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Pereira TJ, De Santiago A, Bik HM. Soil properties predict below-ground community structure, but not nematode microbiome patterns in semi-arid habitats. Mol Ecol 2024:e17501. [PMID: 39175265 DOI: 10.1111/mec.17501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 08/02/2024] [Accepted: 08/07/2024] [Indexed: 08/24/2024]
Abstract
Microbial and microeukaryotic communities are extremely abundant and diverse in soil habitats where they play critical roles in ecosystem functioning and services that are essential to soil health. Soil biodiversity is influenced by above-ground (vegetation) and below-ground factors (soil properties), which together create habitat-specific conditions. However, the compound effects of vegetation and soil properties on soil communities are less studied or often focused on one component of the soil biota. Here, we integrate metabarcoding (16S and 18S rRNA genes) and nematode morphology to assess the effects of habitat and soil properties shaping microbial and microeukaryotic communities as well as nematode-associated microbiomes. We show that both vegetation and soil properties (soil bulk density) were major factors structuring microbial and microeukaryotic communities in semi-arid soil habitats. Despite having lower nutrients and lower pH, denser soils displayed significantly higher alpha diversity than less dense soils across datasets. Nematode-associated microbiomes have lower microbial diversity, strongly differ from soil microbes and are more likely to respond to microscale variations among samples than to vegetation or soil bulk density. Consequently, different nematode lineages and trophic groups are likely to display similar associated microbiomes when sharing the same microhabitat. Different microbiome taxa were enriched within specific nematode lineages (e.g. Mycobacterium, Candidatus Cardinium) highlighting potentially new species-specific associations that may confer benefits to their soil nematode hosts. Our findings highlight the importance of exploring above- and below-ground effects to assess community structure in terrestrial habitats, and how fine-scale analyses are critical for understanding patterns of host-associated microbiomes.
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Affiliation(s)
- Tiago José Pereira
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Alejandro De Santiago
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Holly M Bik
- Department of Marine Sciences, University of Georgia, Athens, Georgia, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
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2
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Alexander H, Hu SK, Krinos AI, Pachiadaki M, Tully BJ, Neely CJ, Reiter T. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 2023; 14:e0167623. [PMID: 37947402 PMCID: PMC10746220 DOI: 10.1128/mbio.01676-23] [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: 06/30/2023] [Accepted: 09/27/2023] [Indexed: 11/12/2023] Open
Abstract
IMPORTANCE Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.
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Affiliation(s)
- Harriet Alexander
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Sarah K. Hu
- Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Arianna I. Krinos
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
| | - Maria Pachiadaki
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Benjamin J. Tully
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Christopher J. Neely
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, USA
| | - Taylor Reiter
- Population Health and Reproduction, University of California, Davis, Davis, California, USA
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3
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Giorgini M, Formisano G, García-García R, Bernat-Ponce S, Beitia F. The Susceptibility of Bemisia tabaci Mediterranean (MED) Species to Attack by a Parasitoid Wasp Changes between Two Whitefly Strains with Different Facultative Endosymbiotic Bacteria. INSECTS 2023; 14:808. [PMID: 37887820 PMCID: PMC10607859 DOI: 10.3390/insects14100808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/22/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
In this study, two strains of the mitochondrial lineage Q1 of Bemisia tabaci MED species, characterized by a different complement of facultative bacterial endosymbionts, were tested for their susceptibility to be attacked by the parasitoid wasp Eretmocerus mundus, a widespread natural enemy of B. tabaci. Notably, the BtHC strain infected with Hamiltonella and Cardinium was more resistant to parasitization than the BtHR strain infected with Hamiltonella and Rickettsia. The resistant phenotype consisted of fewer nymphs successfully parasitized (containing the parasitoid mature larva or pupa) and in a lower percentage of adult wasps emerging from parasitized nymphs. Interestingly, the resistance traits were not evident when E. mundus parasitism was compared between BtHC and BtHR using parasitoids originating from a colony maintained on BtHC. However, when we moved the parasitoid colony on BtHR and tested E. mundus after it was reared on BtHR for four and seven generations, we saw then that BtHC was less susceptible to parasitization than BtHR. On the other hand, we did not detect any difference in the parasitization of the BtHR strain between the three generations of E. mundus tested. Our findings showed that host strain is a factor affecting the ability of E. mundus to parasitize B. tabaci and lay the basis for further studies aimed at disentangling the role of the facultative endosymbiont Cardinium and of the genetic background in the resistance of B. tabaci MED to parasitoid attack. Furthermore, they highlight that counteradaptations to the variation of B. tabaci defence mechanisms may be rapidly selected in E. mundus to maximize the parasitoid fitness.
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Affiliation(s)
- Massimo Giorgini
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 80055 Portici, Italy;
| | - Giorgio Formisano
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), 80055 Portici, Italy;
| | - Rosalía García-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain; (R.G.-G.); (S.B.-P.); (F.B.)
| | - Saúl Bernat-Ponce
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain; (R.G.-G.); (S.B.-P.); (F.B.)
| | - Francisco Beitia
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113 Valencia, Spain; (R.G.-G.); (S.B.-P.); (F.B.)
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Endogenous Plasmids and Chromosomal Genome Reduction in the Cardinium Endosymbiont of Dermatophagoides farinae. mSphere 2023; 8:e0007423. [PMID: 36939349 PMCID: PMC10117132 DOI: 10.1128/msphere.00074-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
Cardinium bacteria are well known as endosymbionts that infect a wide range of arthropods and can manipulate host reproduction to promote their vertical transmission. As intracellular bacteria, Cardinium species undergo dramatic genome evolution, especially their chromosomal genome reduction. Although Cardinium plasmids have been reported to harbor important genes, the role of these plasmids in the genome evolution is yet to be fully understood. In this study, 2 genomes of Cardinium endosymbiont bacteria in astigmatic mites were de novo assembled, including the complete circular chromosomal genome of Cardinium sp. DF that was constructed in high quality using high-coverage long-read sequencing data. Intriguingly, 2 circular plasmids were assembled in Cardinium sp. DF and were identified to be endogenous for over 10 homologous genes shared with the chromosomal genome. Comparative genomics analysis illustrated an outline of the genome evolution of Cardinium bacteria, and the in-depth analysis of Cardinium sp. DF shed light on the multiple roles of endogenous plasmids in the molecular process of the chromosomal genome reduction. The endogenous plasmids of Cardinium sp. DF not only harbor massive homologous sequences that enable homologous recombination with the chromosome, but also can provide necessary functional proteins when the coding genes decayed in the chromosomal genome. IMPORTANCE As bacterial endosymbionts, Cardinium typically undergoes genome reduction, but the molecular process is still unclear, such as how plasmids get involved in chromosome reduction. Here, we de novo assembled 2 genomes of Cardinium in astigmatic mites, especially the chromosome of Cardinium sp. DF was assembled in a complete circular DNA using high-coverage long-read sequencing data. In the genome assembly of Cardinium sp. DF, 2 circular endogenous plasmids were identified to share at least 10 homologous genes with the chromosomal genome. In the comparative analysis, we identified a range of genes decayed in the chromosomal genome of Cardinium sp. DF but preserved in the 2 plasmids. Taken together with in-depth analyses, our results unveil that the endogenous plasmids harbor homologous sequences of chromosomal genome and can provide a structural basis of homologous recombination. Overall, this study reveals that endogenous plasmids participate in the ongoing chromosomal genome reduction of Cardinium sp. DF.
