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Uppal S, Waterworth SC, Nick A, Vogel H, Flórez LV, Kaltenpoth M, Kwan JC. Repeated horizontal acquisition of lagriamide-producing symbionts in Lagriinae beetles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.23.576914. [PMID: 39026795 PMCID: PMC11257431 DOI: 10.1101/2024.01.23.576914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microbial symbionts associate with multicellular organisms on a continuum from facultative associations to mutual codependency. In some of the oldest intracellular symbioses there is exclusive vertical symbiont transmission, and co-diversification of symbiotic partners over millions of years. Such symbionts often undergo genome reduction due to low effective population sizes, frequent population bottlenecks, and reduced purifying selection. Here, we describe multiple independent acquisition events of closely related defensive symbionts followed by genome erosion in a group of Lagriinae beetles. Previous work in Lagria villosa revealed the dominant genome-eroded symbiont of the genus Burkholderia produces the antifungal compound lagriamide and protects the beetle's eggs and larvae from antagonistic fungi. Here, we use metagenomics to assemble 11 additional genomes of lagriamide-producing symbionts from seven different host species within Lagriinae from five countries, to unravel the evolutionary history of this symbiotic relationship. In each host species, we detected one dominant genome-eroded Burkholderia symbiont encoding the lagriamide biosynthetic gene cluster (BGC). Surprisingly, however, we did not find evidence for host-symbiont co-diversification, or for a monophyly of the lagriamide-producing symbionts. Instead, our analyses support at least four independent acquisition events of lagriamide-encoding symbionts and subsequent genome erosion in each of these lineages. By contrast, a clade of plant-associated relatives retained large genomes but secondarily lost the lagriamide BGC. In conclusion, our results reveal a dynamic evolutionary history with multiple independent symbiont acquisitions characterized by high degree of specificity. They highlight the importance of the specialized metabolite lagriamide for the establishment and maintenance of this defensive symbiosis.
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Affiliation(s)
- Siddharth Uppal
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
| | - Samantha C. Waterworth
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
- Current address: National Cancer Institute, Frederick, Maryland, USA
| | - Alina Nick
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Laura V. Flórez
- Department of Plant and Environmental Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Jason C. Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, USA
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2
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Schober I, Bunk B, Carril G, Freese HM, Ojeda N, Riedel T, Meier-Kolthoff JP, Göker M, Spröer C, Flores-Herrera PA, Nourdin-Galindo G, Gómez F, Cárdenas C, Vásquez-Ponce F, Labra A, Figueroa J, Olivares-Pacheco J, Nübel U, Sikorski J, Marshall SH, Overmann J. Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts. THE ISME JOURNAL 2023; 17:2247-2258. [PMID: 37853183 PMCID: PMC10689435 DOI: 10.1038/s41396-023-01531-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/28/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023]
Abstract
The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.
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Affiliation(s)
- Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabriela Carril
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Heike M Freese
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nicolás Ojeda
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Patricio A Flores-Herrera
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Guillermo Nourdin-Galindo
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Fernando Gómez
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Constanza Cárdenas
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Felipe Vásquez-Ponce
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Alvaro Labra
- Laboratorio de Patógenos Acuícolas, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Jaime Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Olivares-Pacheco
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Milenio para la Investigación Colaborativa en Resistencia Antimicrobiana (MICROB-R), Santiago, Chile
| | - Ulrich Nübel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Johannes Sikorski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sergio H Marshall
- Laboratorio de Genética e Inmunología Molecular, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Núcleo Biotecnología Curauma, Pontificia Universidad Católica de Valparaíso, Campus Curauma, Valparaíso, Chile
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.
- Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
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3
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Fourie A, Venter SN, Slippers B, Fourie G. Pantoea bathycoeliae sp. nov and Sodalis sp. are core gut microbiome symbionts of the two-spotted stink bug. Front Microbiol 2023; 14:1284397. [PMID: 38098653 PMCID: PMC10720322 DOI: 10.3389/fmicb.2023.1284397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/04/2023] [Indexed: 12/17/2023] Open
Abstract
Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode.
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Affiliation(s)
| | | | | | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Mfopit YM, Engel JS, Chechet GD, Ibrahim MAM, Signaboubo D, Achukwi DM, Mamman M, Balogun EO, Shuaibu MN, Kabir J, Kelm S. Molecular detection of Sodalis glossinidius, Spiroplasma species and Wolbachia endosymbionts in wild population of tsetse flies collected in Cameroon, Chad and Nigeria. BMC Microbiol 2023; 23:260. [PMID: 37716961 PMCID: PMC10504758 DOI: 10.1186/s12866-023-03005-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Tsetse flies are cyclical vectors of African trypanosomiasis (AT). The flies have established symbiotic associations with different bacteria that influence certain aspects of their physiology. Vector competence of tsetse flies for different trypanosome species is highly variable and is suggested to be affected by bacterial endosymbionts amongst other factors. Symbiotic interactions may provide an avenue for AT control. The current study provided prevalence of three tsetse symbionts in Glossina species from Cameroon, Chad and Nigeria. RESULTS Tsetse flies were collected and dissected from five different locations. DNA was extracted and polymerase chain reaction used to detect presence of Sodalis glossinidius, Spiroplasma species and Wolbachia endosymbionts, using species specific primers. A total of 848 tsetse samples were analysed: Glossina morsitans submorsitans (47.52%), Glossina palpalis palpalis (37.26%), Glossina fuscipes fuscipes (9.08%) and Glossina tachinoides (6.13%). Only 95 (11.20%) were infected with at least one of the three symbionts. Among infected flies, six (6.31%) had Wolbachia and Spiroplasma mixed infection. The overall symbiont prevalence was 0.88, 3.66 and 11.00% respectively, for Sodalis glossinidius, Spiroplasma species and Wolbachia endosymbionts. Prevalence varied between countries and tsetse fly species. Neither Spiroplasma species nor S. glossinidius were detected in samples from Cameroon and Nigeria respectively. CONCLUSION The present study revealed, for the first time, presence of Spiroplasma species infections in tsetse fly populations in Chad and Nigeria. These findings provide useful information on repertoire of bacterial flora of tsetse flies and incite more investigations to understand their implication in the vector competence of tsetse flies.
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Affiliation(s)
- Youssouf Mouliom Mfopit
- Institute of Agricultural Research for Development, Yaounde, Cameroon.
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria.
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria.
| | | | - Gloria Dada Chechet
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | | | | | | | - Mohammed Mamman
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Emmanuel Oluwadare Balogun
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Mohammed Nasir Shuaibu
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Junaidu Kabir
- Africa Centre of Excellence for Neglected Tropical Diseases and Forensic Biotechnology, Ahmadu Bello University, Zaria, Nigeria
- Department of Veterinary Public Health and Preventive Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - Soerge Kelm
- Centre for Biomolecular Interactions Bremen, University of Bremen, Bremen, Germany
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Wang Z, Yong H, Zhang S, Liu Z, Zhao Y. Colonization Resistance of Symbionts in Their Insect Hosts. INSECTS 2023; 14:594. [PMID: 37504600 PMCID: PMC10380809 DOI: 10.3390/insects14070594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/25/2023] [Accepted: 06/29/2023] [Indexed: 07/29/2023]
Abstract
The symbiotic microbiome is critical in promoting insect resistance against colonization by exogenous microorganisms. The mechanisms by which symbionts contribute to the host's immune capacity is referred to as colonization resistance. Symbionts can protect insects from exogenous pathogens through a variety of mechanisms, including upregulating the expression of host immune-related genes, producing antimicrobial substances, and competitively excluding pathogens. Concordantly, insects have evolved fine-tuned regulatory mechanisms to avoid overactive immune responses against symbionts or specialized cells to harbor symbionts. Alternatively, some symbionts have evolved special adaptations, such as the formation of biofilms to increase their tolerance to host immune responses. Here, we provide a review of the mechanisms about colonization resistance of symbionts in their insect hosts. Adaptations of symbionts and their insect hosts that may maintain such symbiotic relationships, and the significance of such relationships in the coevolution of symbiotic systems are also discussed to provide insights into the in-depth study of the contribution of symbionts to host physiology and behavior.
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Affiliation(s)
- Zhengyan Wang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Hanzi Yong
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Shan Zhang
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Zhiyuan Liu
- School of Food and Strategic Reserves, Henan University of Technology, Zhengzhou 450001, China
| | - Yaru Zhao
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
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Rodríguez L, Peñalver M, Casino P, García-del Portillo F. Evolutionary analysis and structure modelling of the Rcs-repressor IgaA unveil a functional role of two cytoplasmic small β-barrel (SBB) domains. Heliyon 2023; 9:e16661. [PMID: 37303533 PMCID: PMC10248123 DOI: 10.1016/j.heliyon.2023.e16661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/17/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
The Rcs sensor system, comprising the RcsB/RcsC/RcsD and RcsF proteins, is used by bacteria of the order Enterobacterales to withstand envelope damage. In non-stress conditions, Rcs is repressed by IgaA, a membrane protein with three cytoplasmic regions (cyt-1, cyt-2 and cyt-3). How the Rcs-IgaA axis evolved within Enterobacterales has not been yet explored. Here, we report phylogenetic data supporting co-evolution of IgaA with RcsC/RcsD. Functional exchange assays showed that IgaA from Shigella and Dickeya, but not from Yersinia or the endosymbionts Photorhabdus and Sodalis, repress the Rcs system of Salmonella. IgaA from Dickeya, however, repress only partially the Rcs system despite being produced at high levels in the complementation assay. The modelled structures of these IgaA variants uncovered one periplasmic and two cytoplasmic conserved β-rich architectures forming partially closed small β-barrel (SBB) domains. Conserved residues map in a connector linking cytoplasmic SSB-1 and SBB-2 domains (E180-R265); a region of cyt-1 facing cyt-2 (R188-E194-D309 and T191-H326); and between cyt-2 and cyt-3 (H293-E328-R686). These structures validated early in vivo studies in Salmonella that assigned a role in function to R188, T191 and G262, and in addition revealed a previously unnoticed "hybrid" SBB-2 domain to which cyt-1 and cyt-2 contribute. IgaA variants not functional or partially functional in Salmonella lack H192-P249 and R255-D313 interactions. Among these variants, only IgaA from Dickeya conserves the helix α6 in SSB-1 that is present in IgaA from Salmonella and Shigella. RcsF and RcsD, which interact directly with IgaA, failed to show structural features linked to specific IgaA variants. Altogether, our data provide new insights into IgaA by mapping residues selected differently during evolution and involved in function. Our data also infer contrasting lifestyles of Enterobacterales bacteria as source of variability in the IgaA-RcsD/IgaA-RcsF interactions.
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Affiliation(s)
- Leticia Rodríguez
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
| | - Marcos Peñalver
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Patricia Casino
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Burjassot, Spain
- Instituto Universitario de Biotecnología y Biomedicina BIOTECMED, Universitat de València, Burjassot, Spain
- CIBER de Enfermedades Raras (CIBERER-ISCIII), Madrid, Spain
| | - Francisco García-del Portillo
- Laboratory of Intracellular Bacterial Pathogens, National Center for Biotechnology-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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Mfopit YM, Weber JS, Chechet GD, Ibrahim MAM, Signaboubo D, Achukwi DM, Mamman M, Balogun EO, Shuaibu MN, Kabir J, Kelm S. Molecular detection of Sodalis glossinidius, Spiroplasma and Wolbachia endosymbionts in wild population of tsetse flies collected in Cameroon, Chad and Nigeria. RESEARCH SQUARE 2023:rs.3.rs-2902767. [PMID: 37214831 PMCID: PMC10197739 DOI: 10.21203/rs.3.rs-2902767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Tsetse flies are cyclical vectors of African trypanosomiasis. They have established symbiotic associations with different bacteria, which influence certain aspects of their physiology. The vector competence of tsetse flies for different trypanosome species is highly variable and is suggested to be affected by various factors, amongst which are bacterial endosymbionts. Symbiotic interactions may provide an avenue for the disease control. The current study provided the prevalence of 3 tsetse symbionts in Glossina species from Cameroon, Chad and Nigeria. Results Tsetse flies were collected from five different locations and dissected. DNA was extracted and polymerase chain reaction PCR was used to detect the presence of Sodalis glossinidius , Spiroplasma sp and Wolbachia using specific primers. A total of 848 tsetse samples were analysed: Glossina morsitans submorsitans (47.52%), Glossina palpalis palpalis (37.26%), Glossina fuscipes fuscipes (9.08%) and Glossina tachinoides (6.13%). Only 95 (11.20%) were infected with at least one of the 3 symbionts. Among the infected, 6 (6.31%) were carrying mixed infection ( Wolbachia and Spiroplasma ). The overall symbiont prevalence was 0.88%, 3.66% and 11.00% respectively, for Sodalis , Spiroplasma and Wolbachia . Prevalence varied between countries and tsetse species. No Spiroplasma was detected in samples from Cameroon and no Sodalis was found in samples from Nigeria. Conclusion The present study revealed for the first time, the presence of infection by Spiroplasma in tsetse in Chad and Nigeria. These findings provide useful information to the repertoire of bacterial flora of tsetse flies and incite to more investigations to understand their implication in the vector competence of tsetse flies.
