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Peng L, Hoban J, Joffe J, Smith AH, Carpenter M, Marcelis T, Patel V, Lynn-Bell N, Oliver KM, Russell JA. Cryptic community structure and metabolic interactions among the heritable facultative symbionts of the pea aphid. J Evol Biol 2023; 36:1712-1730. [PMID: 37702036 DOI: 10.1111/jeb.14216] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 09/14/2023]
Abstract
Most insects harbour influential, yet non-essential heritable microbes in their hemocoel. Communities of these symbionts exhibit low diversity. But their frequent multi-species nature raises intriguing questions on roles for symbiont-symbiont synergies in host adaptation, and on the stability of the symbiont communities, themselves. In this study, we build on knowledge of species-defined symbiont community structure across US populations of the pea aphid, Acyrthosiphon pisum. Through extensive symbiont genotyping, we show that pea aphids' microbiomes can be more precisely defined at the symbiont strain level, with strain variability shaping five out of nine previously reported co-infection trends. Field data provide a mixture of evidence for synergistic fitness effects and symbiont hitchhiking, revealing causes and consequences of these co-infection trends. To test whether within-host metabolic interactions predict common versus rare strain-defined communities, we leveraged the high relatedness of our dominant, community-defined symbiont strains vs. 12 pea aphid-derived Gammaproteobacteria with sequenced genomes. Genomic inference, using metabolic complementarity indices, revealed high potential for cooperation among one pair of symbionts-Serratia symbiotica and Rickettsiella viridis. Applying the expansion network algorithm, through additional use of pea aphid and obligate Buchnera symbiont genomes, Serratia and Rickettsiella emerged as the only symbiont community requiring both parties to expand holobiont metabolism. Through their joint expansion of the biotin biosynthesis pathway, these symbionts may span missing gaps, creating a multi-party mutualism within their nutrient-limited, phloem-feeding hosts. Recent, complementary gene inactivation, within the biotin pathways of Serratia and Rickettsiella, raises further questions on the origins of mutualisms and host-symbiont interdependencies.
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Affiliation(s)
- Linyao Peng
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jessica Hoban
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Jonah Joffe
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Andrew H Smith
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Melissa Carpenter
- Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, Pennsylvania, USA
| | - Tracy Marcelis
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Vilas Patel
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Nicole Lynn-Bell
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Kerry M Oliver
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Jacob A Russell
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
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Li J, An Z, Luo J, Zhu X, Wang L, Zhang K, Li D, Ji J, Niu L, Gao X, Cui J. Parasitization of Aphis gossypii Glover by Binodoxys communis Gahan Causes Shifts in the Ovarian Bacterial Microbiota. INSECTS 2023; 14:314. [PMID: 37103129 PMCID: PMC10142764 DOI: 10.3390/insects14040314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Aphis gossypii Glover is an important agricultural pest distributed worldwide. Binodoxys communis Gahan is the main parasitoid wasp of A. gossypii. Previous studies have shown that parasitization causes reduced egg production in A. gossypii, but the effects of parasitism on the symbiotic bacteria in the host ovaries are unknown. RESULTS In this study, we analyzed the microbial communities in the ovaries of A. gossypii without and after parasitization. Whether parasitized or not, Buchnera was the dominant genus of symbiotic bacteria in the ovaries, followed by facultative symbionts including Arsenophonus, Pseudomonas, and Acinetobacter. The relative abundance of Buchnera in the aphid ovary increased after parasitization for 1 d in both third-instar nymph and adult stages, but decreased after parasitization for 3 d. The shifts in the relative abundance of Arsenophonus in both stages were the same as those observed for Buchnera. In addition, the relative abundance of Serratia remarkably decreased after parasitization for 1 d and increased after parasitization for 3 d. A functional predictive analysis of the control and parasitized ovary microbiomes revealed that pathways primarily enriched in parasitization were "amino acid transport and metabolism" and "energy production and conversion." Finally, RT-qPCR analysis was performed on Buchnera, Arsenophonus, and Serratia. The results of RT-qPCR were the same as the results of 16S rDNA sequencing. CONCLUSIONS These results provide a framework for investigating shifts in the microbial communities in host ovaries, which may be responsible for reduced egg production in aphids. These findings also broaden our understanding of the interactions among aphids, parasitoid wasps, and endosymbionts.