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Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes. Int J Mol Sci 2023; 24:ijms24032905. [PMID: 36769231 PMCID: PMC9918034 DOI: 10.3390/ijms24032905] [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: 12/06/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.
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Halter T, Köstlbacher S, Rattei T, Hendrickx F, Manzano-Marín A, Horn M. One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus. Microb Genom 2023; 9:mgen000943. [PMID: 36757767 PMCID: PMC9997750 DOI: 10.1099/mgen.0.000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, 'Candidatus Tisiphia' (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, 'Ca. Tisiphia' and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, 'Ca. Tisiphia' and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary 'contact-tracing' tool.
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Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria.,Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria.,Doctoral School in Microbiology and Environmental Science, University of Vienna. Universitätsring 1, 1010 Vienna, Austria.,Current address: Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6700 EH Wageningen, The Netherlands
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Frederik Hendrickx
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences. Rue Vautier/Vautierstraat 29,, 1000 Brussels, Belgium
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna. Djerassiplatz 1, 1030 Vienna, Austria
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7
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Halter T, Hendrickx F, Horn M, Manzano-Marín A. A Novel Widespread MITE Element in the Repeat-Rich Genome of the Cardinium Endosymbiont of the Spider Oedothorax gibbosus. Microbiol Spectr 2022; 10:e0262722. [PMID: 36301108 PMCID: PMC9769881 DOI: 10.1128/spectrum.02627-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 09/19/2022] [Indexed: 01/07/2023] Open
Abstract
Free-living bacteria have evolved multiple times to become host-restricted endosymbionts. The transition from a free-living to a host-restricted lifestyle comes with a number of different genomic changes, including a massive loss of genes. In host-restricted endosymbionts, gene inactivation and genome reduction are facilitated by mobile genetic elements, mainly insertion sequences (ISs). ISs are small autonomous mobile elements, and one of, if not the most, abundant transposable elements in bacteria. Proliferation of ISs is common in some facultative endosymbionts, and is likely driven by the transmission bottlenecks, which increase the level of genetic drift. In this study, we present a manually curated genome annotation for a Cardinium endosymbiont of the dwarf spider Oedothorax gibbosus. Cardinium species are host-restricted endosymbionts that, similarly to ColbachiaWolbachia spp., include strains capable of manipulating host reproduction. Through the focus on mobile elements, the annotation revealed a rampant spread of ISs, extending earlier observations in other Cardinium genomes. We found that a large proportion of IS elements are pseudogenized, with many displaying evidence of recent inactivation. Most notably, we describe the lineage-specific emergence and spread of a novel IS-derived Miniature Inverted repeat Transposable Element (MITE), likely being actively maintained by intact copies of its parental IS982-family element. This study highlights the relevance of manual curation of these repeat-rich endosymbiont genomes for the discovery of novel MITEs, as well as the possible role these understudied elements might play in genome streamlining. IMPORTANCE Cardinium bacteria, a widespread symbiont lineage found across insects and nematodes, have been linked to reproductive manipulation of their hosts. However, the study of Cardinium has been hampered by the lack of comprehensive genomic resources. The high content of mobile genetic elements, namely, insertion sequences (ISs), has long complicated the analyses and proper annotations of these genomes. In this study, we present a manually curated annotation of the Cardinium symbiont of the spider Oedothorax gibbosus. Most notably, we describe a novel IS-like element found exclusively in this strain. We show that this mobile element likely evolved from a defective copy of its parental IS and then spread throughout the genome, contributing to the pseudogenization of several other mobile elements. We propose this element is likely being maintained by the intact copies of its parental IS element and that other similar elements in the genome could potentially follow this route.
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Affiliation(s)
- Tamara Halter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Frederik Hendrickx
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Alejandro Manzano-Marín
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
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8
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Swanson MT, Henson MW, Handika H, Achmadi AS, Anita S, Rowe KC, Esselstyn JA. Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture. J Mammal 2022. [DOI: 10.1093/jmammal/gyac098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Faunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.
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Affiliation(s)
- Mark T Swanson
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
| | - Michael W Henson
- Department of Geophysical Sciences, University of Chicago , Illinois 60616 , USA
| | - Heru Handika
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
| | - Anang S Achmadi
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN) , Cibinong 16912 , Indonesia
| | - Syahfitri Anita
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN) , Cibinong 16912 , Indonesia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria Research Institute , G.P.O. Box 666, Melbourne, Victoria 3001 , Australia
- School of Biosciences, University of Melbourne , Royal Parade, Parkville, Melbourne, Victoria 3052 , Australia
| | - Jacob A Esselstyn
- Museum of Natural Science and Department of Biological Sciences, 119 Foster Hall, Louisiana State University , Baton Rouge, Louisiana 70803 , USA
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9
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Martinez J, Ant TH, Murdochy SM, Tong L, da Silva Filipe A, Sinkins SP. Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common. PLoS Genet 2022; 18:e1010406. [PMID: 36121852 PMCID: PMC9560607 DOI: 10.1371/journal.pgen.1010406] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/13/2022] [Accepted: 09/02/2022] [Indexed: 11/18/2022] Open
Abstract
Wolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host's reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus, after eliminating the co-infecting and higher density wAlbB strain that previously made sequencing of wAlbA challenging. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
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Affiliation(s)
- Julien Martinez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Thomas H. Ant
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Shivan M. Murdochy
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Lily Tong
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ana da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Steven P. Sinkins
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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10
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Konecka E. Fifty shades of bacterial endosymbionts and some of them still remain a mystery: Wolbachia and Cardinium in oribatid mites (Acari: Oribatida). J Invertebr Pathol 2022; 189:107733. [DOI: 10.1016/j.jip.2022.107733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/28/2022]
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11
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Selberherr E, Penz T, König L, Conrady B, Siegl A, Horn M, Schmitz-Esser S. The life cycle-dependent transcriptional profile of the obligate intracellular amoeba symbiont Amoebophilus asiaticus. FEMS Microbiol Ecol 2022; 98:6499296. [PMID: 34999767 PMCID: PMC8831229 DOI: 10.1093/femsec/fiac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 12/04/2022] Open
Abstract
Free-living amoebae often harbor obligate intracellular bacterial symbionts. Amoebophilus (A.) asiaticus is a representative of a lineage of amoeba symbionts in the phylum Bacteroidota. Here, we analyse the transcriptome of A. asiaticus strain 5a2 at four time points during its infection cycle and replication within the Acanthamoeba host using RNA sequencing. Our results reveal a dynamic transcriptional landscape throughout different A. asiaticus life cycle stages. Many intracellular bacteria and pathogens utilize eukaryotic-like proteins (ELPs) for host cell interaction and the A. asiaticus 5a2 genome shows a particularly high abundance of ELPs. We show the expression of all genes encoding ELPs and found many ELPs to be differentially expressed. At the replicative stage of A. asiaticus, ankyrin repeat proteins and tetratricopeptide/Sel1-like repeat proteins were upregulated. At the later time points, high expression levels of a type 6 secretion system that likely prepares for a new infection cycle after lysing its host, were found. This study reveals comprehensive insights into the intracellular lifestyle of A. asiaticus and highlights candidate genes for host cell interaction. The results from this study have implications for other intracellular bacteria such as other amoeba-associated bacteria and the arthropod symbionts Cardinium forming the sister lineage of A. asiaticus.