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Danneels B, Blignaut M, Marti G, Sieber S, Vandamme P, Meyer M, Carlier A. Cyclitol metabolism is a central feature of Burkholderia leaf symbionts. Environ Microbiol 2023; 25:454-472. [PMID: 36451580 DOI: 10.1111/1462-2920.16292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Monique Blignaut
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Guillaume Marti
- Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UT3, INP, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Marion Meyer
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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9
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Goffredi SK, Appy RG, Hildreth R, deRogatis J. Marine vampires: Persistent, internal associations between bacteria and blood-feeding marine annelids and crustaceans. Front Microbiol 2023; 13:1113237. [PMID: 36713196 PMCID: PMC9876621 DOI: 10.3389/fmicb.2022.1113237] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
Persistent bacterial presence is believed to play an important role in host adaptation to specific niches that would otherwise be unavailable, including the exclusive consumption of blood by invertebrate parasites. Nearly all blood-feeding animals examined so far host internal bacterial symbionts that aid in some essential aspect of their nutrition. Obligate blood-feeding (OBF) invertebrates exist in the oceans, yet symbiotic associations between them and beneficial bacteria have not yet been explored. This study describes the microbiome of 6 phylogenetically-diverse species of marine obligate blood-feeders, including leeches (both fish and elasmobranch specialists; e.g., Pterobdella, Ostreobdella, and Branchellion), isopods (e.g., Elthusa and Nerocila), and a copepod (e.g., Lernanthropus). Amplicon sequencing analysis revealed the blood-feeding invertebrate microbiomes to be low in diversity, compared to host fish skin surfaces, seawater, and non-blood-feeding relatives, and dominated by only a few bacterial genera, including Vibrio (100% prevalence and comprising 39%-81% of the average total recovered 16S rRNA gene sequences per OBF taxa). Vibrio cells were localized to the digestive lumen in and among the blood meal for all taxa examined via fluorescence microscopy. For Elthusa and Branchellion, Vibrio cells also appeared intracellularly within possible hemocytes, suggesting an interaction with the immune system. Additionally, Vibrio cultivated from four of the obligate blood-feeding marine taxa matched the dominant amplicons recovered, and all but one was able to effectively lyse vertebrate blood cells. Bacteria from 2 additional phyla and 3 families were also regularly recovered, albeit in much lower abundances, including members of the Oceanospirillaceae, Flavobacteriacea, Porticoccaceae, and unidentified members of the gamma-and betaproteobacteria, depending on the invertebrate host. For the leech Pterobdella, the Oceanospirillaceae were also detected in the esophageal diverticula. For two crustacean taxa, Elthusa and Lernanthropus, the microbial communities associated with brooded eggs were very similar to the adults, indicating possible direct transmission. Virtually nothing is known about the influence of internal bacteria on the success of marine blood-feeders, but this evidence suggests their regular presence in marine parasites from several prominent groups.
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Affiliation(s)
- Shana K. Goffredi
- Department of Biology, Occidental College, Los Angeles, CA, United States
| | - Ralph G. Appy
- Cabrillo Marine Aquarium, San Pedro, CA, United States
| | - Rebecca Hildreth
- Department of Biology, Occidental College, Los Angeles, CA, United States
| | - Julia deRogatis
- Department of Biology, Occidental College, Los Angeles, CA, United States
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10
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Runyen-Janecky LJ, Scheutzow JD, Farsin R, Cabo LF, Wall KE, Kuhn KM, Amador R, D’Souza SJ, Vigneron A, Weiss BL. Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut. PLoS Negl Trop Dis 2022; 16:e0010833. [PMID: 36441823 PMCID: PMC9731421 DOI: 10.1371/journal.pntd.0010833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/08/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Tsetse flies (Glossina spp.) feed exclusively on vertebrate blood. After a blood meal, the enteric endosymbiont Sodalis glossinidius is exposed to various environmental stressors including high levels of heme. To investigate how S. glossinidius morsitans (Sgm), the Sodalis subspecies that resides within the gut of G. morsitans, tolerates the heme-induced oxidative environment of tsetse's midgut, we used RNAseq to identify bacterial genes that are differentially expressed in cells cultured in high versus lower heme environments. Our analysis identified 436 genes that were significantly differentially expressed (> or < 2-fold) in the presence of high heme [219 heme-induced genes (HIGs) and 217 heme-repressed genes (HRGs)]. HIGs were enriched in Gene Ontology (GO) terms related to regulation of a variety of biological functions, including gene expression and metabolic processes. We observed that 11 out of 13 Sgm genes that were heme regulated in vitro were similarly regulated in bacteria that resided within tsetse's midgut 24 hr (high heme environment) and 96 hr (low heme environment) after the flies had consumed a blood meal. We used intron mutagenesis to make insertion mutations in 12 Sgm HIGs and observed no significant change in growth in vitro in any of the mutant strains in high versus low heme conditions. However, Sgm strains that carried mutations in genes encoding a putative undefined phosphotransferase sugar (PTS) system component (SG2427), fucose transporter (SG0182), bacterioferritin (SG2280), and a DNA-binding protein (SGP1-0002), presented growth and/or survival defects in tsetse midguts as compared to normal Sgm. These findings suggest that the uptake up of sugars and storage of iron represent strategies that Sgm employs to successfully reside within the high heme environment of its tsetse host's midgut. Our results are of epidemiological relevance, as many hematophagous arthropods house gut-associated bacteria that mediate their host's competency as a vector of disease-causing pathogens.
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Affiliation(s)
| | - Jack D. Scheutzow
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Ruhan Farsin
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Leah F. Cabo
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Katie E. Wall
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Katrina M. Kuhn
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Rashel Amador
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Shaina J. D’Souza
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Aurelien Vigneron
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Brian L. Weiss
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
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11
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Říhová J, Bell KC, Nováková E, Hypša V. Lightella neohaematopini: A new lineage of highly reduced endosymbionts coevolving with chipmunk lice of the genus Neohaematopinus. Front Microbiol 2022; 13:900312. [PMID: 35979496 PMCID: PMC9376444 DOI: 10.3389/fmicb.2022.900312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sucking lice (Anoplura) are known to have established symbiotic associations multiple times with different groups of bacteria as diverse as Enterobacteriales, Legionellales, and Neisseriales. This diversity, together with absence of a common coevolving symbiont (such as Buchnera, in aphids), indicates that sucking lice underwent a series of symbiont acquisitions, losses, and replacements. To better understand evolution and significance of louse symbionts, genomic and phylogenetic data are needed from a broader taxonomic diversity of lice and their symbiotic bacteria. In this study, we extend the known spectrum of the louse symbionts with a new lineage associated with Neohaematopinus pacificus, a louse species that commonly parasitizes North American chipmunks. The recent coevolutionary analysis showed that rather than a single species, these lice form a cluster of unique phylogenetic lineages specific to separate chipmunk species (or group of closely related species). Using metagenomic assemblies, we show that the lice harbor a bacterium which mirrors their phylogeny and displays traits typical for obligate mutualists. Phylogenetic analyses place this bacterium within Enterobacteriaceae on a long branch related to another louse symbiont, “Candidatus Puchtella pedicinophila.” We propose for this symbiotic lineage the name “Candidatus Lightella neohaematopini.” Based on the reconstruction of metabolic pathways, we suggest that like other louse symbionts, L. neohaematopini provides its host with at least some B vitamins. In addition, several samples harbored another symbiotic bacterium phylogenetically affiliated with the Neisseriales-related symbionts described previously from the lice Polyplax serrata and Hoplopleura acanthopus. Characterizing these bacteria further extend the known diversity of the symbiotic associations in lice and show unique complexity and dynamics of the system.
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Affiliation(s)
- Jana Říhová
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Kayce C. Bell
- Department of Mammalogy, Natural History Museum of Los Angeles County, Los Angeles, CA, United States
- Department of Biology, Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, United States
- Department of Zoology, Denver Museum of Nature and Science, Denver, CO, United States
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
- Institute of Parasitology, Biology Centre, ASCR, v.v.i., České Budějovice, Czechia
- *Correspondence: Václav Hypša,
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12
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Syberg-Olsen MJ, Garber AI, Keeling PJ, McCutcheon JP, Husnik F. Pseudofinder: detection of pseudogenes in prokaryotic genomes. Mol Biol Evol 2022; 39:6633826. [PMID: 35801562 PMCID: PMC9336565 DOI: 10.1093/molbev/msac153] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and nonfunctional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogenes, is a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis in bacterial and archaeal genomes. We demonstrate that Pseudofinder’s multi-pronged, reference-based approach can detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes containing only one or a few inactivating mutations. Additionally, Pseudofinder can detect genes that lack inactivating substitutions but experiencing relaxed selection. Implementation of Pseudofinder in annotation pipelines will allow more precise estimations of the functional potential of sequenced microbes, while also generating new hypotheses related to the evolutionary dynamics of bacterial and archaeal genomes.
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Affiliation(s)
| | - Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA.,Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, Maryland, USA
| | - Filip Husnik
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Okinawa Institute of Science and Technology, Okinawa, Japan
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13
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Silva FJ, Santos-Garcia D, Zheng X, Zhang L, Han XY. Construction and Analysis of the Complete Genome Sequence of Leprosy Agent Mycobacterium lepromatosis. Microbiol Spectr 2022; 10:e0169221. [PMID: 35467405 PMCID: PMC9248898 DOI: 10.1128/spectrum.01692-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 04/07/2022] [Indexed: 12/29/2022] Open
Abstract
Leprosy is caused by Mycobacterium leprae and Mycobacterium lepromatosis. We report construction and analyses of the complete genome sequence of M. lepromatosis FJ924. The genome contained 3,271,694 nucleotides to encode 1,789 functional genes and 1,564 pseudogenes. It shared 1,420 genes and 885 pseudogenes (71.4%) with M. leprae but differed in 1,281 genes and pseudogenes (28.6%). In phylogeny, the leprosy bacilli started from a most recent common ancestor (MRCA) that diverged ~30 million years ago (Mya) from environmental organism Mycobacterium haemophilum. The MRCA then underwent reductive evolution with pseudogenization, gene loss, and chromosomal rearrangements. Analysis of the shared pseudogenes estimated the pseudogenization event ~14 Mya, shortly before species bifurcation. Afterwards, genomic changes occurred to lesser extent in each species. Like M. leprae, four major types of highly repetitive sequences were detected in M. lepromatosis, contributing to chromosomal rearrangements within and after MRCA. Variations in genes and copy numbers were noted, such as three copies of the gene encoding bifunctional diguanylate cyclase/phosphodiesterase in M. lepromatosis, but single copy in M. leprae; 6 genes encoding the TetR family transcriptional regulators in M. lepromatosis, but 11 such genes in M. leprae; presence of hemW gene in M. lepromatosis, but absence in M. leprae; and others. These variations likely aid unique pathogenesis, such as diffuse lepromatous leprosy associated with M. lepromatosis, while the shared genomic features should explain the common pathogenesis of dermatitis and neuritis in leprosy. Together, these findings and the genomic data of M. lepromatosis may facilitate future research and care for leprosy. IMPORTANCE Leprosy is a dreaded infection that still affects millions of people worldwide. Mycobacterium lepromatosis is a recently recognized cause in addition to the well-known Mycobacterium leprae. M. lepromatosis is likely specific for diffuse lepromatous leprosy, a severe form of the infection and endemic in Mexico. This study constructed and annotated the complete genome sequence of M. lepromatosis FJ924 and performed comparative genomic analyses with related mycobacteria. The results afford new and refined insights into the genome size, gene repertoire, pseudogenes, phylogenomic relationship, genome organization and plasticity, process and timing of reductive evolution, and genetic and proteomic basis for pathogenesis. The availability of the complete M. lepromatosis genome may prove to be useful for future research and care for the infection.
