman EAP, Santagati S, Gern L, Sambri V, Masuzawa T, Gray JS, Jaenson TGT, Bouattour A, Kenny MJ, Guner ES, Kharitonenkov IG, Bitam I, Bandi C. Widespread distribution and high prevalence of an alpha-proteobacterial symbiont in the tick Ixodes ricinus. Environ Microbiol 2006; 8:1280-7. [PMID: 16817936 DOI: 10.1111/j.1462-2920.2006.01024.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tick Ixodes ricinus is responsible for the transmission of a number of bacterial, protozoan and viral diseases to humans and animals in Europe and Northern Africa. Female I. ricinus from England, Switzerland and Italy have been found to harbour an intracellular alpha-proteobacterium, designated IricES1, within the cells of the ovary. IricES1 is the only prokaryote known to exist within the mitochondria of any animal or multicellular organism. To further examine the distribution, prevalence and mode of transmission of IricES1, we performed polymerase chain reaction screening of I. ricinus adults from 12 countries across its geographic distribution, including tick colonies that have been maintained in the laboratory for varying periods of time. IricES1 was detected in 100% of field-collected female ticks from all countries examined (n = 128), while 44% of males were found to be infected (n = 108). Those males that are infected appear to harbour fewer bacteria than females. Sequencing of fragments of the 16S rRNA and gyrB genes revealed very low nucleotide diversity among various populations of IricES1. Transmission of IricES1 from engorged adult females to eggs was found to be 100% (n = 31). In tick colonies that had been maintained in the laboratory for several years, a relatively low prevalence was found in females (32%; n = 25). To our knowledge, IricES1 is the most widespread and highly prevalent of any tick-associated symbiont.
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Affiliation(s)
- N Lo
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia.
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28
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Abstract
Tight interactions between unrelated organisms such as is seen in plant-insect, host-parasite, or host-symbiont associations may lead to speciation of the smaller partners when their hosts speciate. Totally congruent phylogenies of interacting taxa have not been observed often but a number of studies have provided evidence that various hemipteran insect taxa and their primary bacterial endosymbionts share phylogenetic histories. Like other hemipterans, mealybugs (Pseudococcidae) harbour multiple intracellular bacterial symbionts, which are thought to be strictly vertically inherited, implying codivergence of hosts and symbionts. Here, robust estimates of phylogeny were generated from four fragments of three nuclear genes for mealybugs of the subfamily Pseudococcinae, and a substantial fragment of the 16S-23S rDNA of their P-endosymbionts. Phylogenetic congruence was highly significant, with 75% of nodes on the two trees identical, and significant correlation of branch lengths indicated coincident timing of cladogenesis. It is suggested that the low level of observed incongruence was influenced by uncertainty in phylogenetic estimation, but evolutionary outcomes other than congruence, including host shifts, could not be rejected.
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Affiliation(s)
- D A Downie
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa.
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29
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Affiliation(s)
- Spencer V Nyholm
- Department of Pathology, Stanford University, School of Medicine, Palo Alto, California 94305, USA
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30
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BIRKLE LM, MINTO LB, WALTERS KFA, DOUGLAS AE. Microbial genotype and insect fitness in an aphid-bacterial symbiosis. Funct Ecol 2004. [DOI: 10.1111/j.0269-8463.2004.00871.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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31
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Beninati T, Lo N, Sacchi L, Genchi C, Noda H, Bandi C. A novel alpha-Proteobacterium resides in the mitochondria of ovarian cells of the tick Ixodes ricinus. Appl Environ Microbiol 2004; 70:2596-602. [PMID: 15128508 PMCID: PMC404433 DOI: 10.1128/aem.70.5.2596-2602.2004] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An intracellular bacterium from Ixodes ricinus ticks collected in Italy was characterized by electron microscopy (EM), PCR sequencing of the 16S rRNA gene, molecular phylogenetic analysis, and in situ hybridization (ISH). This bacterium was shown by EM to be present in the cytoplasm, as well as in the mitochondria of ovarian cells. When universal 16S rRNA bacterial primers were used, PCR amplification of ovarian DNA followed by cloning and sequencing resulted in the same sequence being found in each sample. Phylogenetic analysis of this sequence showed that the bacterium from which it was derived, tentatively designated IricES1, is part of a novel clade in the alpha subdivision of the Proteobacterium: ISH and PCR assays of various tissues performed with oligonucleotides specific for the IricES1 16S rRNA showed that IricES1 is restricted to ovarian cells. Based on the results obtained, we inferred that the bacteria seen by EM in ovarian cells are a single type of bacteria, corresponding to IricES1. PCR screening of 166 ticks from various parts of Italy and one site in England showed that IricES1 was present in 96% of adult females and 44% of nymphs (unsexed). No adult males were found to be infected. Despite the apparent parasitism of host mitochondria by IricES1, the available information suggests that the bacterium has an obligate relationship with its host, although this must be confirmed.