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Affiliation(s)
- E Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Austria
| | - T Penz
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.,current affiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - L König
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - B Conrady
- Department of Veterinary and Animal Science, University of Copenhagen, Denmark
| | - A Siegl
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - M Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - S Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, USA
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12
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Buysse M, Floriano AM, Gottlieb Y, Nardi T, Comandatore F, Olivieri E, Giannetto A, Palomar AM, Makepeace BL, Bazzocchi C, Cafiso A, Sassera D, Duron O. A dual endosymbiosis supports nutritional adaptation to hematophagy in the invasive tick Hyalomma marginatum. eLife 2021; 10:e72747. [PMID: 34951405 PMCID: PMC8709577 DOI: 10.7554/elife.72747] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
Many animals are dependent on microbial partners that provide essential nutrients lacking from their diet. Ticks, whose diet consists exclusively on vertebrate blood, rely on maternally inherited bacterial symbionts to supply B vitamins. While previously studied tick species consistently harbor a single lineage of those nutritional symbionts, we evidence here that the invasive tick Hyalomma marginatum harbors a unique dual-partner nutritional system between an ancestral symbiont, Francisella, and a more recently acquired symbiont, Midichloria. Using metagenomics, we show that Francisella exhibits extensive genome erosion that endangers the nutritional symbiotic interactions. Its genome includes folate and riboflavin biosynthesis pathways but deprived functional biotin biosynthesis on account of massive pseudogenization. Co-symbiosis compensates this deficiency since the Midichloria genome encompasses an intact biotin operon, which was primarily acquired via lateral gene transfer from unrelated intracellular bacteria commonly infecting arthropods. Thus, in H. marginatum, a mosaic of co-evolved symbionts incorporating gene combinations of distant phylogenetic origins emerged to prevent the collapse of an ancestral nutritional symbiosis. Such dual endosymbiosis was never reported in other blood feeders but was recently documented in agricultural pests feeding on plant sap, suggesting that it may be a key mechanism for advanced adaptation of arthropods to specialized diets.
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Affiliation(s)
- Marie Buysse
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Univ. Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS) - Institut pour la Recherche et le Développement (IRD)MontpellierFrance
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, FranceMontpellierFrance
| | - Anna Maria Floriano
- Department of Biology and Biotechnology “L. Spallanzani”, University of PaviaPaviaItaly
- Faculty of Science, University of South BohemiaČeské BudějoviceCzech Republic
| | - Yuval Gottlieb
- Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Tiago Nardi
- Department of Biology and Biotechnology “L. Spallanzani”, University of PaviaPaviaItaly
| | - Francesco Comandatore
- Department of Biomedical and Clinical Sciences L. Sacco and Pediatric Clinical Research Center, University of MilanMilanItaly
| | - Emanuela Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of PaviaPaviaItaly
| | - Alessia Giannetto
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of MessinaMessinaItaly
| | - Ana M Palomar
- Center of Rickettsiosis and Arthropod-Borne Diseases (CRETAV), San Pedro University Hospital- Center of Biomedical Research from La Rioja (CIBIR)LogroñoSpain
| | - Benjamin L Makepeace
- Institute of Infection, Veterinary & Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | | | | | - Davide Sassera
- Department of Biology and Biotechnology “L. Spallanzani”, University of PaviaPaviaItaly
| | - Olivier Duron
- MIVEGEC (Maladies Infectieuses et Vecteurs : Ecologie, Génétique, Evolution et Contrôle), Univ. Montpellier (UM) - Centre National de la Recherche Scientifique (CNRS) - Institut pour la Recherche et le Développement (IRD)MontpellierFrance
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, FranceMontpellierFrance
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13
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Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia. PLoS Negl Trop Dis 2021; 15:e0009942. [PMID: 34928947 PMCID: PMC8722730 DOI: 10.1371/journal.pntd.0009942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 01/03/2022] [Accepted: 10/22/2021] [Indexed: 01/04/2023] Open
Abstract
Background Secondary symbionts of insects include a range of bacteria and fungi that perform various functional roles on their hosts, such as fitness, tolerance to heat stress, susceptibility to insecticides and effects on reproduction. These endosymbionts could have the potential to shape microbial communites and high potential to develop strategies for mosquito-borne disease control. Methodology/Principal findings The relative frequency and molecular phylogeny of Wolbachia, Microsporidia and Cardinium were determined of phlebotomine sand flies and mosquitoes in two regions from Colombia. Illumina Miseq using the 16S rRNA gene as a biomarker was conducted to examine the microbiota. Different percentages of natural infection by Wolbachia, Cardinium, and Microsporidia in phlebotomines and mosquitoes were detected. Phylogenetic analysis of Wolbachia shows putative new strains of Lutzomyia gomezi (wLgom), Brumptomyia hamata (wBrham), and a putative new group associated with Culex nigripalpus (Cnig) from the Andean region, located in Supergroup A and Supergroup B, respectively. The sequences of Microsporidia were obtained of Pi. pia and Cx. nigripalpus, which are located on phylogeny in the IV clade (terrestrial origin). The Cardinium of Tr. triramula and Ps. shannoni were located in group C next to Culicoides sequences while Cardinium of Mi. cayennensis formed two putative new subgroups of Cardinium in group A. In total were obtained 550 bacterial amplicon sequence variants (ASVs) and 189 taxa to the genus level. The microbiota profiles of Sand flies and mosquitoes showed mainly at the phylum level to Proteobacteria (67.6%), Firmicutes (17.9%) and Actinobacteria (7.4%). High percentages of relative abundance for Wolbachia (30%-83%) in Lu. gomezi, Ev. dubitans, Mi. micropyga, Br. hamata, and Cx. nigripalpus were found. ASVs assigned as Microsporidia were found in greater abundance in Pi. pia (23%) and Cx. nigripalpus (11%). An important finding is the detection of Rickettsia in Pi. pia (58,8%) and Bartonella sp. in Cx. nigripalpus. Conclusions/Significance We found that Wolbachia infection significantly decreased the alpha diversity and negatively impacts the number of taxa on sand flies and Culex nigripalpus. The Principal Coordinate Analysis (PCoA) is consistent, which showed statistically significant differences (PERMANOVA, F = 2.4744; R2 = 0.18363; p-value = 0.007) between the microbiota of sand flies and mosquitoes depending on its origin, host and possibly for the abundance of some endosymbionts (Wolbachia, Rickettsia). The secondary endosymbionts can positively influence the metabolism of many compounds essential for the survival of the insect vectors, provide resistance to pathogens and impact susceptibility to insecticides, as also the tolerance to heat stress. We provide information from new records of natural infection of secondary endosymbionts, such as Wolbachia, Cardinium, Microsporidia, Flavobacterium, and Rickettsia in phlebotomine sand flies and mosquitoes from Colombia. An important finding is the detection of Bartonella sp. in Cx. nigripalpus. Clear differences were found in the composition and diversity of microbiota at the intra-specific and interspecific levels in sand flies and Cx. nigripalpus, which may depend in the of the load of natural infection of endosymbionts (as Wolbachia), the geographical distribution and host.