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Affiliation(s)
- Francisco J. Silva
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Paterna, Spain
- Genomics and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research, Valencia, Spain
| | - Diego Santos-Garcia
- Laboratory of Biometry and Evolutionary Biology UMR CNRS, University of Lyon, Villeurbanne, France
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiang Y. Han
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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14
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Feng Y, Wang Z, Chien KY, Chen HL, Liang YH, Hua X, Chiu CH. "Pseudo-pseudogenes" in bacterial genomes: Proteogenomics reveals a wide but low protein expression of pseudogenes in Salmonella enterica. Nucleic Acids Res 2022; 50:5158-5170. [PMID: 35489061 PMCID: PMC9122581 DOI: 10.1093/nar/gkac302] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudogenes (genes disrupted by frameshift or in-frame stop codons) are ubiquitously present in the bacterial genome and considered as nonfunctional fossil. Here, we used RNA-seq and mass-spectrometry technologies to measure the transcriptomes and proteomes of Salmonella enterica serovars Paratyphi A and Typhi. All pseudogenes’ mRNA sequences remained disrupted, and were present at comparable levels to their intact homologs. At the protein level, however, 101 out of 161 pseudogenes suggested successful translation, with their low expression regardless of growth conditions, genetic background and pseudogenization causes. The majority of frameshifting detected was compensatory for -1 frameshift mutations. Readthrough of in-frame stop codons primarily involved UAG; and cytosine was the most frequent base adjacent to the codon. Using a fluorescence reporter system, fifteen pseudogenes were confirmed to express successfully in vivo in Escherichia coli. Expression of the intact copy of the fifteen pseudogenes in S. Typhi affected bacterial pathogenesis as revealed in human macrophage and epithelial cell infection models. The above findings suggest the need to revisit the nonstandard translation mechanism as well as the biological role of pseudogenes in the bacterial genome.
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Affiliation(s)
- Ye Feng
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Zeyu Wang
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Kun-Yi Chien
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China
| | - Hsiu-Ling Chen
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Yi-Hua Liang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China
| | - Xiaoting Hua
- Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Cheng-Hsun Chiu
- Graduate Institute of Biomedical Sciences, Chang Gung University College of Medicine, Taoyuan, Republic of China.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Republic of China.,Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Republic of China
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15
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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae). THE ISME JOURNAL 2022; 16:642-654. [PMID: 34508228 PMCID: PMC8857208 DOI: 10.1038/s41396-021-01102-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023]
Abstract
Many plant-sap-feeding insects have maintained a single, obligate, nutritional symbiont over the long history of their lineage. This senior symbiont may be joined by one or more junior symbionts that compensate for gaps in function incurred through genome-degradative forces. Adelgids are sap-sucking insects that feed solely on conifer trees and follow complex life cycles in which the diet fluctuates in nutrient levels. Adelgids are unusual in that both senior and junior symbionts appear to have been replaced repeatedly over their evolutionary history. Genomes can provide clues to understanding symbiont replacements, but only the dual symbionts of hemlock adelgids have been examined thus far. Here, we sequence and compare genomes of four additional dual-symbiont pairs in adelgids. We show that these symbionts are nutritional partners originating from diverse bacterial lineages and exhibiting wide variation in general genome characteristics. Although dual symbionts cooperate to produce nutrients, the balance of contributions varies widely across pairs, and total genome contents reflect a range of ages and degrees of degradation. Most symbionts appear to be in transitional states of genome reduction. Our findings support a hypothesis of periodic symbiont turnover driven by fluctuating selection for nutritional provisioning related to gains and losses of complex life cycles in their hosts.
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16
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Dieng MM, Dera KSM, Moyaba P, Ouedraogo GMS, Demirbas-Uzel G, Gstöttenmayer F, Mulandane FC, Neves L, Mdluli S, Rayaisse JB, Belem AMG, Pagabeleguem S, de Beer CJ, Parker AG, Van Den Abbeele J, Mach RL, Vreysen MJB, Abd-Alla AMM. Prevalence of Trypanosoma and Sodalis in wild populations of tsetse flies and their impact on sterile insect technique programmes for tsetse eradication. Sci Rep 2022; 12:3322. [PMID: 35228552 PMCID: PMC8885713 DOI: 10.1038/s41598-022-06699-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/03/2022] [Indexed: 11/24/2022] Open
Abstract
The sterile insect technique (SIT) is an environment friendly and sustainable method to manage insect pests of economic importance through successive releases of sterile irradiated males of the targeted species to a defined area. A mating of a sterile male with a virgin wild female will result in no offspring, and ultimately lead to the suppression or eradication of the targeted population. Tsetse flies, vectors of African Trypanosoma, have a highly regulated and defined microbial fauna composed of three bacterial symbionts that may have a role to play in the establishment of Trypanosoma infections in the flies and hence, may influence the vectorial competence of the released sterile males. Sodalis bacteria seem to interact with Trypanosoma infection in tsetse flies. Field-caught tsetse flies of ten different taxa and from 15 countries were screened using PCR to detect the presence of Sodalis and Trypanosoma species and analyse their interaction. The results indicate that the prevalence of Sodalis and Trypanosoma varied with country and tsetse species. Trypanosome prevalence was higher in east, central and southern African countries than in west African countries. Tsetse fly infection rates with Trypanosoma vivax and T. brucei sspp were higher in west African countries, whereas tsetse infection with T. congolense and T. simiae, T. simiae (tsavo) and T. godfreyi were higher in east, central and south African countries. Sodalis prevalence was high in Glossina morsitans morsitans and G. pallidipes but absent in G. tachinoides. Double and triple infections with Trypanosoma taxa and coinfection of Sodalis and Trypanosoma were rarely observed but it occurs in some taxa and locations. A significant Chi square value (< 0.05) seems to suggest that Sodalis and Trypanosoma infection correlate in G. palpalis gambiensis, G. pallidipes and G. medicorum. Trypanosoma infection seemed significantly associated with an increased density of Sodalis in wild G. m. morsitans and G. pallidipes flies, however, there was no significant impact of Sodalis infection on trypanosome density.
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Affiliation(s)
- Mouhamadou M Dieng
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria
| | - Kiswend-Sida M Dera
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria.,Insectarium de Bobo Dioulasso-Campagne d'Eradication de la mouche tsetse et de la Trypanosomose (IBD-CETT), 01 BP 1087, Bobo Dioulasso 01, Burkina Faso
| | - Percy Moyaba
- Epidemiology, Vectors and Parasites, Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa
| | - Gisele M S Ouedraogo
- Insectarium de Bobo Dioulasso-Campagne d'Eradication de la mouche tsetse et de la Trypanosomose (IBD-CETT), 01 BP 1087, Bobo Dioulasso 01, Burkina Faso
| | - Guler Demirbas-Uzel
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria
| | - Fabian Gstöttenmayer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria
| | - Fernando C Mulandane
- University Eduardo Mondlane, Centro de Biotecnologia, Av. de Moçambique Km 1.5, Maputo, Mozambique
| | - Luis Neves
- University Eduardo Mondlane, Centro de Biotecnologia, Av. de Moçambique Km 1.5, Maputo, Mozambique.,Department of Veterinary Tropical Diseases, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Sihle Mdluli
- Epidemiology Unit, Department of Veterinary Services, PO Box 4192, Manzini, Eswatini
| | - Jean-Baptiste Rayaisse
- Centre International de Recherche-Développement sur l'Elevage en zone Subhumide (CIRDES), 01 BP 454, Bobo-Dioulasso 01, Burkina Faso
| | | | - Soumaïla Pagabeleguem
- Insectarium de Bobo Dioulasso-Campagne d'Eradication de la mouche tsetse et de la Trypanosomose (IBD-CETT), 01 BP 1087, Bobo Dioulasso 01, Burkina Faso.,University of Dedougou, B.P. 176, Dédougou 01, Burkina Faso
| | - Chantel J de Beer
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria.,Epidemiology, Vectors and Parasites, Agricultural Research Council-Onderstepoort Veterinary Research, Pretoria, South Africa
| | | | | | - Robert L Mach
- Institute of Chemical, Environmental, and Bioscience Engineering, Vienna University of Technology, Gumpendorfer Straße 1a, 1060, Vienna, Austria
| | - Marc J B Vreysen
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, 1400, Vienna, Austria.
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17
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Cooper WR, Horton DR, Swisher-Grimm K, Krey K, Wildung MR. Bacterial Endosymbionts of Bactericera maculipennis and Three Mitochondrial Haplotypes of B. cockerelli (Hemiptera: Psylloidea: Triozidae). ENVIRONMENTAL ENTOMOLOGY 2022; 51:94-107. [PMID: 34864906 DOI: 10.1093/ee/nvab133] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Indexed: 06/13/2023]
Abstract
Insects harbor bacterial endosymbionts that provide their hosts with nutritional benefit or with protection against natural enemies, plant defenses, insecticides, or abiotic stresses. We used directed sequencing of 16S rDNA to identify and compare endosymbionts of Bactericera maculipennis (Crawford) and the western, central, and northwestern haplotypes of B. cockerelli (Šulc) (Hemiptera: Psylloidea: Triozidae). Both species are native to North America, are known to harbor the plant pathogen 'Candidatus Liberibacter solanacearum' and develop on shared host plants within the Convolvulaceae. The Old-World species Heterotrioza chenopodii (Reuter) (Psylloidea: Triozidae), now found in North America, was included as an outgroup. 16S sequencing confirmed that both Bactericera species harbor 'Candidatus Liberibacter solanacearum' and revealed that both species harbor unique strains of Wolbachia and Sodalis. However, the presence of Wolbachia and Sodalis varied among haplotypes of B. cockerelli. The central and western haplotypes harbored the same strains of Wolbachia, which was confirmed by Sanger sequencing of the wsp and ftsZ genes. Wolbachia was also detected in very low abundance from the northwestern haplotype by high-throughput sequencing of 16S but was not detected from this haplotype by PCR screening. The northwestern and central haplotypes also harbored Sodalis, which was not detected in the western haplotype. Heterotrioza chenopodii harbored an entirely different community of potential endosymbionts compared with the Bactericera spp. that included Rickettsia and an unidentified bacterium in the Enterobacteriaceae. Results of this study provide a foundation for further research on the interactions between psyllids and their bacterial endosymbionts.
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Affiliation(s)
- W Rodney Cooper
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, 5230 Konnowac Pass Road, Wapato, WA 98951, USA
| | - David R Horton
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, 5230 Konnowac Pass Road, Wapato, WA 98951, USA
| | - Kylie Swisher-Grimm
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, Prosser, WA 99350, USA
| | - Karol Krey
- Temperate Tree Fruit and Vegetable Research Unit, USDA-ARS, 5230 Konnowac Pass Road, Wapato, WA 98951, USA
| | - Mark R Wildung
- Laboratory for Bioinformatics and Bioanalysis, Washington State University, Pullman, WA 99164, USA
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18
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Diversity and dynamics of bacteria at the Chrysomya megacephala pupal stage revealed by third-generation sequencing. Sci Rep 2022; 12:2006. [PMID: 35132164 PMCID: PMC8821589 DOI: 10.1038/s41598-022-06311-7] [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: 10/08/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022] Open
Abstract
Characterization of the microbial community is essential for understanding the symbiotic relationships between microbes and host insects. Chrysomya megacephala is a vital resource, a forensic insect, a pollinator, and a vector for enteric bacteria, protozoa, helminths, and viruses. However, research on its microbial community is incomprehensive, particularly at the pupal stage, which comprises approximately half of the entire larval development stage and is important entomological evidence in forensic medicine. For the first time, this study investigated the bacterial communities of C. megacephala pupae at different ages using third-generation sequencing technology. The results showed that C. megacephala has a diverse and dynamic bacterial community. Cluster analysis at ≥ 97% similarity produced 154 operational taxonomic units (OTUs) that belonged to 10 different phyla and were distributed into 15 classes, 28 orders, 50 families, 88 genera, and 130 species. Overall, the number of bacterial OTUs increased with the development of pupae, and the relative abundance of Wolbachia in the Day5 group was significantly lower than that in the other groups. Within the pupal stage, Proteobacteria, Firmicutes, and Bacteroidetes were the dominant phyla of bacteria. At the genus level, Wolbachia and Ignatzschineria coexisted, a rarely known feature. In addition, we found Erysipelothrix rhusiopathiae, the etiological agent of swine erysipelas, which is rarely identified in insects. This study enriches the understanding of the microbial community of C. megacephala and provides a reference for better utilization and control of C. megacephala.
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19
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Prigot-Maurice C, Beltran-Bech S, Braquart-Varnier C. Why and how do protective symbionts impact immune priming with pathogens in invertebrates? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 126:104245. [PMID: 34453995 DOI: 10.1016/j.dci.2021.104245] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Growing evidence demonstrates that invertebrates display adaptive-like immune abilities, commonly known as "immune priming". Immune priming is a process by which a host improves its immune defences following an initial pathogenic exposure, leading to better protection after a subsequent infection with the same - or different - pathogens. Nevertheless, beneficial symbionts can enhance similar immune priming processes in hosts, such as when they face repeated infections with pathogens. This "symbiotic immune priming" protects the host against pathogenic viruses, bacteria, fungi, or eukaryotic parasites. In this review, we explore the extent to which protective symbionts interfere and impact immune priming against pathogens from both a mechanical (proximal) and an evolutionary (ultimate) point of view. We highlight that the immune priming of invertebrates is the cornerstone of the tripartite interaction of hosts/symbionts/pathogens. The main shared mechanism of immune priming (induced by symbionts or pathogens) is the sustained immune response at the beginning of host-microbial interactions. However, the evolutionary outcome of immune priming leads to a specific discrimination, which provides enhanced tolerance or resistance depending on the type of microbe. Based on several studies testing immune priming against pathogens in the presence or absence of protective symbionts, we observed that both types of immune priming could overlap and affect each other inside the same hosts. As protective symbionts could be an evolutionary force that influences immune priming, they may help us to better understand the heterogeneity of pathogenic immune priming across invertebrate populations and species.