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Affiliation(s)
- Tiziana Beninati
- DIPAV, Sezione di Patologia Generale e Parassitologia, Università degli Studi di Milano, Milan
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32
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Sabater-Muñoz B, van Ham RCHJ, Moya A, Silva FJ, Latorre A. Evolution of the leucine gene cluster in Buchnera aphidicola: insights from chromosomal versions of the cluster. J Bacteriol 2004; 186:2646-54. [PMID: 15090505 PMCID: PMC387811 DOI: 10.1128/jb.186.9.2646-2654.2004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In Buchnera aphidicola strains associated with the aphid subfamilies Thelaxinae, Lachninae, Pterocommatinae, and Aphidinae, the four leucine genes (leuA, -B, -C, and -D) are located on a plasmid. However, these genes are located on the main chromosome in B. aphidicola strains associated with the subfamilies Pemphiginae and Chaitophorinae. The sequence of the chromosomal fragment containing the leucine cluster and flanking genes has different positions in the chromosome in B. aphidicola strains associated with three tribes of the subfamily Pemphiginae and one tribe of the subfamily Chaitophorinae. Due to the extreme gene order conservation of the B. aphidicola genomes, the variability in the position of the leucine cluster in the chromosome may be interpreted as resulting from independent insertions from an ancestral plasmid-borne leucine gene. These findings do not support a chromosomal origin for the leucine genes in the ancestral B. aphidicola and do support a back transfer evolutionary scenario from a plasmid to the main chromosome.
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Affiliation(s)
- Beatriz Sabater-Muñoz
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, 46071 Valencia, Spain
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33
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Plague GR, Dale C, Moran NA. Low and homogeneous copy number of plasmid-borne symbiont genes affecting host nutrition in Buchnera aphidicola of the aphid Uroleucon ambrosiae. Mol Ecol 2003; 12:1095-100. [PMID: 12753227 DOI: 10.1046/j.1365-294x.2003.01782.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The bacterial endosymbiont of aphids, Buchnera aphidicola, often provides amino acids to its hosts. Plasmid amplification of leucine (leuABCD) and tryptophan (trpEG) biosynthesis genes may be a mechanism by which some Buchnera over-produce these nutrients. We used quantitative polymerase chain reaction to assess the leuABCD/trpEG copy variability within Uroleucon ambrosiae, an aphid with a wide diet breadth and range. Both leuABCD and trpEG abundances are: (i) similar for aphids across 15 populations, and (ii) low compared to Buchnera from other aphid species (particularly trpEG). Consequently, the plasmid location of trpEG combined with Buchnera's chromosomal polyploidy may functionally limit, rather than increase, tryptophan production within Uroleucon ambrosiae.
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Affiliation(s)
- Gordon R Plague
- Center for Insect Science, University of Arizona, Tucson, AZ 85721, USA.