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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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Milenovic M, Ghanim M, Hoffmann L, Rapisarda C. Whitefly endosymbionts: IPM opportunity or tilting at windmills? JOURNAL OF PEST SCIENCE 2021; 95:543-566. [PMID: 34744550 PMCID: PMC8562023 DOI: 10.1007/s10340-021-01451-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 05/23/2023]
Abstract
Whiteflies are sap-sucking insects responsible for high economic losses. They colonize hundreds of plant species and cause direct feeding damage and indirect damage through transmission of devastating viruses. Modern agriculture has seen a history of invasive whitefly species and populations that expand to novel regions, bringing along fierce viruses. Control efforts are hindered by fast virus transmission, insecticide-resistant populations, and a wide host range which permits large natural reservoirs for whiteflies. Augmentative biocontrol by parasitoids while effective in suppressing high population densities in greenhouses falls short when it comes to preventing virus transmission and is ineffective in the open field. A potential source of much needed novel control strategies lays within a diverse community of whitefly endosymbionts. The idea to exploit endosymbionts for whitefly control is as old as identification of these bacteria, yet it still has not come to fruition. We review where our knowledge stands on the aspects of whitefly endosymbiont evolution, biology, metabolism, multitrophic interactions, and population dynamics. We show how these insights are bringing us closer to the goal of better integrated pest management strategies. Combining most up to date understanding of whitefly-endosymbiont interactions and recent technological advances, we discuss possibilities of disrupting and manipulating whitefly endosymbionts, as well as using them for pest control.
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Affiliation(s)
- Milan Milenovic
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 41, Rue du Brill, L-4422 Belvaux, Luxembourg
- Dipartimento di Agricoltura, Università degli Studi di Catania, Alimentazione e Ambiente (Di3A), via Santa Sofia 100, 95123 Catania, Italy
| | - Murad Ghanim
- Department of Entomology, Volcani Center, ARO, HaMaccabim Road 68, PO Box 15159, 7528809 Rishon Le Tsiyon, Israel
| | - Lucien Hoffmann
- Environmental Research and Innovation Department (ERIN), Luxembourg Institute of Science and Technology (LIST), 41, Rue du Brill, L-4422 Belvaux, Luxembourg
| | - Carmelo Rapisarda
- Dipartimento di Agricoltura, Università degli Studi di Catania, Alimentazione e Ambiente (Di3A), via Santa Sofia 100, 95123 Catania, Italy
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Yang K, Yuan MY, Liu Y, Guo CL, Liu TX, Zhang YJ, Chu D. First evidence for thermal tolerance benefits of the bacterial symbiont Cardinium in an invasive whitefly, Bemisia tabaci. PEST MANAGEMENT SCIENCE 2021; 77:5021-5031. [PMID: 34216527 DOI: 10.1002/ps.6543] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUD Cardinium symbiont is a maternally inherited bacterial endosymbiont and widely spreads in arthropods including Bemisia tabaci (Hemiptera: Aleyrodidae). However, the potential role of Cardinium played in the biology of their hosts is largely unknown. In two genetic lines (i.e. LS and SG lines) of B. tabaci MED, collected from different locations in China, we tested the effects of Cardinium on the performance of the host whitefly under a constant high temperature (31 °C) using the age-stage two-sex life table method, and explored the genes influenced by Cardinium-infection by RNA-sequencing. RESULTS We found that Cardinium did provide protection of B. tabaci against heat stress under 31 °C. However, there was a significant connection between Cardinium-infection and whitefly genetic backgrounds. Performance revealed that Cardinium infection can increase the longevity of both female and male adults and oviposition periods in both lines, but it also conferred benefits of fecundity and pre-adult period to LS line. Additionally, the population parameters such as intrinsic rate of increase (r), finite rate of increase (λ) and mean generation time (T) demonstrated that Cardinium infection conferred fitness benefits to LS line but not to SG line. Transcriptome analysis indicated that several genes related to homeostasis and metamorphosis such as ubiquitin-related genes were highly expressed in Cardinium-infected B. tabaci. CONCLUSION The research provided the first evidence that Cardinium can increase the thermal tolerance of whitefly, which may be associated with host genetic background.
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Affiliation(s)
- Kun Yang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Meng-Ying Yuan
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ying Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chen-Liang Guo
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - You-Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, |Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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17
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Haselkorn TS, Jimenez D, Bashir U, Sallinger E, Queller DC, Strassmann JE, DiSalvo S. Novel Chlamydiae and Amoebophilus endosymbionts are prevalent in wild isolates of the model social amoeba Dictyostelium discoideum. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:708-719. [PMID: 34159734 PMCID: PMC8518690 DOI: 10.1111/1758-2229.12985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 06/12/2021] [Indexed: 05/24/2023]
Abstract
Amoebae interact with bacteria in multifaceted ways. Amoeba predation can serve as a selective pressure for the development of bacterial virulence traits. Bacteria may also adapt to life inside amoebae, resulting in symbiotic relationships. Indeed, particular lineages of obligate bacterial endosymbionts have been found in different amoebae. Here, we screened an extensive collection of Dictyostelium discoideum wild isolates for the presence of these bacterial symbionts using endosymbiont specific PCR primers. We find that these symbionts are surprisingly common, identified in 42% of screened isolates (N = 730). Members of the Chlamydiae phylum are particularly prevalent, occurring in 27% of the amoeba isolated. They are novel and phylogenetically distinct from other Chlamydiae. We also found Amoebophilus symbionts in 8% of screened isolates (N = 730). Antibiotic-cured amoebae behave similarly to their Chlamydiae or Amoebophilus-infected counterparts, suggesting that these endosymbionts do not significantly impact host fitness, at least in the laboratory. We found several natural isolates were co-infected with multiple endosymbionts, with no obvious fitness effect of co-infection under laboratory conditions. The high prevalence and novelty of amoeba endosymbiont clades in the model organism D. discoideum opens the door to future research on the significance and mechanisms of amoeba-symbiont interactions.
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Affiliation(s)
- Tamara S. Haselkorn
- Department of BiologyUniversity of Central Arkansas201 Donaghey Avenue, ConwayAR72035USA
| | - Daniela Jimenez
- Department of BiologyWashington University in St. LouisOne Brookings Drive St. LouisMO63130USA
| | - Usman Bashir
- Department of BiologyWashington University in St. LouisOne Brookings Drive St. LouisMO63130USA
| | - Eleni Sallinger
- Department of BiologyUniversity of Central Arkansas201 Donaghey Avenue, ConwayAR72035USA
| | - David C. Queller
- Department of BiologyWashington University in St. LouisOne Brookings Drive St. LouisMO63130USA
| | - Joan E. Strassmann
- Department of BiologyWashington University in St. LouisOne Brookings Drive St. LouisMO63130USA
| | - Susanne DiSalvo
- Department of Biological SciencesSouthern Illinois University Edwardsville44 Circle Drive, EdwardsvilleIL62026USA
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Hubert J, Nesvorna M, Pekar S, Green SJ, Klimov PB. Cardinium inhibits Wolbachia in its mite host, Tyrophagus putrescentiae, and affects host fitness. FEMS Microbiol Ecol 2021; 97:6358523. [PMID: 34448854 DOI: 10.1093/femsec/fiab123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/24/2021] [Indexed: 12/14/2022] Open
Abstract
Interactions among endosymbiotic bacteria inside their eukaryotic hosts are poorly understood, particularly in mites. The mite Tyrophagus putrescentiae is a common, medically important generalist species that has many intracellular and gut bacterial symbionts. In the experiments, we examined bacterial abundances and composition in mite populations obtained by controlled mixing of stock mite populations that differed in the presence/absence of the major intracellular bacteria Wolbachia and Cardinium. Changes in microbial communities were characterized using 16S ribosomal RNA high-throughput sequencing (pooled mite individuals) and quantitative PCR for key microbial taxa (individual mites). Mite fitness was estimated as a parameter of population growth. We detected that in mixed mite populations, Cardinium and Wolbachia can co-occur in the same mite individual. The presence of Cardinium was negatively correlated with the presence of Wolbachia and Bartonella, while the Bartonella and Wolbachia were positively correlated in individual level samples. Since mixed populations had lower abundances of Wolbachia, while the abundance of Cardinium did not change, we suggest that the presence of Cardinium inhibits the growth of Wolbachia. The mixed mite populations had lower population growth than parental populations. The possible effect of symbionts on the fitness of mixed population is discussed.