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Affiliation(s)
- Cybèle Prigot-Maurice
- Université de Poitiers - UFR Sciences Fondamentales et Appliquées, Laboratoire Écologie et Biologie des Interactions - UMR CNRS 7267, Bâtiment B8-B35, 5 rue Albert Turpin, TSA 51106, F, 86073, POITIERS Cedex 9, France.
| | - Sophie Beltran-Bech
- Université de Poitiers - UFR Sciences Fondamentales et Appliquées, Laboratoire Écologie et Biologie des Interactions - UMR CNRS 7267, Bâtiment B8-B35, 5 rue Albert Turpin, TSA 51106, F, 86073, POITIERS Cedex 9, France
| | - Christine Braquart-Varnier
- Université de Poitiers - UFR Sciences Fondamentales et Appliquées, Laboratoire Écologie et Biologie des Interactions - UMR CNRS 7267, Bâtiment B8-B35, 5 rue Albert Turpin, TSA 51106, F, 86073, POITIERS Cedex 9, France
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Interactions of the Intracellular Bacterium Cardinium with Its Host, the House Dust Mite Dermatophagoides farinae, Based on Gene Expression Data. mSystems 2021; 6:e0091621. [PMID: 34726490 PMCID: PMC8562489 DOI: 10.1128/msystems.00916-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dermatophagoides farinae is inhabited by an intracellular bacterium, Cardinium. Using correlations between host and symbiont gene expression profiles, we identified several important molecular pathways that potentially regulate/facilitate their interactions. The expression of Cardinium genes collectively explained 95% of the variation in the expression of mite genes assigned to pathways for phagocytosis, apoptosis, the MAPK signaling cascade, endocytosis, the tumor necrosis factor (TNF) pathway, the transforming growth factor beta (TGF-β) pathway, lysozyme, and the Toll/Imd pathway. In addition, expression of mite genes explained 76% of the variability in Cardinium gene expression. In particular, the expression of the Cardinium genes encoding the signaling molecules BamD, LepA, SymE, and VirD4 was either positively or negatively correlated with the expression levels of mite genes involved in endocytosis, phagocytosis, and apoptosis. We also found that Cardinium possesses a complete biosynthetic pathway for lipoic acid and may provide lipoate, but not biotin, to mites. Cardinium gene expression collectively explained 84% of the variation in expression related to several core mite metabolic pathways, and, most notably, a negative correlation was observed between bacterial gene expression and expression of mite genes assigned to the glycolysis and citric acid cycle pathways. Furthermore, we showed that Cardinium gene expression is correlated with expression levels of genes associated with terpenoid backbone biosynthesis. This pathway is important for the synthesis of pheromones, thus providing an opportunity for Cardinium to influence mite reproductive behavior to facilitate transmission of the bacterium. Overall, our study provided correlational gene expression data that can be useful for future research on mite-Cardinium interactions. IMPORTANCE The molecular mechanisms of mite-symbiont interactions and their impacts on human health are largely unknown. Astigmatid mites, such as house dust and stored-product mites, are among the most significant allergen sources worldwide. Although mites themselves are the main allergen sources, recent studies have indicated that mite-associated microbiomes may have implications for allergen production and human health. The major medically important house dust mite, D. farinae, is known to harbor a highly abundant intracellular bacterium belonging to the genus Cardinium. Expression analysis of the mite and symbiont genes can identify key mite molecular pathways that facilitate interactions with this endosymbiont and possibly shed light on how this bacterium affects mite allergen production and physiology in general.
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Kennedy SJ, Atkinson CGF, Tomlinson BR, Hammond L, Eswara P, Baker BJ, Shaw LN. Phenogenomic Characterization of a Newly Domesticated and Novel Species from the Genus Verrucosispora. Appl Environ Microbiol 2021; 87:e0132721. [PMID: 34495705 PMCID: PMC8552891 DOI: 10.1128/aem.01327-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/31/2021] [Indexed: 11/20/2022] Open
Abstract
The concept of bacterial dark matter stems from our inability to culture most microbes and represents a fundamental gap in our knowledge of microbial diversity. Here, we present the domestication of such an organism: a previously uncultured, novel species from the rare Actinomycetes genus Verrucosispora. Although initial recovery took >4 months, isolation of phenotypically distinct, domesticated generations occurred within weeks. Two isolates were subjected to phenogenomic analyses, revealing domestication correlated with enhanced growth rates in nutrient-rich media but diminished capacity to metabolize diverse amino acids. This is seemingly mediated by genomic atrophy through a mixed approach of pseudogenization and reversion of pseudogenization of amino acid metabolism genes. Conversely, later generational strains had enhanced spore germination rates, potentially through the reversion of a sporulation-associated kinase from pseudogene to true gene status. We observed that our most wild-type isolate had the greatest potential for antibacterial activity, which correlated with extensive mutational attrition of biosynthetic gene clusters in domesticated strains. Comparative analyses revealed wholesale genomic reordering in strains, with widespread single nucleotide polymorphism, indel, and pseudogene-impactful mutations observed. We hypothesize that domestication of this previously unculturable organism resulted from the shedding of genomic flexibility required for life in a dynamic marine environment, parsing out genetic redundancy to allow for a newfound cultivable amenability. IMPORTANCE The majority of environmental bacteria cannot be cultured within the laboratory. Understanding why only certain environmental isolates can be recovered is key to unlocking the abundant microbial dark matter that is widespread on our planet. In this study, we present not only the culturing but domestication of just such an organism. Although initial recovery took >4 months, we were able to isolate distinct, subpassaged offspring from the originating colony within mere weeks. A phenotypic and genotypic analysis of our generational strains revealed that adaptation to life in the lab occurred as a result of wholesale mutational changes. These permitted an enhanced ability for growth in nutrient rich media but came at the expense of reduced genomic flexibility. We suggest that without dynamic natural environmental stressors our domesticated strains effectively underwent genomic atrophy as they adapted to static conditions experienced in the laboratory.
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Affiliation(s)
- Sarah J. Kennedy
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Celine Grace F. Atkinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Brooke R. Tomlinson
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Lauren Hammond
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Prahathees Eswara
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
| | - Bill J. Baker
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Lindsey N. Shaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida, Tampa, Florida, USA
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22
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Garber AI, Kupper M, Laetsch DR, Weldon SR, Ladinsky MS, Bjorkman PJ, McCutcheon JP. The Evolution of Interdependence in a Four-Way Mealybug Symbiosis. Genome Biol Evol 2021; 13:evab123. [PMID: 34061185 PMCID: PMC8331144 DOI: 10.1093/gbe/evab123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 01/03/2023] Open
Abstract
Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a single betaproteobacterial endosymbiont, a Candidatus Tremblaya species (hereafter Tremblaya) that alone provides the insect with its required nutrients. Other mealybugs have two nutritional endosymbionts that together provision these same nutrients, where Tremblaya has gained a gammaproteobacterial partner that resides in its cytoplasm. Previous work had established that Pseudococcus longispinus mealybugs maintain not one but two species of gammaproteobacterial endosymbionts along with Tremblaya. Preliminary genomic analyses suggested that these two gammaproteobacterial endosymbionts have large genomes with features consistent with a relatively recent origin as insect endosymbionts, but the patterns of genomic complementarity between members of the symbiosis and their relative cellular locations were unknown. Here, using long-read sequencing and various types of microscopy, we show that the two gammaproteobacterial symbionts of P. longispinus are mixed together within Tremblaya cells, and that their genomes are somewhat reduced in size compared with their closest nonendosymbiotic relatives. Both gammaproteobacterial genomes contain thousands of pseudogenes, consistent with a relatively recent shift from a free-living to an endosymbiotic lifestyle. Biosynthetic pathways of key metabolites are partitioned in complex interdependent patterns among the two gammaproteobacterial genomes, the Tremblaya genome, and horizontally acquired bacterial genes that are encoded on the mealybug nuclear genome. Although these two gammaproteobacterial endosymbionts have been acquired recently in evolutionary time, they have already evolved codependencies with each other, Tremblaya, and their insect host.
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Affiliation(s)
- Arkadiy I Garber
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Maria Kupper
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephanie R Weldon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Mark S Ladinsky
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Pamela J Bjorkman
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - John P McCutcheon
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Biodesign Center for Mechanisms of Evolution and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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Tláskal V, Pylro VS, Žifčáková L, Baldrian P. Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood. Front Microbiol 2021; 12:668644. [PMID: 34177846 PMCID: PMC8226273 DOI: 10.3389/fmicb.2021.668644] [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] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 11/19/2022] Open
Abstract
The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.
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Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Victor Satler Pylro
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
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Medina Munoz M, Brenner C, Richmond D, Spencer N, Rio RVM. The holobiont transcriptome of teneral tsetse fly species of varying vector competence. BMC Genomics 2021; 22:400. [PMID: 34058984 PMCID: PMC8166097 DOI: 10.1186/s12864-021-07729-5] [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] [Received: 11/29/2020] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Background Tsetse flies are the obligate vectors of African trypanosomes, which cause Human and Animal African Trypanosomiasis. Teneral flies (newly eclosed adults) are especially susceptible to parasite establishment and development, yet our understanding of why remains fragmentary. The tsetse gut microbiome is dominated by two Gammaproteobacteria, an essential and ancient mutualist Wigglesworthia glossinidia and a commensal Sodalis glossinidius. Here, we characterize and compare the metatranscriptome of teneral Glossina morsitans to that of G. brevipalpis and describe unique immunological, physiological, and metabolic landscapes that may impact vector competence differences between these two species. Results An active expression profile was observed for Wigglesworthia immediately following host adult metamorphosis. Specifically, ‘translation, ribosomal structure and biogenesis’ followed by ‘coenzyme transport and metabolism’ were the most enriched clusters of orthologous genes (COGs), highlighting the importance of nutrient transport and metabolism even following host species diversification. Despite the significantly smaller Wigglesworthia genome more differentially expressed genes (DEGs) were identified between interspecific isolates (n = 326, ~ 55% of protein coding genes) than between the corresponding Sodalis isolates (n = 235, ~ 5% of protein coding genes) likely reflecting distinctions in host co-evolution and adaptation. DEGs between Sodalis isolates included genes involved in chitin degradation that may contribute towards trypanosome susceptibility by compromising the immunological protection provided by the peritrophic matrix. Lastly, G. brevipalpis tenerals demonstrate a more immunologically robust background with significant upregulation of IMD and melanization pathways. Conclusions These transcriptomic differences may collectively contribute to vector competence differences between tsetse species and offers translational relevance towards the design of novel vector control strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07729-5.
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Affiliation(s)
- Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Caitlyn Brenner
- Department of Biology, Washington and Jefferson College, Washington, PA, 15301, USA
| | - Dylan Richmond
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Noah Spencer
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Rita V M Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, 26505, USA.
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25
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Demirbas-Uzel G, Augustinos AA, Doudoumis V, Parker AG, Tsiamis G, Bourtzis K, Abd-Alla AMM. Interactions Between Tsetse Endosymbionts and Glossina pallidipes Salivary Gland Hypertrophy Virus in Glossina Hosts. Front Microbiol 2021; 12:653880. [PMID: 34122367 PMCID: PMC8194091 DOI: 10.3389/fmicb.2021.653880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
Tsetse flies are the sole cyclic vector for trypanosomosis, the causative agent for human African trypanosomosis or sleeping sickness and African animal trypanosomosis or nagana. Tsetse population control is the most efficient strategy for animal trypanosomosis control. Among all tsetse control methods, the Sterile Insect Technique (SIT) is one of the most powerful control tactics to suppress or eradicate tsetse flies. However, one of the challenges for the implementation of SIT is the mass production of target species. Tsetse flies have a highly regulated and defined microbial fauna composed of three bacterial symbionts (Wigglesworthia, Sodalis and Wolbachia) and a pathogenic Glossina pallidipes Salivary Gland Hypertrophy Virus (GpSGHV) which causes reproduction alterations such as testicular degeneration and ovarian abnormalities with reduced fertility and fecundity. Interactions between symbionts and GpSGHV might affect the performance of the insect host. In the present study, we assessed the possible impact of GpSGHV on the prevalence of tsetse endosymbionts under laboratory conditions to decipher the bidirectional interactions on six Glossina laboratory species. The results indicate that tsetse symbiont densities increased over time in tsetse colonies with no clear impact of the GpSGHV infection on symbionts density. However, a positive correlation between the GpSGHV and Sodalis density was observed in Glossina fuscipes species. In contrast, a negative correlation between the GpSGHV density and symbionts density was observed in the other taxa. It is worth noting that the lowest Wigglesworthia density was observed in G. pallidipes, the species which suffers most from GpSGHV infection. In conclusion, the interactions between GpSGHV infection and tsetse symbiont infections seems complicated and affected by the host and the infection density of the GpSGHV and tsetse symbionts.