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34
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Nishiguchi MK. Host-symbiont recognition in the environmentally transmitted sepiolid squid-Vibrio mutualism. MICROBIAL ECOLOGY 2002; 44:10-8. [PMID: 12019463 DOI: 10.1007/bf03036870] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2002] [Accepted: 01/25/2003] [Indexed: 05/23/2023]
Abstract
Associations between environmentally transmitted symbionts and their hosts provide a unique opportunity to study the evolution of specificity and subsequent radiation of tightly coupled host-symbiont assemblages [3, 8, 24]. The evidence provided here from the environmentally transmitted bacterial symbiont Vibrio fischeri and its sepiolid squid host (Sepiolidae: Euprymna) demonstrates how host-symbiont specificity can still evolve without vertical transmission of the symbiont [1]. Infection by intraspecific V. fischeri symbionts exhibited preferential colonization over interspecific V. fischeri symbionts, indicating a high degree of specificity for the native symbiotic strains. Inoculation with symbiotic bacteria from other taxa (monocentrid fish and loliginid squids) produced little or no colonization in two species of Euprymna, despite their presence in the same or similar habitats as these squids. These findings of host specificity between native Vibrios and sepiolid squids provides evidence that the presence of multiple strains of symbionts does not dictate the composition of bacterial symbionts in the host.
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Affiliation(s)
- M K Nishiguchi
- Department of Biology, New Mexico State University, Box 30001, MSC 3AF, Las Cruces, New Mexico 88003-8001, USA.
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35
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Martinez-Torres D, Buades C, Latorre A, Moya A. Molecular systematics of aphids and their primary endosymbionts. Mol Phylogenet Evol 2001; 20:437-49. [PMID: 11527469 DOI: 10.1006/mpev.2001.0983] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aphids constitute a monophyletic group within the order Homoptera (i.e., superfamily Aphidoidea). The Aphidoidea originated in the Jurassic about 150 my ago from some aphidiform ancestor whose origin can be traced back to about 250 my ago. They exhibit a mutualistic association with intracellular bacteria (Buchnera sp.) related to Escherichia coli. Buchnera is usually considered the aphids' primary endosymbiont. The association is obligate for both partners. The 16S rDNA-based phylogeny of Buchnera from four aphid families showed complete concordance with the morphology-based phylogeny of their aphid hosts, which pointed to a single original infection in a common ancestor of aphids some 100-250 my ago followed by cospeciation of aphids and Buchnera. This study concentrated on the molecular phylogeny of both the aphids and their primary endosymbionts of five aphid families including for the first time representatives of the family Lachnidae. We discuss results based on two Buchnera genes (16S rDNA and the beta subunit of the F-ATPase complex) and on one host mitochondrial gene (the subunit 6 of the F-ATPase complex). Although our data do not allow definitive evolutionary relationships to be established among the different aphid families, some traditionally accepted groupings are put into question from both bacterial and insect data. In particular, the Lachnidae and the Aphididae, which from morphological data are considered recently evolved sister groups, do not seem to be as closely related as is usually accepted. Finally, we discuss our results in the light of the proposed parallel evolution of aphids and their endosymbionts.
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Affiliation(s)
- D Martinez-Torres
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Apartado de Correos 2085, 46071, Spain
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36
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McFall-Ngai MJ. Identifying 'prime suspects': symbioses and the evolution of multicellularity. Comp Biochem Physiol B Biochem Mol Biol 2001; 129:711-23. [PMID: 11435126 DOI: 10.1016/s1096-4959(01)00406-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The possible involvement of symbioses in the evolution of multicellularity is explored. Evidence is drawn principally from the biology of present day associations of plants and animals with prokaryotes. A particular emphasis is placed on future research opportunities in this area of biology that have been provided by the advent of specific molecular techniques and new model systems. With the application of new approaches that result from these advances, a more holistic understanding of the biology of the coevolved communities, composed of animals or plants and their associated prokaryotes, is within the reach of biologists over the next few decades.