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Affiliation(s)
- Jan Hubert
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, CZ-165 00 Prague 6-Suchdol, Czechia
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, CZ-611 37 Brno, Czechia
| | - Stefan J Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL 60612, USA
| | - Pavel B Klimov
- School of Natural Sciences, Bangor University, Bangor, LL57 2 UW, UK.,Institute of Biology, University of Tyumen, Pirogova 3, 625043 Tyumen, Russia
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Selvaraj G, Santos-Garcia D, Mozes-Daube N, Medina S, Zchori-Fein E, Freilich S. An eco-systems biology approach for modeling tritrophic networks reveals the influence of dietary amino acids on symbiont dynamics of Bemisia tabaci. FEMS Microbiol Ecol 2021; 97:6348090. [PMID: 34379764 DOI: 10.1093/femsec/fiab117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/09/2021] [Indexed: 01/12/2023] Open
Abstract
Metabolic conversions allow organisms to produce essential metabolites from the available nutrients in an environment, frequently requiring metabolic exchanges among co-inhabiting organisms. Here, we applied genomic-based simulations for exploring tri-trophic interactions among the sap-feeding insect whitefly (Bemisia tabaci), its host-plants, and symbiotic bacteria. The simplicity of this ecosystem allows capturing the interacting organisms (based on genomic data) and the environmental content (based on metabolomics data). Simulations explored the metabolic capacities of insect-symbiont combinations under environments representing natural phloem. Predictions were correlated with experimental data on the dynamics of symbionts under different diets. Simulation outcomes depict a puzzle of three-layer origins (plant-insect-symbionts) for the source of essential metabolites across habitats and stratify interactions enabling the whitefly to feed on diverse hosts. In parallel to simulations, natural and artificial feeding experiments provide supporting evidence for an environment-based effect on symbiont dynamics. Based on simulations, a decrease in the relative abundance of a symbiont can be associated with a loss of fitness advantage due to an environmental excess in amino-acids whose production in a deprived environment used to depend on the symbiont. The study demonstrates that genomic-based predictions can bridge environment and community dynamics and guide the design of symbiont manipulation strategies.
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Affiliation(s)
- Gopinath Selvaraj
- Institute of Plant Sciences, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel.,Institute of Plant Protection, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel
| | - Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Netta Mozes-Daube
- Institute of Plant Protection, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel
| | - Shlomit Medina
- Institute of Plant Sciences, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel
| | - Einat Zchori-Fein
- Institute of Plant Protection, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel
| | - Shiri Freilich
- Institute of Plant Sciences, Newe Ya'ar Research Center, The Agricultural Research Organization, P.O.B. 1021, Ramat Yishay, 30095, Israel
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20
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Renoz F, Foray V, Ambroise J, Baa-Puyoulet P, Bearzatto B, Mendez GL, Grigorescu AS, Mahillon J, Mardulyn P, Gala JL, Calevro F, Hance T. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica. Front Cell Infect Microbiol 2021; 11:660007. [PMID: 34268133 PMCID: PMC8275996 DOI: 10.3389/fcimb.2021.660007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/14/2021] [Indexed: 01/10/2023] Open
Abstract
Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial associates of insects that are at the gateway to a host-dependent lifestyle.
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Affiliation(s)
- François Renoz
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Vincent Foray
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
- Institut de Recherche sur la Biologie de l’insecte, UMR 7261, CNRS, Université de Tours, Tours, France
| | - Jérôme Ambroise
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | | | - Bertrand Bearzatto
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Gipsi Lima Mendez
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Jean-Luc Gala
- Center for Applied Molecular Technologies, Institute of Experimental and Clinical Research, Université catholique de Louvain (UCLouvain), Woluwe-Saint-Lambert, Belgium
| | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2i, UMR203, F-69621, Villeurbanne, France
| | - Thierry Hance
- Biodiversity Research Centre, Earth and Life Institute, Université catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium
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21
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Andreason SA, Shelby EA, Moss JB, Moore PJ, Moore AJ, Simmons AM. Whitefly Endosymbionts: Biology, Evolution, and Plant Virus Interactions. INSECTS 2020; 11:insects11110775. [PMID: 33182634 PMCID: PMC7696030 DOI: 10.3390/insects11110775] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/07/2020] [Indexed: 11/16/2022]
Abstract
Whiteflies (Hemiptera: Aleyrodidae) are sap-feeding global agricultural pests. These piercing-sucking insects have coevolved with intracellular endosymbiotic bacteria that help to supplement their nutrient-poor plant sap diets with essential amino acids and carotenoids. These obligate, primary endosymbionts have been incorporated into specialized organs called bacteriomes where they sometimes coexist with facultative, secondary endosymbionts. All whitefly species harbor the primary endosymbiont Candidatus Portiera aleyrodidarum and have a variable number of secondary endosymbionts. The secondary endosymbiont complement harbored by the cryptic whitefly species Bemisia tabaci is particularly complex with various assemblages of seven different genera identified to date. In this review, we discuss whitefly associated primary and secondary endosymbionts. We focus on those associated with the notorious B. tabaci species complex with emphasis on their biological characteristics and diversity. We also discuss their interactions with phytopathogenic begomoviruses (family Geminiviridae), which are transmitted exclusively by B. tabaci in a persistent-circulative manner. Unraveling the complex interactions of these endosymbionts with their insect hosts and plant viruses could lead to advancements in whitefly and whitefly transmitted virus management.
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Affiliation(s)
- Sharon A. Andreason
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA;
| | - Emily A. Shelby
- Department of Entomology, University of Georgia, Athens, GA 30602, USA; (E.A.S.); (J.B.M.); (P.J.M.); (A.J.M.)
| | - Jeanette B. Moss
- Department of Entomology, University of Georgia, Athens, GA 30602, USA; (E.A.S.); (J.B.M.); (P.J.M.); (A.J.M.)
| | - Patricia J. Moore
- Department of Entomology, University of Georgia, Athens, GA 30602, USA; (E.A.S.); (J.B.M.); (P.J.M.); (A.J.M.)
| | - Allen J. Moore
- Department of Entomology, University of Georgia, Athens, GA 30602, USA; (E.A.S.); (J.B.M.); (P.J.M.); (A.J.M.)
| | - Alvin M. Simmons
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Vegetable Laboratory, Charleston, SC 29414, USA;
- Correspondence:
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Ren FR, Sun X, Wang TY, Yao YL, Huang YZ, Zhang X, Luan JB. Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits. THE ISME JOURNAL 2020; 14:2542-2553. [PMID: 32572143 PMCID: PMC7490365 DOI: 10.1038/s41396-020-0704-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/01/2020] [Accepted: 06/11/2020] [Indexed: 12/15/2022]
Abstract
Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.