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Affiliation(s)
- Güler Demirbas-Uzel
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Antonios A Augustinos
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Vangelis Doudoumis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, Agrinio, Greece
| | - Andrew G Parker
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, Agrinio, Greece
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | - Adly M M Abd-Alla
- Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria
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Incipient genome erosion and metabolic streamlining for antibiotic production in a defensive symbiont. Proc Natl Acad Sci U S A 2021; 118:2023047118. [PMID: 33883280 PMCID: PMC8092579 DOI: 10.1073/pnas.2023047118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genome reduction is commonly observed in bacteria of several phyla engaging in obligate nutritional symbioses with insects. In Actinobacteria, however, little is known about the process of genome evolution, despite their importance as prolific producers of antibiotics and their increasingly recognized role as defensive partners of insects and other organisms. Here, we show that “Streptomyces philanthi,” a defensive symbiont of digger wasps, has a G+C-enriched genome in the early stages of erosion, with inactivating mutations in a large proportion of genes, causing dependency on its hosts for certain nutrients, which was validated in axenic symbiont cultures. Additionally, overexpressed catabolic and biosynthetic pathways of the bacteria inside the host indicate host–symbiont metabolic integration for streamlining and control of antibiotic production. Genome erosion is a frequently observed result of relaxed selection in insect nutritional symbionts, but it has rarely been studied in defensive mutualisms. Solitary beewolf wasps harbor an actinobacterial symbiont of the genus Streptomyces that provides protection to the developing offspring against pathogenic microorganisms. Here, we characterized the genomic architecture and functional gene content of this culturable symbiont using genomics, transcriptomics, and proteomics in combination with in vitro assays. Despite retaining a large linear chromosome (7.3 Mb), the wasp symbiont accumulated frameshift mutations in more than a third of its protein-coding genes, indicative of incipient genome erosion. Although many of the frameshifted genes were still expressed, the encoded proteins were not detected, indicating post-transcriptional regulation. Most pseudogenization events affected accessory genes, regulators, and transporters, but “Streptomyces philanthi” also experienced mutations in central metabolic pathways, resulting in auxotrophies for biotin, proline, and arginine that were confirmed experimentally in axenic culture. In contrast to the strong A+T bias in the genomes of most obligate symbionts, we observed a significant G+C enrichment in regions likely experiencing reduced selection. Differential expression analyses revealed that—compared to in vitro symbiont cultures—“S. philanthi” in beewolf antennae showed overexpression of genes for antibiotic biosynthesis, the uptake of host-provided nutrients and the metabolism of building blocks required for antibiotic production. Our results show unusual traits in the early stage of genome erosion in a defensive symbiont and suggest tight integration of host–symbiont metabolic pathways that effectively grants the host control over the antimicrobial activity of its bacterial partner.
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Gabrieli P, Caccia S, Varotto-Boccazzi I, Arnoldi I, Barbieri G, Comandatore F, Epis S. Mosquito Trilogy: Microbiota, Immunity and Pathogens, and Their Implications for the Control of Disease Transmission. Front Microbiol 2021; 12:630438. [PMID: 33889137 PMCID: PMC8056039 DOI: 10.3389/fmicb.2021.630438] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
In mosquitoes, the interaction between the gut microbiota, the immune system, and the pathogens that these insects transmit to humans and animals is regarded as a key component toward the development of control strategies, aimed at reducing the burden of severe diseases, such as malaria and dengue fever. Indeed, different microorganisms from the mosquito microbiota have been investigated for their ability to affect important traits of the biology of the host insect, related with its survival, development and reproduction. Furthermore, some microorganisms have been shown to modulate the immune response of mosquito females, significantly shaping their vector competence. Here, we will review current knowledge in this field, focusing on i) the complex interaction between the intestinal microbiota and mosquito females defenses, both in the gut and at humoral level; ii) how knowledge on these issues contributes to the development of novel and targeted strategies for the control of mosquito-borne diseases such as the use of paratransgenesis or taking advantage of the relationship between Wolbachia and mosquito hosts. We conclude by providing a brief overview of available knowledge on microbiota-immune system interplay in major insect vectors.
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Affiliation(s)
- Paolo Gabrieli
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Silvia Caccia
- Department of Agricultural Sciences, University of Naples "Federico II", Naples, Italy.,Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Ilaria Varotto-Boccazzi
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Irene Arnoldi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Giulia Barbieri
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Francesco Comandatore
- "L. Sacco" Department of Biomedical and Clinical Sciences, Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
| | - Sara Epis
- Department of Biosciences and Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", University of Milan, Milan, Italy
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Abstract
Bacteriophages (phages) are ubiquitous in nature. These viruses play a number of central roles in microbial ecology and evolution by, for instance, promoting horizontal gene transfer (HGT) among bacterial species. The ability of phages to mediate HGT through transduction has been widely exploited as an experimental tool for the genetic study of bacteria. As such, bacteriophage P1 represents a prototypical generalized transducing phage with a broad host range that has been extensively employed in the genetic manipulation of Escherichia coli and a number of other model bacterial species. Here we demonstrate that P1 is capable of infecting, lysogenizing, and promoting transduction in members of the bacterial genus Sodalis, including the maternally inherited insect endosymbiont Sodalis glossinidius. While establishing new tools for the genetic study of these bacterial species, our results suggest that P1 may be used to deliver DNA to many Gram-negative endosymbionts in their insect host, thereby circumventing a culturing requirement to genetically manipulate these organisms. IMPORTANCE A large number of economically important insects maintain intimate associations with maternally inherited endosymbiotic bacteria. Due to the inherent nature of these associations, insect endosymbionts cannot be usually isolated in pure culture or genetically manipulated. Here we use a broad-host-range bacteriophage to deliver exogenous DNA to an insect endosymbiont and a closely related free-living species. Our results suggest that broad-host-range bacteriophages can be used to genetically alter insect endosymbionts in their insect host and, as a result, bypass a culturing requirement to genetically alter these bacteria.
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Bacterial Symbionts of Tsetse Flies: Relationships and Functional Interactions Between Tsetse Flies and Their Symbionts. Results Probl Cell Differ 2021; 69:497-536. [PMID: 33263885 DOI: 10.1007/978-3-030-51849-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Tsetse flies (Glossina spp.) act as the sole vectors of the African trypanosome species that cause Human African Trypanosomiasis (HAT or African Sleeping Sickness) and Nagana in animals. These flies have undergone a variety of specializations during their evolution including an exclusive diet consisting solely of vertebrate blood for both sexes as well as an obligate viviparous reproductive biology. Alongside these adaptations, Glossina species have developed intricate relationships with specific microbes ranging from mutualistic to parasitic. These relationships provide fundamental support required to sustain the specializations associated with tsetse's biology. This chapter provides an overview on the knowledge to date regarding the biology behind these relationships and focuses primarily on four bacterial species that are consistently associated with Glossina species. Here their interactions with the host are reviewed at the morphological, biochemical and genetic levels. This includes: the obligate symbiont Wigglesworthia, which is found in all tsetse species and is essential for nutritional supplementation to the blood-specific diet, immune system maturation and facilitation of viviparous reproduction; the commensal symbiont Sodalis, which is a frequently associated symbiont optimized for survival within the fly via nutritional adaptation, vertical transmission through mating and may alter vectorial capacity of Glossina for trypanosomes; the parasitic symbiont Wolbachia, which can manipulate Glossina via cytoplasmic incompatibility and shows unique interactions at the genetic level via horizontal transmission of its genetic material into the genome in two Glossina species; finally, knowledge on recently observed relations between Spiroplasma and Glossina is explored and potential interactions are discussed based on knowledge of interactions between this bacterial Genera and other insect species. These flies have a simple microbiome relative to that of other insects. However, these relationships are deep, well-studied and provide a window into the complexity and function of host/symbiont interactions in an important disease vector.
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Sontowski R, Gerth M, Richter S, Gruppe A, Schlegel M, van Dam NM, Bleidorn C. Infection Patterns and Fitness Effects of Rickettsia and Sodalis Symbionts in the Green Lacewing Chrysoperla carnea. INSECTS 2020; 11:insects11120867. [PMID: 33297293 PMCID: PMC7762206 DOI: 10.3390/insects11120867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Bacteria have occupied a wide range of habitats including insect hosts. There they can strongly affect host physiology and ecology in a positive or negative way. Bacteria living exclusively inside other organisms are called endosymbionts. They often establish a long-term and stable association with their host. Although more and more studies focus on endosymbiont–insect interactions, the group of Neuroptera is largely neglected in such studies. We were interested in the common green lacewing (Chrysoperla carnea), a representative of Neuroptera, which is mainly known for its use in biological pest control. We asked ourselves which endosymbionts are present in these lacewings. By screening natural and laboratory populations, we found that the endosymbiont Rickettsia is present in all populations but the symbiont Sodalis only occurred in laboratory populations. We were curious whether both endosymbionts affect reproduction success. Through establishing and studying green lacewing lines carrying different endosymbionts, we found that Rickettsia had no effect on the insect reproduction, while Sodalis reduced the number of eggs laid by lacewings, alone and in co-infections with Rickettsia. The economic and ecological importance of green lacewings in biological pest control warrants a more profound understanding of its biology, which might be strongly influenced by symbionts. Abstract Endosymbionts are widely distributed in insects and can strongly affect their host ecology. The common green lacewing (Chrysoperla carnea) is a neuropteran insect which is widely used in biological pest control. However, their endosymbionts and their interactions with their hosts have not been very well studied. Therefore, we screened for endosymbionts in natural and laboratory populations of Ch. carnea using diagnostic PCR amplicons. We found the endosymbiont Rickettsia to be very common in all screened natural and laboratory populations, while a hitherto uncharacterized Sodalis strain was found only in laboratory populations. By establishing lacewing lines with no, single or co-infections of Sodalis and Rickettsia, we found a high vertical transmission rate for both endosymbionts (>89%). However, we were only able to estimate these numbers for co-infected lacewings. Sodalis negatively affected the reproductive success in single and co-infected Ch. carnea, while Rickettsia showed no effect. We hypothesize that the fitness costs accrued by Sodalis infections might be more tolerable in the laboratory than in natural populations, as the latter are also prone to fluctuating environmental conditions and natural enemies. The economic and ecological importance of lacewings in biological pest control warrants a more profound understanding of its biology, which might be influenced by symbionts.
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Affiliation(s)
- Rebekka Sontowski
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; (R.S.); (M.S.); (N.M.v.D.)
- Institute of Biodiversity, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Michael Gerth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK;
| | - Sandy Richter
- Department of Basic and Clinical Neuroscience, King’s College London, 5 Cutcombe Road, London SE5 9RT, UK;
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, 04109 Leipzig, Germany
| | - Axel Gruppe
- Chair of Zoology—Entomology Group, Technical University of Munich, 85354 Freising, Germany;
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; (R.S.); (M.S.); (N.M.v.D.)
- Institute of Biology, Molecular Evolution and Systematics of Animals, University of Leipzig, 04109 Leipzig, Germany
| | - Nicole M. van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; (R.S.); (M.S.); (N.M.v.D.)
- Institute of Biodiversity, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Christoph Bleidorn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; (R.S.); (M.S.); (N.M.v.D.)
- Animal Evolution and Biodiversity, Georg-Augustus-University, 37073 Göttingen, Germany
- Correspondence: ; Tel.: +49-5513925459
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Abstract
Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission. Stable associations between insects and bacterial species are widespread in nature. This is the case for many economically important insects, such as tsetse flies. Tsetse flies are the vectors of Trypanosoma brucei, the etiological agent of African trypanosomiasis—a zoonotic disease that incurs a high socioeconomic cost in regions of endemicity. Populations of tsetse flies are often infected with the bacterium Sodalis glossinidius. Following infection, S. glossinidius establishes a chronic, stable association characterized by vertical (maternal) and horizontal (paternal) modes of transmission. Due to the stable nature of this association, S. glossinidius has been long sought as a means for the implementation of anti-Trypanosoma paratransgenesis in tsetse flies. However, the lack of tools for the genetic modification of S. glossinidius has hindered progress in this area. Here, we establish that S. glossinidius is amenable to DNA uptake by conjugation. We show that conjugation can be used as a DNA delivery method to conduct forward and reverse genetic experiments in this bacterium. This study serves as an important step in the development of genetic tools for S. glossinidius. The methods highlighted here should guide the implementation of genetics for the study of the tsetse-Sodalis association and the evaluation of S. glossinidius-based tsetse fly paratransgenesis strategies. IMPORTANCE Tsetse flies are the insect vectors of T. brucei, the causative agent of African sleeping sickness—a zoonotic disease that inflicts a substantial economic cost on a broad region of sub-Saharan Africa. Notably, tsetse flies can be infected with the bacterium S. glossinidius to establish an asymptomatic chronic infection. This infection can be inherited by future generations of tsetse flies, allowing S. glossinidius to spread and persist within populations. To this effect, S. glossinidius has been considered a potential expression platform to create flies which reduce T. brucei stasis and lower overall parasite transmission to humans and animals. However, the efficient genetic manipulation of S. glossinidius has remained a technical challenge due to its complex growth requirements and uncharacterized physiology. Here, we exploit a natural mechanism of DNA transfer among bacteria and develop an efficient technique to genetically manipulate S. glossinidius for future studies in reducing trypanosome transmission.