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Affiliation(s)
- M J McFall-Ngai
- Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, 41 Ahui Street, 96813, Honolulu, HI, USA
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37
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Funk DJ, Wernegreen JJ, Moran NA. Intraspecific variation in symbiont genomes: bottlenecks and the aphid-buchnera association. Genetics 2001; 157:477-89. [PMID: 11156972 PMCID: PMC1461510 DOI: 10.1093/genetics/157.2.477] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Buchnera are maternally transmitted bacterial endosymbionts that synthesize amino acids that are limiting in the diet of their aphid hosts. Previous studies demonstrated accelerated sequence evolution in Buchnera compared to free-living bacteria, especially for nonsynonymous substitutions. Two mechanisms may explain this acceleration: relaxed purifying selection and increased fixation of slightly deleterious alleles under drift. Here, we test the divergent predictions of these hypotheses for intraspecific polymorphism using Buchnera associated with natural populations of the ragweed aphid, Uroleucon ambrosiae. Contrary to expectations under relaxed selection, U. ambrosiae from across the United States yielded strikingly low sequence diversity at three Buchnera loci (dnaN, trpBC, trpEG), revealing polymorphism three orders of magnitude lower than in enteric bacteria. An excess of nonsynonymous polymorphism and of rare alleles was also observed. Local sampling of additional dnaN sequences revealed similar patterns of polymorphism and no evidence of food plant-associated genetic structure. Aphid mitochondrial sequences further suggested that host bottlenecks and large-scale dispersal may contribute to genetic homogenization of aphids and symbionts. Together, our results support reduced N(e) as a primary cause of accelerated sequence evolution in Buchnera. However, our study cannot rule out the possibility that mechanisms other than bottlenecks also contribute to reduced N(e) at aphid and endosymbiont loci.
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Affiliation(s)
- D J Funk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
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38
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Ishikawa H. Symbiotic microoiganisms in aphids (Homoptera, Insecta): A secret of one thriving insect group. ACTA ACUST UNITED AC 2001. [DOI: 10.1080/12265071.2001.9647599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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Funk DJ, Helbling L, Wernegreen JJ, Moran NA. Intraspecific phylogenetic congruence among multiple symbiont genomes. Proc Biol Sci 2000; 267:2517-21. [PMID: 11197128 PMCID: PMC1690841 DOI: 10.1098/rspb.2000.1314] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eukaryotes often form intimate endosymbioses with prokaryotic organisms. Cases in which these symbionts are transmitted cytoplasmically to host progeny create the potential for co-speciation or congruent evolution among the distinct genomes of these partners. If symbionts do not move horizontally between different eukaryotic hosts, strict phylogenetic congruence of their genomes is predicted and should extend to relationships within a single host species. Conversely, even rare 'host shifts' among closely related lineages should yield conflicting tree topologies at the intraspecific level. Here, we investigate the historical associations among four symbiotic genomes residing within an aphid host: the mitochondrial DNA of Uroleucon ambrosiae aphids, the bacterial chromosome of their Buchnera bacterial endosymbionts, and two plasmids associated with Buchnera. DNA sequence polymorphisms provided a significant phylogenetic signal and no homoplasy for each data set, yielding completely and significantly congruent phylogenies for these four genomes and no evidence of horizontal transmission. This study thus provides the first evidence for strictly vertical transmission and 'co-speciation' of symbiotic organisms at the intraspecific level, and represents the lowest phylogenetic level at which such coevolution has been demonstrated. These results may reflect the obligate nature of this intimate mutualism and indicate opportunities for adaptive coevolution among linked symbiont genomes.
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Affiliation(s)
- D J Funk
- Department of Ecology and Evolutionary Biology, and Center for Insect Science, University of Arizona, Tucson 85721, USA.