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Affiliation(s)
- Jinming Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhe An
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Junyu Luo
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiangzhen Zhu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Li Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kaixin Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Dongyang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jichao Ji
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Lin Niu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xueke Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jinjie Cui
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Liu W, Yu SH, Zhang HP, Fu ZY, An JQ, Zhang JY, Yang P. Two Cladosporium Fungi with Opposite Functions to the Chinese White Wax Scale Insect Have Different Genome Characters. J Fungi (Basel) 2022; 8:jof8030286. [PMID: 35330288 PMCID: PMC8949958 DOI: 10.3390/jof8030286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/05/2023] Open
Abstract
Insects encounter infection of microorganisms, and they also harbor endosymbiosis to participate in nutrition providing and act as a defender against pathogens. We previously found the Chinese white wax scale insect, Ericerus pela, was infected and killed by Cladosporium sp. (pathogen). We also found it harbored Cladosporium sp. (endogensis). In this study, we cultured these two Cladosporium fungi and sequenced their genome. The results showed Cladosporium sp. (endogensis) has a larger genome size and more genes than Cladosporium sp. (pathogen). Pan-genome analysis showed Cladosporium sp. (endogensis)-specific genes enriched in pathways related to nutrition production, such as amino acid metabolism, carbohydrate metabolism, and energy metabolism. These pathways were absent in that of Cladosporium sp. (pathogen). Gene Ontology analysis showed Cladosporium sp. (pathogen)-specific genes enriched in the biosynthesis of asperfuranone, emericellamide, and fumagillin. These terms were not found in that of Cladosporium sp. (endogensis). Pathogen Host Interactions analysis found Cladosporium sp. (endogensis) had more genes related to loss of pathogenicity and reduced virulence than Cladosporium sp. (pathogen). Cytotoxicity assay indicated Cladosporium sp. (pathogen) had cytotoxicity, while Cladosporium sp. (endogensis) had no cytotoxicity. These characters reflect the adaptation of endosymbiosis to host-restricted lifestyle and the invader of the entomopathogen to the host.
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Affiliation(s)
- Wei Liu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (W.L.); (Z.-Y.F.); (J.-Q.A.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Shu-Hui Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China; (S.-H.Y.); (H.-P.Z.)
| | - Hong-Ping Zhang
- College of Agriculture and Life Sciences, Kunming University, Kunming 650214, China; (S.-H.Y.); (H.-P.Z.)
| | - Zuo-Yi Fu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (W.L.); (Z.-Y.F.); (J.-Q.A.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Jia-Qi An
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (W.L.); (Z.-Y.F.); (J.-Q.A.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
| | - Jin-Yang Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
| | - Pu Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming 650224, China; (W.L.); (Z.-Y.F.); (J.-Q.A.)
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming 650224, China
- Correspondence:
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Renoz F, Foray V, Ambroise J, Baa-Puyoulet P, Bearzatto B, Mendez GL, Grigorescu AS, Mahillon J, Mardulyn P, Gala JL, Calevro F, Hance T. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front Cell Infect Microbiol 2021; 11:660007. [PMID: 34268133 PMCID: PMC8275996 DOI: 10.3389/fcimb.2021.660007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
- Institut de Recherche sur la Biologie de l’insecte, UMR 7261, CNRS, Université de Tours, Tours, France
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Gipsi Lima Mendez
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2i, UMR203, F-69621, Villeurbanne, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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Brenner AE, Muñoz-Leal S, Sachan M, Labruna MB, Raghavan R. Coxiella burnetii and Related Tick Endosymbionts Evolved from Pathogenic Ancestors. Genome Biol Evol 2021; 13:6278299. [PMID: 34009306 PMCID: PMC8290121 DOI: 10.1093/gbe/evab108] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Both symbiotic and pathogenic bacteria in the family Coxiellaceae cause morbidity and mortality in humans and animals. For instance, Coxiella-like endosymbionts (CLEs) improve the reproductive success of ticks—a major disease vector, while Coxiella burnetii causes human Q fever, and uncharacterized coxiellae infect both animals and humans. To better understand the evolution of pathogenesis and symbiosis in this group of intracellular bacteria, we sequenced the genome of a CLE present in the soft tick Ornithodoros amblus (CLEOA) and compared it to the genomes of other bacteria in the order Legionellales. Our analyses confirmed that CLEOA is more closely related to C. burnetii, the human pathogen, than to CLEs in hard ticks, and showed that most clades of CLEs contain both endosymbionts and pathogens, indicating that several CLE lineages have evolved independently from pathogenic Coxiella. We also determined that the last common ancestorof CLEOA and C. burnetii was equipped to infect macrophages and that even though horizontal gene transfer (HGT) contributed significantly to the evolution of C. burnetii, most acquisition events occurred primarily in ancestors predating the CLEOA–C. burnetii divergence. These discoveries clarify the evolution of C. burnetii, which previously was assumed to have emerged when an avirulent tick endosymbiont recently gained virulence factors via HGT. Finally, we identified several metabolic pathways, including heme biosynthesis, that are likely critical to the intracellular growth of the human pathogen but not the tick symbiont, and show that the use of heme analog is a promising approach to controlling C. burnetii infections.