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De Maayer P, Pillay T, Coutinho TA. Flagella by numbers: comparative genomic analysis of the supernumerary flagellar systems among the Enterobacterales. BMC Genomics 2020; 21:670. [PMID: 32993503 PMCID: PMC7526173 DOI: 10.1186/s12864-020-07085-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/21/2020] [Indexed: 01/17/2023] Open
Abstract
Background Flagellar motility is an efficient means of movement that allows bacteria to successfully colonize and compete with other microorganisms within their respective environments. The production and functioning of flagella is highly energy intensive and therefore flagellar motility is a tightly regulated process. Despite this, some bacteria have been observed to possess multiple flagellar systems which allow distinct forms of motility. Results Comparative genomic analyses showed that, in addition to the previously identified primary peritrichous (flag-1) and secondary, lateral (flag-2) flagellar loci, three novel types of flagellar loci, varying in both gene content and gene order, are encoded on the genomes of members of the order Enterobacterales. The flag-3 and flag-4 loci encode predicted peritrichous flagellar systems while the flag-5 locus encodes a polar flagellum. In total, 798/4028 (~ 20%) of the studied taxa incorporate dual flagellar systems, while nineteen taxa incorporate three distinct flagellar loci. Phylogenetic analyses indicate the complex evolutionary histories of the flagellar systems among the Enterobacterales. Conclusions Supernumerary flagellar loci are relatively common features across a broad taxonomic spectrum in the order Enterobacterales. Here, we report the occurrence of five (flag-1 to flag-5) flagellar loci on the genomes of enterobacterial taxa, as well as the occurrence of three flagellar systems in select members of the Enterobacterales. Considering the energetic burden of maintaining and operating multiple flagellar systems, they are likely to play a role in the ecological success of members of this family and we postulate on their potential biological functions.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular & Cell Biology, University of the Witwatersrand, Wits, 2050, South Africa.
| | - Talia Pillay
- School of Molecular & Cell Biology, University of the Witwatersrand, Wits, 2050, South Africa
| | - Teresa A Coutinho
- Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
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Duan R, Xu H, Gao S, Gao Z, Wang N. Effects of Different Hosts on Bacterial Communities of Parasitic Wasp Nasonia vitripennis. Front Microbiol 2020; 11:1435. [PMID: 32774328 PMCID: PMC7381354 DOI: 10.3389/fmicb.2020.01435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 06/03/2020] [Indexed: 01/08/2023] Open
Abstract
Parasitism is a special interspecific relationship in insects. Unlike most other ectoparasites, Nasonia vitripennis spend most of its life cycle (egg, larvae, pupae, and early adult stage) inside the pupae of flies, which is covered with hard puparium. Microbes play important roles in host development and help insect hosts to adapt to various environments. How the microbes of parasitic wasp respond to different fly hosts living in such close relationships motivated this investigation. In this study, we used N. vitripennis and three different fly pupa hosts (Lucilia sericata, Sarcophaga marshalli, and Musca domestica) to address this question, as well as to illustrate the potential transfer of bacteria through the trophic food chains. We found that N. vitripennis from different fly pupa hosts showed distinct microbiota, which means that the different fly hosts could affect the bacterial communities of their parasitic wasps. Some bacteria showed potential horizontal transfer through the trophic food chains, from the food through the fly to the parasitic wasp. We also found that the heritable endosymbiont Wolbachia could transferred from the fly host to the parasite and correlated with the bacterial communities of the corresponding parasitic wasps. Our findings provide new insight to the microbial interactions between parasite and host.
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Affiliation(s)
- Ruxin Duan
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Department of Entomology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Heng Xu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Department of Entomology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Shanshan Gao
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Department of Entomology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
| | - Zheng Gao
- College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Ningxin Wang
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, Department of Entomology, College of Plant Protection, Shandong Agricultural University, Tai'an, China
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Medina Munoz M, Spencer N, Enomoto S, Dale C, Rio RVM. Quorum sensing sets the stage for the establishment and vertical transmission of Sodalis praecaptivus in tsetse flies. PLoS Genet 2020; 16:e1008992. [PMID: 32797092 PMCID: PMC7449468 DOI: 10.1371/journal.pgen.1008992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/26/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Bacterial virulence factors facilitate host colonization and set the stage for the evolution of parasitic and mutualistic interactions. The Sodalis-allied clade of bacteria exhibit striking diversity in the range of both plant and animal feeding insects they inhabit, suggesting the appropriation of universal molecular mechanisms that facilitate establishment. Here, we report on the infection of the tsetse fly by free-living Sodalis praecaptivus, a close relative of many Sodalis-allied symbionts. Key genes involved in quorum sensing, including the homoserine lactone synthase (ypeI) and response regulators (yenR and ypeR) are integral for the benign colonization of S. praecaptivus. Mutants lacking ypeI, yenR and ypeR compromised tsetse survival as a consequence of their inability to repress virulence. Genes under quorum sensing, including homologs of the binary insecticidal toxin PirAB and a putative symbiosis-promoting factor CpmAJ, demonstrated negative and positive impacts, respectively, on tsetse survival. Taken together with results obtained from experiments involving weevils, this work shows that quorum sensing virulence suppression plays an integral role in facilitating the establishment of Sodalis-allied symbionts in diverse insect hosts. This knowledge contributes to the understanding of the early evolutionary steps involved in the formation of insect-bacterial symbiosis. Further, despite having no established history of interaction with tsetse, S. praecaptivus can infect reproductive tissues, enabling vertical transmission through adenotrophic viviparity within a single host generation. This creates an option for the use of S. praecaptivus in the biocontrol of insect disease vectors via paratransgenesis.
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Affiliation(s)
- Miguel Medina Munoz
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Noah Spencer
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
| | - Shinichiro Enomoto
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Colin Dale
- Department of Biology, University of Utah, Salt Lake City, UT, United States of America
| | - Rita V. M. Rio
- Department of Biology, Eberly College of Arts and Sciences, West Virginia University, Morgantown, WV, United States of America
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Hall RJ, Thorpe S, Thomas GH, Wood AJ. Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. Microb Genom 2020; 6:mgen000378. [PMID: 32543366 PMCID: PMC7478623 DOI: 10.1099/mgen.0.000378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 04/27/2020] [Indexed: 01/13/2023] Open
Abstract
Insect-bacterial symbioses are ubiquitous, but there is still much to uncover about how these relationships establish, persist and evolve. The tsetse endosymbiont Sodalis glossinidius displays intriguing metabolic adaptations to its microenvironment, but the process by which this relationship evolved remains to be elucidated. The recent chance discovery of the free-living species of the genus Sodalis, Sodalis praecaptivus, provides a serendipitous starting point from which to investigate the evolution of this symbiosis. Here, we present a flux balance model for S. praecaptivus and empirically verify its predictions. Metabolic modelling is used in combination with a multi-objective evolutionary algorithm to explore the trajectories that S. glossinidius may have undertaken from this starting point after becoming internalized. The order in which key genes are lost is shown to influence the evolved populations, providing possible targets for future in vitro genetic manipulation. This method provides a detailed perspective on possible evolutionary trajectories for S. glossinidius in this fundamental process of evolutionary and ecological change.
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Affiliation(s)
- Rebecca J. Hall
- Department of Biology, University of York, York, YO10 5NG, UK
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2TQ, UK
| | - Stephen Thorpe
- Department of Biology, University of York, York, YO10 5NG, UK
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Gavin H. Thomas
- Department of Biology, University of York, York, YO10 5NG, UK
| | - A. Jamie Wood
- Department of Biology, University of York, York, YO10 5NG, UK
- Department of Mathematics, University of York, York, YO10 5DD, UK
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Cossolin JFS, Lopes DRG, Martínez LC, Santos HCP, Fiaz M, Pereira MJB, Vivan LM, Mantovani HC, Serrão JE. Morphology and composition of the midgut bacterial community of Scaptocoris castanea Perty, 1830 (Hemiptera: Cydnidae). Cell Tissue Res 2020; 382:337-349. [PMID: 32447450 DOI: 10.1007/s00441-020-03197-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 03/03/2020] [Indexed: 11/26/2022]
Abstract
The burrower bug Scaptocoris castanea is an important soybean and pasture pest in Brazil, with an underground habit feeding directly on the sap of the roots. Underground habit hinders control and knowledge of the biology and physiology of this pest. This study describes the anatomy, histology, ultrastructure and symbionts of the midgut of S. castanea. The midgut of S. castanea is anatomically divided into five regions (ventricles). Ventricles 1-3 are similar between males and females, with cells specialized in digestion and absorption of nutrients, water transport and homeostasis. Ventricle 4 has squamous epithelium forming crypts and harboring bacteria in the lumen. Ventricle 5 of males is small with cells containing apical microvilli and broad basal folds with many openings for hemocoel, while in females, this region of the midgut is well developed and colonized by intracellular bacteria, characterizing bacteriocytes. The main bacteria are Gammaproteobacteria. The results show sexual dimorphism in ventricle 5 of the midgut of S. castanea, with formation of bacteriocytes in the females, while the other regions are involved in digestive processes in both sexes.
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Affiliation(s)
| | - Déborah Romaskevis Gomes Lopes
- Laboratório de Microbiologia de Anaeróbios, Departamento de Microbiologia, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-000, Brazil
| | - Luis Carlos Martínez
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-000, Brazil
| | - Helen Cristina Pinto Santos
- Instituto Federal de Educação, Ciência e Tecnologia de Minas Gerais IFMG - Campus Congonhas, Congonhas, Minas Gerais, 36415-000, Brazil
| | - Muhammad Fiaz
- Departamento de Entomologia, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-000, Brazil
| | | | - Lucia Madalena Vivan
- Fundação de Apoio a Pesquisa Agropecuária de Mato Grosso, Rondonopolis, MT, 78750-360, Brazil
| | - Hilário Cuquetto Mantovani
- Laboratório de Microbiologia de Anaeróbios, Departamento de Microbiologia, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-000, Brazil
| | - José Eduardo Serrão
- Departamento de Biologia Geral, Universidade Federal de Viçosa, Vicosa, Minas Gerais, 36570-000, Brazil.
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Rose C, Casas-Sánchez A, Dyer NA, Solórzano C, Beckett AJ, Middlehurst B, Marcello M, Haines LR, Lisack J, Engstler M, Lehane MJ, Prior IA, Acosta-Serrano Á. Trypanosoma brucei colonizes the tsetse gut via an immature peritrophic matrix in the proventriculus. Nat Microbiol 2020; 5:909-916. [DOI: 10.1038/s41564-020-0707-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/09/2020] [Indexed: 01/10/2023]
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Cervantes-Rivera R, Tronnet S, Puhar A. Complete genome sequence and annotation of the laboratory reference strain Shigella flexneri serotype 5a M90T and genome-wide transcriptional start site determination. BMC Genomics 2020; 21:285. [PMID: 32252626 PMCID: PMC7132871 DOI: 10.1186/s12864-020-6565-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 02/07/2020] [Indexed: 01/19/2023] Open
Abstract
Background Shigella is a Gram-negative facultative intracellular bacterium that causes bacillary dysentery in humans. Shigella invades cells of the colonic mucosa owing to its virulence plasmid-encoded Type 3 Secretion System (T3SS), and multiplies in the target cell cytosol. Although the laboratory reference strain S. flexneri serotype 5a M90T has been extensively used to understand the molecular mechanisms of pathogenesis, its complete genome sequence is not available, thereby greatly limiting studies employing high-throughput sequencing and systems biology approaches. Results We have sequenced, assembled, annotated and manually curated the full genome of S. flexneri 5a M90T. This yielded two complete circular contigs, the chromosome and the virulence plasmid (pWR100). To obtain the genome sequence, we have employed long-read PacBio DNA sequencing followed by polishing with Illumina RNA-seq data. This provides a new hybrid strategy to prepare gapless, highly accurate genome sequences, which also cover AT-rich tracks or repetitive sequences that are transcribed. Furthermore, we have performed genome-wide analysis of transcriptional start sites (TSS) and determined the length of 5′ untranslated regions (5′-UTRs) at typical culture conditions for the inoculum of in vitro infection experiments. We identified 6723 primary TSS (pTSS) and 7328 secondary TSS (sTSS). The S. flexneri 5a M90T annotated genome sequence and the transcriptional start sites are integrated into RegulonDB (http://regulondb.ccg.unam.mx) and RSAT (http://embnet.ccg.unam.mx/rsat/) databases to use their analysis tools in the S. flexneri 5a M90T genome. Conclusions We provide the first complete genome for S. flexneri serotype 5a, specifically the laboratory reference strain M90T. Our work opens the possibility of employing S. flexneri M90T in high-quality systems biology studies such as transcriptomic and differential expression analyses or in genome evolution studies. Moreover, the catalogue of TSS that we report here can be used in molecular pathogenesis studies as a resource to know which genes are transcribed before infection of host cells. The genome sequence, together with the analysis of transcriptional start sites, is also a valuable tool for precise genetic manipulation of S. flexneri 5a M90T. Further, we present a new hybrid strategy to prepare gapless, highly accurate genome sequences. Unlike currently used hybrid strategies combining long- and short-read DNA sequencing technologies to maximize accuracy, our workflow using long-read DNA sequencing and short-read RNA sequencing provides the added value of using non-redundant technologies, which yield distinct, exploitable datasets.