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40
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Rispe C, Moran NA. Accumulation of Deleterious Mutations in Endosymbionts: Muller’s Ratchet with Two Levels of Selection. Am Nat 2000; 156:425-441. [DOI: 10.1086/303396] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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41
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Moran NA, Wernegreen JJ. Lifestyle evolution in symbiotic bacteria: insights from genomics. Trends Ecol Evol 2000; 15:321-326. [PMID: 10884696 DOI: 10.1016/s0169-5347(00)01902-9] [Citation(s) in RCA: 241] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bacteria that live only in eukaryotic cells and tissues, including chronic pathogens and mutualistic bacteriocyte associates, often possess a distinctive set of genomic traits, including reduced genome size, biased nucleotide base composition and fast polypeptide evolution. These phylogenetically diverse bacteria have lost certain functional categories of genes, including DNA repair genes, which affect mutational patterns. However, pathogens and mutualistic symbionts retain loci that underlie their unique interaction types, such as genes enabling nutrient provisioning by mutualistic bacteria-inhabiting animals. Recent genomic studies suggest that many of these bacteria are irreversibly specialized, precluding shifts between pathogenesis and mutualism.
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42
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Nishiguchi MK. Temperature affects species distribution in symbiotic populations of Vibrio spp. Appl Environ Microbiol 2000; 66:3550-5. [PMID: 10919820 PMCID: PMC92184 DOI: 10.1128/aem.66.8.3550-3555.2000] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genus Sepiola (Cephalopoda: Sepiolidae) contains 10 known species that occur in the Mediterranean Sea today. All Sepiola species have a light organ that contains at least one of two species of luminous bacteria, Vibrio fischeri and Vibrio logei. The two Vibrio species coexist in at least four Sepiola species (S. affinis, S. intermedia, S. ligulata, and S. robusta), and their concentrations in the light organ depend on changes in certain abiotic factors, including temperature. Strains of V. fischeri grew faster in vitro and in Sepiola juveniles when they were incubated at 26 degrees C. In contrast, strains of V. logei grew faster at 18 degrees C in culture and in Sepiola juveniles. When aposymbiotic S. affinis or S. ligulata juveniles were inoculated with one Vibrio species, all strains of V. fischeri and V. logei were capable of infecting both squid species at the optimum growth temperatures, regardless of the squid host from which the bacteria were initially isolated. However, when two different strains of V. fischeri and V. logei were placed in direct competition with each other at either 18 or 26 degrees C, strains of V. fischeri were present in sepiolid light organs in greater concentrations at 26 degrees C, whereas strains of V. logei were present in greater concentrations at 18 degrees C. In addition to the competition experiments, the ratios of the two bacterial species in adult Sepiola specimens caught throughout the season at various depths differed, and these differences were correlated with the temperature in the surrounding environment. My findings contribute additional data concerning the ecological and environmental factors that affect host-symbiont recognition and may provide insight into the evolution of animal-bacterium specificity.
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Affiliation(s)
- M K Nishiguchi
- Department of Biology, New Mexico State University, Las Cruces 88003-8001, USA.
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43
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Wernegreen JJ, Moran NA. Decay of mutualistic potential in aphid endosymbionts through silencing of biosynthetic loci: Buchnera of Diuraphis. Proc Biol Sci 2000; 267:1423-31. [PMID: 10983826 PMCID: PMC1690690 DOI: 10.1098/rspb.2000.1159] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Buchnera, the primary bacterial endosymbiont of aphids, is known to provision essential amino acids lacking in the hosts' diet of plant sap. The recent discovery of silenced copies of genes for tryptophan biosynthesis (trpEG) in certain Buchnera lineages suggests a decay in symbiotic functions in some aphid species. However, neither the distribution of pseudogenes among lineages nor the impact of this gene silencing on amino-acid availability in hosts has been assessed. In Buchnera of the aphid Diuraphis noxia, tandem repeats of these pseudogenes have persisted in diverse lineages, and thpEG pseudogenes have originated at least twice within this aphid genus. Measures of amino-acid concentrations in Diuraphis species have shown that the presence of the pseudogene is associated with a decreased availability of tryptophan, indicating that gene silencing decreases nutrient provisioning by symbionts. In Buchnera of Diuraphis, rates of nonsynonymous substitutions are elevated in functional trpE copies, supporting the hypothesis that pseudogene origin and persistence reflect a reduced selection for symbiont biosynthetic contributions. The parallel evolution of trpEG pseudogenes in Buchnera of Diuraphis and certain other aphid hosts suggests that either selection at the host level is not effective or that fitness in these aphids is not limited by tryptophan availability.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, Center for Insect Science, University of Arizona, Tucson 85721, USA.