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Affiliation(s)
- Fei-Rong Ren
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiang Sun
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Tian-Yu Wang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ya-Lin Yao
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yan-Zhen Huang
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xue Zhang
- China Agricultural University, Beijing, 100083, China
| | - Jun-Bo Luan
- Liaoning Key Laboratory of Economic and Applied Entomology, College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China.
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Stouthamer CM, Kelly SE, Mann E, Schmitz-Esser S, Hunter MS. Development of a multi-locus sequence typing system helps reveal the evolution of Cardinium hertigii, a reproductive manipulator symbiont of insects. BMC Microbiol 2019; 19:266. [PMID: 31775631 PMCID: PMC6882061 DOI: 10.1186/s12866-019-1638-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022] Open
Abstract
Background Cardinium is an intracellular bacterial symbiont in the phylum Bacteroidetes that is found in many different species of arthropods and some nematodes. This symbiont is known to be able to induce three reproductive manipulation phenotypes, including cytoplasmic incompatibility. Placing individual strains of Cardinium within a larger evolutionary context has been challenging because only two, relatively slowly evolving genes, 16S rRNA gene and Gyrase B, have been used to generate phylogenetic trees, and consequently, the relationship of different strains has been elucidated in only its roughest form. Results We developed a Multi Locus Sequence Typing (MLST) system that provides researchers with three new genes in addition to Gyrase B for inferring phylogenies and delineating Cardinium strains. From our Cardinium phylogeny, we confirmed the presence of a new group D, a Cardinium clade that resides in the arachnid order harvestmen (Opiliones). Many Cardinium clades appear to display a high degree of host affinity, while some show evidence of host shifts to phylogenetically distant hosts, likely associated with ecological opportunity. Like the unrelated reproductive manipulator Wolbachia, the Cardinium phylogeny also shows no clear phylogenetic signal associated with particular reproductive manipulations. Conclusions The Cardinium phylogeny shows evidence of diversification within particular host lineages, and also of host shifts among trophic levels within parasitoid-host communities. Like Wolbachia, the relatedness of Cardinium strains does not necessarily predict their reproductive phenotypes. Lastly, the genetic tools proposed in this study may help future authors to characterize new strains and add to our understanding of Cardinium evolution.
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Affiliation(s)
- Corinne M Stouthamer
- Department of Entomology, University of Arizona, 410 Forbes Building, Tucson, AZ, 85721, USA
| | - Suzanne E Kelly
- Department of Entomology, University of Arizona, 410 Forbes Building, Tucson, AZ, 85721, USA
| | - Evelyne Mann
- Milk Technology and Food Science, Institute for Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | | | - Martha S Hunter
- Department of Entomology, University of Arizona, 410 Forbes Building, Tucson, AZ, 85721, USA.
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Klimov P, Molva V, Nesvorna M, Pekar S, Shcherbachenko E, Erban T, Hubert J. Dynamics of the microbial community during growth of the house dust mite Dermatophagoides farinae in culture. FEMS Microbiol Ecol 2019; 95:5581497. [DOI: 10.1093/femsec/fiz153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 10/01/2019] [Indexed: 12/27/2022] Open
Abstract
ABSTRACTThe variation in house dust mite microbial communities is important because various microorganisms modulate the production of allergens by their mite hosts and/or contaminate immunotherapeutic extracts. Temporal changes in mite microbiomes and the mite culture environment occurring at different stages of mite culture development are particularly understudied in this system. Here, we analyzed the dynamics of microbial communities during the culture growth of Dermatophagoides farinae. Changes in microbiomes were related to three key variables: the mite population density, microbial microcosm respiration and concentration of guanine (the mite nitrogenous waste metabolite). Mite populations exhibited the following phases: exponential growth, plateau and exponential decline. The intracellular bacterium Cardinium and the yeast Saccharomyces cerevisiae prevailed in the internal mite microbiomes, and the bacterium Lactobacillus fermentum was prevalent in the mite diet. The reduction in the mite population size during the late phases of culture development was related to the changes in their microbial profiles: the intracellular bacterium Cardinium was replaced by Staphylococcus, Oceanobacillus and Virgibacillus, and S. cerevisiae was replaced by the antagonistic fungi Aspergillus penicillioides and Candida. Increases in the guanine content were positively correlated with increases in the Staphylococcus and A. penicillioides profiles in the culture environment. Our results show that the mite microbiome exhibits strong, dynamic alterations in its profiles across different mite culture growth stages.
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Affiliation(s)
- Pavel Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 3600 Varsity Drive, Ann Arbor, MI 48109, USA
- Institute of Biology, University of Tyumen, Pirogova 3, 625043 Tyumen, Russia
| | - Vit Molva
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 1594/7, CZ-12800 Prague 2, Czechia
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia
| | - Stano Pekar
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 267/2, CZ-61137 Brno, Czechia
| | | | - Tomas Erban
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia
| | - Jan Hubert
- Crop Research Institute, Drnovska 507/73, CZ-16106 Prague 6-Ruzyne, Czechia
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First Evidence of Intracellular Bacteria Cardinium in Thermophilic Mite Microzetorchestes emeryi (Acari: Oribatida): Molecular Screening of Bacterial Endosymbiont Species. Curr Microbiol 2019; 76:1038-1044. [PMID: 31214820 PMCID: PMC6663925 DOI: 10.1007/s00284-019-01717-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/06/2019] [Indexed: 11/02/2022]
Abstract
We undertook the issue of the distribution of intracellular bacteria among Oribatida (Acari). Six genera of bacteria were detected by PCR and Sanger DNA sequencing: Wolbachia, Cardinium, Rickettsia, Spiroplasma, Arsenophonus, and Hamiltonella. Our research, for the first time, revealed the presence of Cardinium in Microzetorchestes emeryi in two subpopulations separated from each other by 300 m. The percentages of infected animals were the same in both subpopulations-ca. 20%. The identity of 16S rDNA sequences of Cardinium between these two subpopulations of M. emeryi was 97%. Phylogenetic analysis showed that the Cardinium in M. emeryi was clustered into the group A. The occurrence of M. emeryi in Poland has not been reported before and our report is the first one. Cardinium maybe help the thermophilic M. emeryi to adapt to low temperatures in the Central Europe.