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Affiliation(s)
- Amanda E Brenner
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA
| | - Sebastián Muñoz-Leal
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Ñuble, Chile
| | - Madhur Sachan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA
| | - Marcelo B Labruna
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Rahul Raghavan
- Department of Biology and Center for Life in Extreme Environments, Portland State University, Portland, OR, USA.,Department of Biology and South Texas Center for Emerging Infectious Diseases, The University of Texas at San Antonio, San Antonio, TX, USA
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Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest. mSystems 2021; 6:6/1/e01048-20. [PMID: 33531407 PMCID: PMC7857533 DOI: 10.1128/msystems.01048-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.
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Patel V, Chevignon G, Manzano-Marín A, Brandt JW, Strand MR, Russell JA, Oliver KM. Cultivation-Assisted Genome of Candidatus Fukatsuia symbiotica; the Enigmatic "X-Type" Symbiont of Aphids. Genome Biol Evol 2020; 11:3510-3522. [PMID: 31725149 PMCID: PMC7145644 DOI: 10.1093/gbe/evz252] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
Heritable symbionts are common in terrestrial arthropods and often provide beneficial services to hosts. Unlike obligate, nutritional symbionts that largely persist under strict host control within specialized host cells, heritable facultative symbionts exhibit large variation in within-host lifestyles and services rendered with many retaining the capacity to transition among roles. One enigmatic symbiont, Candidatus Fukatsuia symbiotica, frequently infects aphids with reported roles ranging from pathogen, defensive symbiont, mutualism exploiter, and nutritional co-obligate symbiont. Here, we used an in vitro culture-assisted protocol to sequence the genome of a facultative strain of Fukatsuia from pea aphids (Acyrthosiphon pisum). Phylogenetic and genomic comparisons indicate that Fukatsuia is an aerobic heterotroph, which together with Regiella insecticola and Hamiltonella defensa form a clade of heritable facultative symbionts within the Yersiniaceae (Enterobacteriales). These three heritable facultative symbionts largely share overlapping inventories of genes associated with housekeeping functions, metabolism, and nutrient acquisition, while varying in complements of mobile DNA. One unusual feature of Fukatsuia is its strong tendency to occur as a coinfection with H. defensa. However, the overall similarity of gene inventories among aphid heritable facultative symbionts suggests that metabolic complementarity is not the basis for coinfection, unless playing out on a H. defensa strain-specific basis. We also compared the pea aphid Fukatsuia with a strain from the aphid Cinara confinis (Lachninae) where it is reported to have transitioned to co-obligate status to support decaying Buchnera function. Overall, the two genomes are very similar with no clear genomic signatures consistent with such a transition, which suggests co-obligate status in C. confinis was a recent event.
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Affiliation(s)
- Vilas Patel
- Department of Entomology, University of Georgia
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Santos-Garcia D, Juravel K, Freilich S, Zchori-Fein E, Latorre A, Moya A, Morin S, Silva FJ. To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies. Front Microbiol 2018; 9:2254. [PMID: 30319574 PMCID: PMC6167482 DOI: 10.3389/fmicb.2018.02254] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Diego Santos-Garcia
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat-Yishai, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, Agricultural Research Organization, Volcani Center, Ramat-Yishai, Israel
| | - Amparo Latorre
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco J. Silva
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
- Francisco J. Silva
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Wernegreen JJ. In it for the long haul: evolutionary consequences of persistent endosymbiosis. Curr Opin Genet Dev 2017; 47:83-90. [PMID: 28934627 DOI: 10.1016/j.gde.2017.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/27/2017] [Accepted: 08/31/2017] [Indexed: 11/30/2022]
Abstract
Phylogenetically independent bacterial lineages have undergone a profound lifestyle shift: from a free-living to obligately host-associated existence. Among these lineages, intracellular bacterial mutualists of insects are among the most intimate, constrained symbioses known. These obligate endosymbionts exhibit severe gene loss and apparent genome deterioration. Evolutionary theory provides a basis to link their unusual genomic features with shifts in fundamental mechanisms - selection, genetic drift, mutation, and recombination. This mini-review highlights recent comparative and experimental research of processes shaping ongoing diversification within these ancient associations. Recent work supports clear contributions of stochastic processes, including genetic drift and exceptionally strong mutational pressure, toward degenerative evolution. Despite possible compensatory mechanisms, genome degradation may constrain how persistent endosymbionts (and their hosts) respond to environmental fluctuations.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment, Duke University, Durham, NC, United States; Center for Genomic and Computational Biology, Duke University, Durham, NC, United States.
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