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Affiliation(s)
- Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Sophie Tronnet
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden.,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), 901 87 Umeå, Sweden. .,Umeå Centre for Microbial Research (UCMR), 901 87, Umeå, Sweden. .,Department of Molecular Biology, Umeå University, 901 87, Umeå, Sweden.
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Abstract
Microorganisms that reside within or transmit through arthropod reproductive tissues have profound impacts on host reproduction, health and evolution. In this Review, we discuss select principles of the biology of microorganisms in arthropod reproductive tissues, including bacteria, viruses, protists and fungi. We review models of specific symbionts, routes of transmission, and the physiological and evolutionary outcomes for both hosts and microorganisms. We also identify areas in need of continuing research, to answer the fundamental questions that remain in fields within and beyond arthropod-microorganism associations. New opportunities for research in this area will drive a broader understanding of major concepts as well as the biodiversity, mechanisms and translational applications of microorganisms that interact with host reproductive tissues.
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Goodhead I, Blow F, Brownridge P, Hughes M, Kenny J, Krishna R, McLean L, Pongchaikul P, Beynon R, Darby AC. Large-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont. Microb Genom 2020; 6:e000285. [PMID: 31922467 PMCID: PMC7067036 DOI: 10.1099/mgen.0.000285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 07/10/2019] [Indexed: 01/30/2023] Open
Abstract
The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.
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Affiliation(s)
- Ian Goodhead
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- School of Science, Engineering and Environment, Peel Building, University of Salford, M5 4WT, UK
| | - Frances Blow
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Philip Brownridge
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Margaret Hughes
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - John Kenny
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Ritesh Krishna
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- IBM Research UK, STFC Daresbury Laboratory, Warrington, WA4 4AD, UK
| | - Lynn McLean
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Pisut Pongchaikul
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Rob Beynon
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
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Roma JS, D’Souza S, Somers PJ, Cabo LF, Farsin R, Aksoy S, Runyen-Janecky LJ, Weiss BL. Thermal stress responses of Sodalis glossinidius, an indigenous bacterial symbiont of hematophagous tsetse flies. PLoS Negl Trop Dis 2019; 13:e0007464. [PMID: 31738754 PMCID: PMC6887450 DOI: 10.1371/journal.pntd.0007464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 12/02/2019] [Accepted: 10/24/2019] [Indexed: 11/22/2022] Open
Abstract
Tsetse flies (Diptera: Glossinidae) house a taxonomically diverse microbiota that includes environmentally acquired bacteria, maternally transmitted symbiotic bacteria, and pathogenic African trypanosomes. Sodalis glossinidius, which is a facultative symbiont that resides intra and extracellularly within multiple tsetse tissues, has been implicated as a mediator of trypanosome infection establishment in the fly’s gut. Tsetse’s gut-associated population of Sodalis are subjected to marked temperature fluctuations each time their ectothermic fly host imbibes vertebrate blood. The molecular mechanisms that Sodalis employs to deal with this heat stress are unknown. In this study, we examined the thermal tolerance and heat shock response of Sodalis. When grown on BHI agar plates, the bacterium exhibited the most prolific growth at 25oC, and did not grow at temperatures above 30oC. Growth on BHI agar plates at 31°C was dependent on either the addition of blood to the agar or reduction in oxygen levels. Sodalis was viable in liquid cultures for 24 hours at 30oC, but began to die upon further exposure. The rate of death increased with increased temperature. Similarly, Sodalis was able to survive for 48 hours within tsetse flies housed at 30oC, while a higher temperature (37oC) was lethal. Sodalis’ genome contains homologues of the heat shock chaperone protein-encoding genes dnaK, dnaJ, and grpE, and their expression was up-regulated in thermally stressed Sodalis, both in vitro and in vivo within tsetse fly midguts. Arrested growth of E. coli dnaK, dnaJ, or grpE mutants under thermal stress was reversed when the cells were transformed with a low copy plasmid that encoded the Sodalis homologues of these genes. The information contained in this study provides insight into how arthropod vector enteric commensals, many of which mediate their host’s ability to transmit pathogens, mitigate heat shock associated with the ingestion of a blood meal. Microorganisms associated with insects must cope with fluctuating temperatures. Because symbiotic bacteria influence the biology of their host, how they respond to temperature changes will have an impact on the host and other microorganisms in the host. The tsetse fly and its symbionts represent an important model system for studying thermal tolerance because the fly feeds exclusively on vertebrate blood and is thus exposed to dramatic temperature shifts. Tsetse flies house a microbial community that can consist of symbiotic and environmentally acquired bacteria, viruses, and parasitic African trypanosomes. This work, which makes use of tsetse’s commensal endosymbiont, Sodalis glossinidius, is significance because it represents the only examination of thermal tolerance mechanisms in a bacterium that resides indigenously within an arthropod disease vector. A better understanding of the biology of thermal tolerance in Sodalis provides insight into thermal stress survival in other insect symbionts and may yield information to help control vector-borne disease.
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Affiliation(s)
- Jose Santinni Roma
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Shaina D’Souza
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Patrick J. Somers
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Leah F. Cabo
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Ruhan Farsin
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Serap Aksoy
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Laura J. Runyen-Janecky
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
- * E-mail: (LJR-J); (BLW)
| | - Brian L. Weiss
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
- * E-mail: (LJR-J); (BLW)
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Fukatsu T. Grand Challenges to Launching an Ideal Platform for Publishing Microbe-Insect Symbiosis Studies. Front Microbiol 2019; 10:2542. [PMID: 31781062 PMCID: PMC6859797 DOI: 10.3389/fmicb.2019.02542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/21/2019] [Indexed: 11/13/2022] Open
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Trappeniers K, Matetovici I, Van Den Abbeele J, De Vooght L. The Tsetse Fly Displays an Attenuated Immune Response to Its Secondary Symbiont, Sodalis glossinidius. Front Microbiol 2019; 10:1650. [PMID: 31396178 PMCID: PMC6668328 DOI: 10.3389/fmicb.2019.01650] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/03/2019] [Indexed: 11/13/2022] Open
Abstract
Sodalis glossinidius, a vertically transmitted facultative symbiont of the tsetse fly, is a bacterium in the early/intermediate state of its transition toward symbiosis, representing an important model for investigating how the insect host immune defense response is regulated to allow endosymbionts to establish a chronic infection within their hosts without being eliminated. In this study, we report on the establishment of a tsetse fly line devoid of S. glossinidius only, allowing us to experimentally investigate (i) the complex immunological interactions between a single bacterial species and its host, (ii) how the symbiont population is kept under control, and (iii) the impact of the symbiont on the vector competence of the tsetse fly to transmit the sleeping sickness parasite. Comparative transcriptome analysis showed no difference in the expression of genes involved in innate immune processes between symbiont-harboring (GmmSod+) and S. glossinidius-free (GmmSod–) flies. Re-exposure of (GmmSod–) flies to the endosymbiotic bacterium resulted in a moderate immune response, whereas exposure to pathogenic E. coli or to a close non-insect associated relative of S. glossinidius, i.e., S. praecaptivus, resulted in full immune activation. We also showed that S. glossinidius densities are not affected by experimental activation or suppression of the host immune system, indicating that S. glossinidius is resistant to mounted immune attacks and that the host immune system does not play a major role in controlling S. glossinidius proliferation. Finally, we demonstrate that the absence or presence of S. glossinidius in the tsetse fly does not alter its capacity to mount an immune response to pathogens nor does it affect the fly’s susceptibility toward trypanosome infection.
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Affiliation(s)
- Katrien Trappeniers
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Irina Matetovici
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jan Van Den Abbeele
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Linda De Vooght
- Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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Abstract
Parasites elicit several physiological changes in their host to enhance transmission. Little is known about the functional association between parasitism and microbiota-provisioned resources typically dedicated to animal hosts and how these goods may be rerouted to optimize parasite development. This study is the first to identify a specific symbiont-generated metabolite that impacts insect vector competence by facilitating parasite establishment and, thus, eventual transmission. Specifically, we demonstrate that the tsetse fly obligate mutualist Wigglesworthia provisions folate (vitamin B9) that pathogenic African trypanosomes exploit in an effort to successfully establish an infection in the vector’s MG. This process is essential for the parasite to complete its life cycle and be transmitted to a new vertebrate host. Disrupting metabolic contributions provided by the microbiota of arthropod disease vectors may fuel future innovative control strategies while also offering minimal nontarget effects. Many symbionts supplement their host’s diet with essential nutrients. However, whether these nutrients also enhance parasitism is unknown. In this study, we investigated whether folate (vitamin B9) production by the tsetse fly (Glossina spp.) essential mutualist, Wigglesworthia, aids auxotrophic African trypanosomes in completing their life cycle within this obligate vector. We show that the expression of Wigglesworthia folate biosynthesis genes changes with the progression of trypanosome infection within tsetse. The disruption of Wigglesworthia folate production caused a reduction in the percentage of flies that housed midgut (MG) trypanosome infections. However, decreased folate did not prevent MG trypanosomes from migrating to and establishing an infection in the fly’s salivary glands, thus suggesting that nutrient requirements vary throughout the trypanosome life cycle. We further substantiated that trypanosomes rely on symbiont-generated folate by feeding this vitamin to Glossina brevipalpis, which exhibits low trypanosome vector competency and houses Wigglesworthia incapable of producing folate. Folate-supplemented G. brevipalpis flies were significantly more susceptible to trypanosome infection, further demonstrating that this vitamin facilitates parasite infection establishment. Our cumulative results provide evidence that Wigglesworthia provides a key metabolite (folate) that is “hijacked” by trypanosomes to enhance their infectivity, thus indirectly impacting tsetse species vector competency. Parasite dependence on symbiont-derived micronutrients, which likely also occurs in other arthropod vectors, represents a relationship that may be exploited to reduce disease transmission.
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Blow F, Douglas AE. The hemolymph microbiome of insects. JOURNAL OF INSECT PHYSIOLOGY 2019; 115:33-39. [PMID: 30953618 DOI: 10.1016/j.jinsphys.2019.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/27/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Hemolymph has long been recognized as a key mediator of nutritional and immunological homeostasis in insects, with the tacit understanding that hemolymph is a hostile environment for microorganisms, and microbiologically sterile in healthy insects. Recent research is overturning the conventional wisdom, and there is now overwhelming evidence that various non-pathogenic microorganisms can stably or transiently inhabit hemolymph in a diversity of insects. Most is known about Spiroplasma, especially in Drosophila species, and secondary symbionts of the Enterobacteriaceae, notably Hamiltonella defensa, in aphids. These bacteria require many nutrients, representing a likely drain on host nutritional resources, and they persist in the hemolymph by a combination of evasion and tolerance of insect immune effectors. These traits can be costly to the insect host. For some hemolymph microorganisms, these costs are balanced by other traits beneficial to the insect, notably protection against natural enemies mediated by specific toxins or competition for key nutrients. Three key priorities for future research are: to investigate the prevalence and taxonomic diversity of hemolymph microorganisms in insects; to establish the role of host nutritional and immune factors as determinants of the abundance and proliferation rates of hemolymph microorganisms; and to integrate the developing understanding of these microorganisms and their impacts (both costs and benefits) on insect nutrition and immune function into the wider study of insect physiology.