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Hubert J, Nesvorna M, Kopecky J, Erban T, Klimov P. Population and Culture Age Influence the Microbiome Profiles of House Dust Mites. MICROBIAL ECOLOGY 2019; 77:1048-1066. [PMID: 30465068 DOI: 10.1007/s00248-018-1294-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/13/2018] [Indexed: 05/09/2023]
Abstract
Interactions with microorganisms might enable house dust mites (HDMs) to derive nutrients from difficult-to-digest structural proteins and to flourish in human houses. We tested this hypothesis by investigating the effects of changes in the mite culture growth and population of two HDM species on HDM microbiome composition and fitness. Growing cultures of laboratory and industrial allergen-producing populations of Dermatophagoides farinae (DFL and DFT, respectively) and Dermatophagoides pteronyssinus (DPL and DPT, respectively) were sampled at four time points. The symbiotic microorganisms of the mites were characterized by DNA barcode sequencing and quantified by qPCR using universal/specific primers. The population growth of mites and nutrient contents of mite bodies were measured and correlated with the changes in bacteria in the HDM microbiome. The results showed that both the population and culture age significantly influenced the microbiome profiles. Cardinium formed 93% and 32% of the total sequences of the DFL and DFT bacterial microbiomes, respectively, but this bacterial species was less abundant in the DPL and DPT microbiomes. Staphylococcus abundance was positively correlated with increased glycogen contents in the bodies of mites, and increased abundances of Aspergillus, Candida, and Kocuria were correlated with increased lipid contents in the bodies of mites. The xerophilic fungus Wallemia accounted for 39% of the fungal sequences in the DPL microbiome, but its abundance was low in the DPT, DFL, and DFT microbiomes. With respect to the mite culture age, we made three important observations: the mite population growth from young cultures was 5-8-fold higher than that from old cultures; specimens from old cultures had greater abundances of fungi and bacteria in their bodies; and yeasts predominated in the gut contents of specimens from young cultures, whereas filamentous mycelium prevailed in specimens from old cultures. Our results are consistent with the hypothesis that mites derive nutrients through associations with microorganisms.
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Affiliation(s)
- Jan Hubert
- Crop Research Institute, Drnovska 507/73, CZ-16106, Prague 6-Ruzyne, Czechia.
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, CZ-16106, Prague 6-Ruzyne, Czechia
| | - Jan Kopecky
- Crop Research Institute, Drnovska 507/73, CZ-16106, Prague 6-Ruzyne, Czechia
| | - Tomas Erban
- Crop Research Institute, Drnovska 507/73, CZ-16106, Prague 6-Ruzyne, Czechia
| | - Pavel Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 3600 Varsity Drive, Ann Arbor, MI, 48109-2228, USA
- Institute of Biology, University of Tyumen, Pirogova 3, Tyumen, Russia, 625043
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Siozios S, Pilgrim J, Darby AC, Baylis M, Hurst GD. The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont. PeerJ 2019; 7:e6448. [PMID: 30809447 PMCID: PMC6387759 DOI: 10.7717/peerj.6448] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/15/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A-D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors. METHODS We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens. RESULTS The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set-characterized by DUF1703 domains-not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin. DISCUSSION These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.
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Affiliation(s)
- Stefanos Siozios
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Jack Pilgrim
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Alistair C. Darby
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Matthew Baylis
- Institute of Infection and Global Health, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections (HPRU-EZI), University of Liverpool, Liverpool, UK
| | - Gregory D.D. Hurst
- Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
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A new Cardinium group of bacteria found in Achipteria coleoptrata (Acari: Oribatida). Mol Phylogenet Evol 2018; 131:64-71. [PMID: 30391314 DOI: 10.1016/j.ympev.2018.10.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/15/2018] [Accepted: 10/31/2018] [Indexed: 11/20/2022]
Abstract
The understanding of the biology of arthropods requires an understanding of their bacterial associates. We determined the distribution of bacteria Wolbachia sp., Rickettsia sp., Cardinium sp., Spiroplasma sp., Arsenophonus sp., Hamiltonella sp., and Flavobacterium in oribatid mites (Acari: Oribatida). We identified Cardinium sp. in Achipteria coleoptrata. This is the first report of this bacterium in A. coleoptrata. Approximately 30% of the mite population was infected by Cardinium sp. The Cardinium 16S rDNA was examined for the presence of two sequences unique for this microorganism. One of them was noted in Cardinium sp. of A. coleoptrata. In the second sequence, we found nucleotide substitution in the 7th position: A instead of T. In our opinion, this demonstrated the unique nature of Cardinium sp. of A. coleoptrata. We also determined phylogenetic relationship between Cardinium sp., including the strain found in A. coleoptrata by studying the 16S rRNA and gyrB gene sequences. It revealed that Cardinium from A. coleoptrata did not cluster together with strains from groups A, B, C or D, and constituted a separate clade E. These observations make A. coleoptrata a unique Cardinium host in terms of the distinction of the strain.
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29
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Brown AMV, Wasala SK, Howe DK, Peetz AB, Zasada IA, Denver DR. Comparative Genomics of Wolbachia- Cardinium Dual Endosymbiosis in a Plant-Parasitic Nematode. Front Microbiol 2018; 9:2482. [PMID: 30459726 PMCID: PMC6232779 DOI: 10.3389/fmicb.2018.02482] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/28/2018] [Indexed: 12/11/2022] Open
Abstract
Wolbachia and Cardinium are among the most important and widespread of all endosymbionts, occurring in nematodes and more than half of insect and arachnid species, sometimes as coinfections. These symbionts are of significant interest as potential biocontrol agents due to their abilities to cause major effects on host biology and reproduction through cytoplasmic incompatibility, sex ratio distortion, or obligate mutualism. The ecological and metabolic effects of coinfections are not well understood. This study examined a Wolbachia-Cardinium coinfection in the plant-parasitic nematode (PPN), Pratylenchus penetrans, producing the first detailed study of such a coinfection using fluorescence in situ hybridization (FISH), polymerase chain reaction (PCR), and comparative genomic analysis. Results from FISH and single-nematode PCR showed 123/127 individuals in a focal population carried Cardinium (denoted strain cPpe), and 48% were coinfected with Wolbachia strain wPpe. Both endosymbionts showed dispersed tissue distribution with highest densities in the anterior intestinal walls and gonads. Phylogenomic analyses confirmed an early place of cPpe and long distance from a sister strain in another PPN, Heterodera glycines, supporting a long history of both Cardinium and Wolbachia in PPNs. The genome of cPpe was 1.36 Mbp with 35.8% GC content, 1,131 predicted genes, 41% having no known function, and missing biotin and lipoate synthetic capacity and a plasmid present in other strains, despite having a slightly larger genome compared to other sequenced Cardinium. The larger genome revealed expansions of gene families likely involved in host-cellular interactions. More than 2% of the genes of cPpe and wPpe were identified as candidate horizontally transferred genes, with some of these from eukaryotes, including nematodes. A model of the possible Wolbachia-Cardinium interaction is proposed with possible complementation in function for pathways such as methionine and fatty acid biosynthesis and biotin transport.