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44
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Wernegreen JJ, Ochman H, Jones IB, Moran NA. Decoupling of genome size and sequence divergence in a symbiotic bacterium. J Bacteriol 2000; 182:3867-9. [PMID: 10851009 PMCID: PMC94565 DOI: 10.1128/jb.182.13.3867-3869.2000] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In contrast to genome size variation in most bacterial taxa, the small genome size of Buchnera sp. was shown to be highly conserved across genetically diverse isolates (630 to 643 kb). This exceptional size conservation may reflect the inability of this obligate mutualist to acquire foreign DNA and reduced selection for genetic novelty within a static intracellular environment.
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Affiliation(s)
- J J Wernegreen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA.
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45
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Thao ML, Moran NA, Abbot P, Brennan EB, Burckhardt DH, Baumann P. Cospeciation of psyllids and their primary prokaryotic endosymbionts. Appl Environ Microbiol 2000; 66:2898-905. [PMID: 10877784 PMCID: PMC92089 DOI: 10.1128/aem.66.7.2898-2905.2000] [Citation(s) in RCA: 178] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. Four-kilobase DNA fragments containing 16S and 23S ribosomal DNA (rDNA) were amplified from the primary (P) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. In addition, 0.54-kb fragments of the psyllid nuclear gene wingless were also amplified from 26 species. Phylogenetic trees derived from 16S-23S rDNA and from the host wingless gene are very similar, and tests of compatibility of the data sets show no significant conflict between host and endosymbiont phylogenies. This result is consistent with a single infection of a shared psyllid ancestor and subsequent cospeciation of the host and the endosymbiont. In addition, the phylogenies based on DNA sequences generally agreed with psyllid taxonomy based on morphology. The 3' end of the 16S rDNA of the P endosymbionts differs from that of other members of the domain Bacteria in the lack of a sequence complementary to the mRNA ribosome binding site. The rate of sequence change in the 16S-23S rDNA of the psyllid P endosymbiont was considerably higher than that of other bacteria, including other fast-evolving insect endosymbionts. The lineage consisting of the P endosymbionts of psyllids was given the designation Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.).
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Affiliation(s)
- M L Thao
- Microbiology Section, University of California, Davis, California 95616-8665, USA
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Clark MA, Moran NA, Baumann P, Wernegreen JJ. Cospeciation between bacterial endosymbionts (Buchnera) and a recent radiation of aphids (Uroleucon) and pitfalls of testing for phylogenetic congruence. Evolution 2000; 54:517-25. [PMID: 10937228 DOI: 10.1111/j.0014-3820.2000.tb00054.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies of phylogenetic congruence between aphids and their symbiotic bacteria (Buchnera) supported long-term vertical transmission of symbionts. However, those studies were based on distantly related aphids and would not have revealed horizontal transfer of symbionts among closely related hosts. Aphid species of the genus Uroleucon are closely related phylogenetically and overlap in geographic ranges, habitats, and parasitoids. To examine support for congruence of phylogenies of Buchnera and Uroleucon, sequences from four mitochondrial, one nuclear, and one endosymbiont gene (trpB) were obtained. Congruence of phylogenies based on pooled aphid genes with phylogenies based on trpB was highly significant: Most nodes resolved by trpB corresponded to nodes resolved by the pooled aphid genes. Furthermore, no nodes were both inconsistent between the trees and strongly supported in both trees. Two kinds of analyses testing the null hypothesis of perfect congruence between pairwise combinations of datasets and tree topologies were performed: the Kishino-Hasegawa test and the likelihood-ratio test. Both tests indicated significant disagreement among most pairwise combinations of mitochondrial, nuclear, and symbiont datasets. Because rampant recombination among mitochondrial genomes of different aphid species is unlikely, inaccurate assumptions in the evolutionary models underlying these tests appear to be causing the hypothesis of a shared history to be incorrectly rejected. Moreover, trpB was more consistent with the aphid genes as a set than any single aphid gene was with the others, suggesting that the symbionts show the same phylogeny as the aphids. Overall, analyses support the interpretation that symbionts and aphids have undergone strict cospeciation, with no horizontal transmission of symbionts even among closely related, ecologically similar aphid hosts.