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Affiliation(s)
- Frances Blow
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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Bohlin J, Pettersson JHO. Evolution of Genomic Base Composition: From Single Cell Microbes to Multicellular Animals. Comput Struct Biotechnol J 2019; 17:362-370. [PMID: 30949307 PMCID: PMC6429543 DOI: 10.1016/j.csbj.2019.03.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/07/2023] Open
Abstract
Whole genome sequencing (WGS) of thousands of microbial genomes has provided considerable insight into evolutionary mechanisms in the microbial world. While substantially fewer eukaryotic genomes are available for analyses the number is rapidly increasing. This mini-review summarizes broadly evolutionary dynamics of base composition in the different domains of life from the perspective of prokaryotes. Common and different evolutionary mechanisms influencing genomic base composition in eukaryotes and prokaryotes are discussed. The conclusion from the data currently available suggests that while there are similarities there are also striking differences in how genomic base composition has evolved within prokaryotes and eukaryotes. For instance, homologous recombination appears to increase GC content locally in eukaryotes due to a non-selective process termed GC-biased gene conversion (gBGC). For prokaryotes on the other hand, increase in genomic GC content seems to be driven by the environment and selection. We find that similar phenomena observed for some organisms in each respective domain may be caused by very different mechanisms: while gBGC and recombination rates appear to explain the negative correlation between GC3 (GC content based on the third codon nucleotides) and genome size in some eukaryotes uptake of AT rich DNA sequences is the main reason for a similar negative correlation observed in prokaryotes. We provide further examples that indicate that base composition in prokaryotes and eukaryotes have evolved under very different constraints.
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Affiliation(s)
- Jon Bohlin
- Norwegian Institute of Public Health, Division of Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Lovisenberggata 8, 0456 Oslo, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, PO-Box 222 Skøyen, N-0213 Oslo, Norway.,Norwegian University of Life Sciences, Faculty of Veterinary Sciences, Production Animal Clinical Sciences, Ullevålsveien 72, 0454 Oslo, Norway
| | - John H-O Pettersson
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School the University of Sydney, New South Wales 2006, Australia.,Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Public Health Agency of Sweden, Nobels vg 18, SE-171 82 Solna, Sweden
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Weiss BL, Maltz MA, Vigneron A, Wu Y, Walter KS, O’Neill MB, Wang J, Aksoy S. Colonization of the tsetse fly midgut with commensal Kosakonia cowanii Zambiae inhibits trypanosome infection establishment. PLoS Pathog 2019; 15:e1007470. [PMID: 30817773 PMCID: PMC6394900 DOI: 10.1371/journal.ppat.1007470] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/27/2018] [Indexed: 11/18/2022] Open
Abstract
Tsetse flies (Glossina spp.) vector pathogenic trypanosomes (Trypanosoma spp.) in sub-Saharan Africa. These parasites cause human and animal African trypanosomiases, which are debilitating diseases that inflict an enormous socio-economic burden on inhabitants of endemic regions. Current disease control strategies rely primarily on treating infected animals and reducing tsetse population densities. However, relevant programs are costly, labor intensive and difficult to sustain. As such, novel strategies aimed at reducing tsetse vector competence require development. Herein we investigated whether Kosakonia cowanii Zambiae (Kco_Z), which confers Anopheles gambiae with resistance to Plasmodium, is able to colonize tsetse and induce a trypanosome refractory phenotype in the fly. Kco_Z established stable infections in tsetse’s gut and exhibited no adverse effect on the fly’s survival. Flies with established Kco_Z infections in their gut were significantly more refractory to infection with two distinct trypanosome species (T. congolense, 6% infection; T. brucei, 32% infection) than were age-matched flies that did not house the exogenous bacterium (T. congolense, 36% infected; T. brucei, 70% infected). Additionally, 52% of Kco_Z colonized tsetse survived infection with entomopathogenic Serratia marcescens, compared with only 9% of their wild-type counterparts. These parasite and pathogen refractory phenotypes result from the fact that Kco_Z acidifies tsetse’s midgut environment, which inhibits trypanosome and Serratia growth and thus infection establishment. Finally, we determined that Kco_Z infection does not impact the fecundity of male or female tsetse, nor the ability of male flies to compete with their wild-type counterparts for mates. We propose that Kco_Z could be used as one component of an integrated strategy aimed at reducing the ability of tsetse to transmit pathogenic trypanosomes. Tsetse flies transmit pathogenic African trypanosomes, which are the causative agents of socio-economically devastating human and animal African trypanosomiases. These diseases are currently controlled in large part by reducing the population size of tsetse vectors through the use of insecticides, traps and sterile insect technique. However, logistic and monetary hurdles often preclude the prolonged application of procedures necessary to maintain these control programs. Thus, novel strategies, including those aimed at sustainably reducing the ability of tsetse to transmit trypanosomes, are presently under development. Herein we stably colonize tsetse flies with a bacterium (Kosakonia cowanii Zambiae, Kco_Z) that acidifies their midgut, thus rendering the environment inhospitable to infection with two distinct, epidemiologically important trypanosome strains as well as an entomopathogenic bacteria. In addition to inducing a trypanosome refractory phenotype, colonization of tsetse with Kco_Z exerts only a modest fitness cost on the fly. Taken together, these findings suggest that Kco_Z could be applied to enhance the effectiveness of currently employed tsetse control programs.
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Affiliation(s)
- Brian L. Weiss
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
- * E-mail: (BLW); (SA)
| | - Michele A. Maltz
- Southern Connecticut State University, New Haven, Connecticut, United States of America
| | - Aurélien Vigneron
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Yineng Wu
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Katharine S. Walter
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Michelle B. O’Neill
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Jingwen Wang
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
| | - Serap Aksoy
- Yale School of Public Health, Department of Epidemiology of Microbial Diseases, New Haven, Connecticut, United States of America
- * E-mail: (BLW); (SA)
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Hall RJ, Flanagan LA, Bottery MJ, Springthorpe V, Thorpe S, Darby AC, Wood AJ, Thomas GH. A Tale of Three Species: Adaptation of Sodalis glossinidius to Tsetse Biology, Wigglesworthia Metabolism, and Host Diet. mBio 2019; 10:e02106-18. [PMID: 30602581 PMCID: PMC6315101 DOI: 10.1128/mbio.02106-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 11/20/2018] [Indexed: 12/22/2022] Open
Abstract
The tsetse fly is the insect vector for the Trypanosoma brucei parasite, the causative agent of human African trypanosomiasis. The colonization and spread of the trypanosome correlate positively with the presence of a secondary symbiotic bacterium, Sodalis glossinidius The metabolic requirements and interactions of the bacterium with its host are poorly understood, and herein we describe a metabolic model of S. glossinidius metabolism. The model enabled the design and experimental verification of a defined medium that supports S. glossinidius growth ex vivo This has been used subsequently to analyze in vitro aspects of S. glossinidius metabolism, revealing multiple unique adaptations of the symbiont to its environment. Continued dependence on a sugar, and the importance of the chitin monomer N-acetyl-d-glucosamine as a carbon and energy source, suggests adaptation to host-derived molecules. Adaptation to the amino acid-rich blood diet is revealed by a strong dependence on l-glutamate as a source of carbon and nitrogen and by the ability to rescue a predicted l-arginine auxotrophy. Finally, the selective loss of thiamine biosynthesis, a vitamin provided to the host by the primary symbiont Wigglesworthia glossinidia, reveals an intersymbiont dependence. The reductive evolution of S. glossinidius to exploit environmentally derived metabolites has resulted in multiple weaknesses in the metabolic network. These weaknesses may become targets for reagents that inhibit S. glossinidius growth and aid the reduction of trypanosomal transmission.IMPORTANCE Human African trypanosomiasis is caused by the Trypanosoma brucei parasite. The tsetse fly vector is of interest for its potential to prevent disease spread, as it is essential for T. brucei life cycle progression and transmission. The tsetse's mutualistic endosymbiont Sodalis glossinidius has a link to trypanosome establishment, providing a disease control target. Here, we describe a new, experimentally verified model of S. glossinidius metabolism. This model has enabled the development of a defined growth medium that was used successfully to test aspects of S. glossinidius metabolism. We present S. glossinidius as uniquely adapted to life in the tsetse, through its reliance on the blood diet and host-derived sugars. Additionally, S. glossinidius has adapted to the tsetse's obligate symbiont Wigglesworthia glossinidia by scavenging a vitamin it produces for the insect. This work highlights the use of metabolic modeling to design defined growth media for symbiotic bacteria and may provide novel inhibitory targets to block trypanosome transmission.
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Affiliation(s)
- Rebecca J Hall
- Department of Biology, University of York, York, United Kingdom
| | | | | | | | - Stephen Thorpe
- Department of Biology, University of York, York, United Kingdom
| | - Alistair C Darby
- University of Liverpool, Institute of Integrative Biology, Liverpool, United Kingdom
| | - A Jamie Wood
- Department of Biology, University of York, York, United Kingdom
- Department of Mathematics, University of York, York, United Kingdom
| | - Gavin H Thomas
- Department of Biology, University of York, York, United Kingdom
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Finer-Scale Phylosymbiosis: Insights from Insect Viromes. mSystems 2018; 3:mSystems00131-18. [PMID: 30574559 PMCID: PMC6299154 DOI: 10.1128/msystems.00131-18] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia. Phylosymbiosis was recently proposed to describe the eco-evolutionary pattern whereby the ecological relatedness (e.g., beta diversity relationships) of host-associated microbial communities parallels the phylogeny of the host species. Representing the most abundant biological entities on the planet and common members of the animal-associated microbiome, viruses can be influential members of host-associated microbial communities that may recapitulate, reinforce, or ablate phylosymbiosis. Here we sequence the metagenomes of purified viral communities from three different parasitic wasp Nasonia species, one cytonuclear introgression line of Nasonia, and the flour moth outgroup Ephestia kuehniella. Results demonstrate complete phylosymbiosis between the viral metagenome and insect phylogeny. Across all Nasonia contigs, 69% of the genes in the viral metagenomes are either new to the databases or uncharacterized, yet over 99% of the contigs have at least one gene with similarity to a known sequence. The core Nasonia virome spans 21% of the total contigs, and the majority of that core is likely derived from induced prophages residing in the genomes of common Nasonia-associated bacterial genera: Proteus, Providencia, and Morganella. We also assemble the first complete viral particle genomes from Nasonia-associated gut bacteria. Taken together, results reveal the first complete evidence for phylosymbiosis in viral metagenomes, new genome sequences of viral particles from Nasonia-associated gut bacteria, and a large set of novel or uncharacterized genes in the Nasonia virome. This work suggests that phylosymbiosis at the host-microbiome level will likely extend to the host-virome level in other systems as well. IMPORTANCE Viruses are the most abundant biological entity on the planet and interact with microbial communities with which they associate. The virome of animals is often dominated by bacterial viruses, known as bacteriophages or phages, which can (re)structure bacterial communities potentially vital to the animal host. Beta diversity relationships of animal-associated bacterial communities in laboratory and wild populations frequently parallel animal phylogenetic relationships, a pattern termed phylosymbiosis. However, little is known about whether viral communities also exhibit this eco-evolutionary pattern. Metagenomics of purified viruses from recently diverged species of Nasonia parasitoid wasps reared in the lab indicates for the first time that the community relationships of the virome can also exhibit complete phylosymbiosis. Therefore, viruses, particularly bacteriophages here, may also be influenced by animal evolutionary changes either directly or indirectly through the tripartite interactions among hosts, bacteria, and phage communities. Moreover, we report several new bacteriophage genomes from the common gut bacteria in Nasonia.
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50
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What can a weevil teach a fly, and reciprocally? Interaction of host immune systems with endosymbionts in Glossina and Sitophilus. BMC Microbiol 2018; 18:150. [PMID: 30470176 PMCID: PMC6251153 DOI: 10.1186/s12866-018-1278-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The tsetse fly (Glossina genus) is the main vector of African trypanosomes, which are protozoan parasites that cause human and animal African trypanosomiases in Sub-Saharan Africa. In the frame of the IAEA/FAO program ‘Enhancing Vector Refractoriness to Trypanosome Infection’, in addition to the tsetse, the cereal weevil Sitophilus has been introduced as a comparative system with regards to immune interactions with endosymbionts. The cereal weevil is an agricultural pest that destroys a significant proportion of cereal stocks worldwide. Tsetse flies are associated with three symbiotic bacteria, the multifunctional obligate Wigglesworthia glossinidia, the facultative commensal Sodalis glossinidius and the parasitic Wolbachia. Cereal weevils house an obligatory nutritional symbiosis with the bacterium Sodalis pierantonius, and occasionally Wolbachia. Studying insect host-symbiont interactions is highly relevant both for understanding the evolution of symbiosis and for envisioning novel pest control strategies. In both insects, the long co-evolution between host and endosymbiont has led to a stringent integration of the host-bacteria partnership. These associations were facilitated by the development of specialized host traits, including symbiont-housing cells called bacteriocytes and specific immune features that enable both tolerance and control of the bacteria. In this review, we compare the tsetse and weevil model systems and compile the latest research findings regarding their biological and ecological similarities, how the immune system controls endosymbiont load and location, and how host-symbiont interactions impact developmental features including cuticle synthesis and immune system maturation. We focus mainly on the interactions between the obligate symbionts and their host’s immune systems, a central theme in both model systems. Finally, we highlight how parallel studies on cereal weevils and tsetse flies led to mutual discoveries and stimulated research on each model, creating a pivotal example of scientific improvement through comparison between relatively distant models.
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