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Affiliation(s)
- M A Clark
- Microbiology Section, University of California, Davis 95616-8665, USA
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Visick KL, McFall-Ngai MJ. An exclusive contract: specificity in the Vibrio fischeri-Euprymna scolopes partnership. J Bacteriol 2000; 182:1779-87. [PMID: 10714980 PMCID: PMC101858 DOI: 10.1128/jb.182.7.1779-1787.2000] [Citation(s) in RCA: 131] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- K L Visick
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA.
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van Hoek AH, van Alen TA, Sprakel VS, Leunissen JA, Brigge T, Vogels GD, Hackstein JH. Multiple acquisition of methanogenic archaeal symbionts by anaerobic ciliates. Mol Biol Evol 2000; 17:251-8. [PMID: 10677847 DOI: 10.1093/oxfordjournals.molbev.a026304] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Anaerobic heterotrichous ciliates (Armophoridae and Clevelandellidae) possess hydrogenosomes that generate molecular hydrogen and ATP. This intracellular source of hydrogen provides the basis for a stable endosymbiotic association with methanogenic archaea. We analyzed the SSU rRNA genes of 18 heterotrichous anaerobic ciliates and their methanogenic endosymbionts in order to unravel the evolution of this mutualistic association. Here, we show that the anaerobic heterotrichous ciliates constitute at least three evolutionary lines. One group consists predominantly of gut-dwelling ciliates, and two to three, potentially four, additional clades comprise ciliates that thrive in freshwater sediments. Their methanogenic endosymbionts belong to only two different taxa that are closely related to free-living methanogenic archaea from the particular ecological niches. The close phylogenetic relationships between the endosymbionts and free-living methanogenic archaea argue for multiple acquisitions from environmental sources, notwithstanding the strictly vertical transmission of the endosymbionts. Since phylogenetic analysis of the small-subunit (SSU) rRNA genes of the hydrogenosomes of these ciliates indicates a descent from the mitochondria of aerobic ciliates, it is likely that anaerobic heterotrichous ciliates hosted endosymbiotic methanogens prior to their radiation. Therefore, our data strongly suggest multiple acquisitions and replacements of endosymbiotic methanogenic archaea during their host's adaptation to the various ecological niches.
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Affiliation(s)
- A H van Hoek
- Department of Microbiology and Evolutionary Biology, Faculty of Science, University of Nijmegen, The Netherlands
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Clark MA, Moran NA, Baumann P, Wernegreen JJ. COSPECIATION BETWEEN BACTERIAL ENDOSYMBIONTS (BUCHNERA) AND A RECENT RADIATION OF APHIDS (UROLEUCON) AND PITFALLS OF TESTING FOR PHYLOGENETIC CONGRUENCE. Evolution 2000. [DOI: 10.1554/0014-3820(2000)054[0517:cbbeba]2.0.co;2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ruby EG, McFall-Ngai MJ. Oxygen-utilizing reactions and symbiotic colonization of the squid light organ by Vibrio fischeri. Trends Microbiol 1999; 7:414-20. [PMID: 10498950 DOI: 10.1016/s0966-842x(99)01588-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A major goal in microbiology is to understand the processes by which bacteria successfully colonize host tissue. Although a wealth of studies focusing on pathogenic microorganisms has revealed much about the rare interactions that result in disease, far less is known about the regulation of the ubiquitous, long-term, cooperative associations of bacteria with their animal hosts.
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Affiliation(s)
- E G Ruby
- Pacific Biomedical Research Center, Kewalo Marine Laboratory, University of Hawaii, Honolulu, HI 96813, USA.
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