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Affiliation(s)
- Amanda M V Brown
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, United States
| | - Sulochana K Wasala
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, OR, United States
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
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30
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Zeng Z, Fu Y, Guo D, Wu Y, Ajayi OE, Wu Q. Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host. BMC Genomics 2018; 19:688. [PMID: 30231855 PMCID: PMC6147030 DOI: 10.1186/s12864-018-5078-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 09/13/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sogatella furcifera is a migratory pest that damages rice plants and causes severe economic losses. Due to its ability to annually migrate long distances, S. furcifera has emerged as a major pest of rice in several Asian countries. Symbiotic relationships of inherited bacteria with terrestrial arthropods have significant implications. The genus Cardinium is present in many types of arthropods, where it influences some host characteristics. We present a report of a newly identified strain of the bacterial endosymbiont Cardinium cSfur in S. furcifera. RESULT From the whole genome of S. furcifera previously sequenced by our laboratory, we assembled the whole genome sequence of Cardinium cSfur. The sequence comprised 1,103,593 bp with a GC content of 39.2%. The phylogenetic tree of the Bacteroides phylum to which Cardinium cSfur belongs suggests that Cardinium cSfur is closely related to the other strains (Cardinium cBtQ1 and cEper1) that are members of the Amoebophilaceae family. Genome comparison between the host-dependent endosymbiont including Cardinium cSfur and free-living bacteria revealed that the endosymbiont has a smaller genome size and lower GC content, and has lost some genes related to metabolism because of its special environment, which is similar to the genome pattern observed in other insect symbionts. Cardinium cSfur has limited metabolic capability, which makes it less contributive to metabolic and biosynthetic processes in its host. From our findings, we inferred that, to compensate for its limited metabolic capability, Cardinium cSfur harbors a relatively high proportion of transport proteins, which might act as the hub between it and its host. With its acquisition of the whole operon related to biotin synthesis and glycolysis related genes through HGT event, Cardinium cSfur seems to be undergoing changes while establishing a symbiotic relationship with its host. CONCLUSION A novel bacterial endosymbiont strain (Cardinium cSfur) has been discovered. A genomic analysis of the endosymbiont in S. furcifera suggests that its genome has undergone certain changes to facilitate its settlement in the host. The envisaged potential reproduction manipulative ability of the new endosymbiont strain in its S. furcifera host has vital implications in designing eco-friendly approaches to combat the insect pest.
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Affiliation(s)
- Zhen Zeng
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230027 China
| | - Yating Fu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230027 China
| | - Dongyang Guo
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230027 China
| | - Yuxuan Wu
- Department of Computer Science, University of Nottingham Ningbo China, Zhejiang, 315100 China
| | - Olugbenga Emmanuel Ajayi
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230027 China
| | - Qingfa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, 230027 China
- CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, 230027 China
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Gillespie JJ, Driscoll TP, Verhoeve VI, Rahman MS, Macaluso KR, Azad AF. A Tangled Web: Origins of Reproductive Parasitism. Genome Biol Evol 2018; 10:2292-2309. [PMID: 30060072 PMCID: PMC6133264 DOI: 10.1093/gbe/evy159] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/13/2022] Open
Abstract
While typically a flea parasite and opportunistic human pathogen, the presence of Rickettsia felis (strain LSU-Lb) in the non-blood-feeding, parthenogenetically reproducing booklouse, Liposcelis bostrychophila, provides a system to ascertain factors governing not only host transitions but also obligate reproductive parasitism (RP). Analysis of plasmid pLbAR, unique to R. felis str. LSU-Lb, revealed a toxin–antitoxin module with similar features to prophage-encoded toxin–antitoxin modules utilized by parasitic Wolbachia strains to induce another form of RP, cytoplasmic incompatibility, in their arthropod hosts. Curiously, multiple deubiquitinase and nuclease domains of the large (3,841 aa) pLbAR toxin, as well the entire antitoxin, facilitated the detection of an assortment of related proteins from diverse intracellular bacteria, including other reproductive parasites. Our description of these remarkable components of the intracellular mobilome, including their presence in certain arthropod genomes, lends insight on the evolution of RP, while invigorating research on parasite-mediated biocontrol of arthropod-borne viral and bacterial pathogens.
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Affiliation(s)
- Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine
| | | | | | | | - Kevin R Macaluso
- Vector-borne Disease Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University
| | - Abdu F Azad
- Department of Microbiology and Immunology, University of Maryland School of Medicine
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Showmaker KC, Walden KKO, Fields CJ, Lambert KN, Hudson ME. Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) Endosymbiont "Candidatus Cardinium hertigii" Strain cHgTN10. GENOME ANNOUNCEMENTS 2018; 6:e00624-18. [PMID: 29954916 PMCID: PMC6025951 DOI: 10.1128/genomea.00624-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/02/2018] [Indexed: 02/01/2023]
Abstract
In this study, we present the genome sequence of the "Candidatus Cardinium hertigii" strain cHgTN10, an endosymbiotic bacterium of the plant-parasitic nematode Heterodera glycines This is the first genome assembly reported for an endosymbiont directly sequenced from a tylenchid nematode.
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Affiliation(s)
- Kurt C Showmaker
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kimberly K O Walden
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher J Fields
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kris N Lambert
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew E Hudson
- Department of Crop Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Opatovsky I, Santos-Garcia D, Ruan Z, Lahav T, Ofaim S, Mouton L, Barbe V, Jiang J, Zchori-Fein E, Freilich S. Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment. BMC Genomics 2018; 19:402. [PMID: 29801436 PMCID: PMC5970531 DOI: 10.1186/s12864-018-4786-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 05/11/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Individual organisms are linked to their communities and ecosystems via metabolic activities. Metabolic exchanges and co-dependencies have long been suggested to have a pivotal role in determining community structure. In phloem-feeding insects such metabolic interactions with bacteria enable complementation of their deprived nutrition. The phloem-feeding whitefly Bemisia tabaci (Hemiptera: Aleyrodidae) harbors an obligatory symbiotic bacterium, as well as varying combinations of facultative symbionts. This well-defined bacterial community in B. tabaci serves here as a case study for a comprehensive and systematic survey of metabolic interactions within the bacterial community and their associations with documented occurrences of bacterial combinations. We first reconstructed the metabolic networks of five common B. tabaci symbionts genera (Portiera, Rickettsia, Hamiltonella, Cardinium and Wolbachia), and then used network analysis approaches to predict: (1) species-specific metabolic capacities in a simulated bacteriocyte-like environment; (2) metabolic capacities of the corresponding species' combinations, and (3) dependencies of each species on different media components. RESULTS The predictions for metabolic capacities of the symbionts in the host environment were in general agreement with previously reported genome analyses, each focused on the single-species level. The analysis suggests several previously un-reported routes for complementary interactions and estimated the dependency of each symbiont in specific host metabolites. No clear association was detected between metabolic co-dependencies and co-occurrence patterns. CONCLUSIONS The analysis generated predictions for testable hypotheses of metabolic exchanges and co-dependencies in bacterial communities and by crossing them with co-occurrence profiles, contextualized interaction patterns into a wider ecological perspective.
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Affiliation(s)
- Itai Opatovsky
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
- Agricultural Research and Development Center, Southern Branch (Besor), Israel
| | | | - Zhepu Ruan
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tamar Lahav
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Shany Ofaim
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Laurence Mouton
- CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR CNRS 5558, Université de Lyon, Université Claude Bernard, F-69622 Villeurbanne, France
| | - Valérie Barbe
- Institut de biologie François-Jacob, GenoscopeCEA, Genoscope, Evry, France
| | - Jiandong Jiang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095 China
| | - Einat Zchori-Fein
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
| | - Shiri Freilich
- Newe Ya’ar Research Center, The Agricultural Research Organization, Ramat Yishay, Israel
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Gardner M, Dhroso A, Johnson N, Davis EL, Baum TJ, Korkin D, Mitchum MG. Novel global effector mining from the transcriptome of early life stages of the soybean cyst nematode Heterodera glycines. Sci Rep 2018; 8:2505. [PMID: 29410430 PMCID: PMC5802810 DOI: 10.1038/s41598-018-20536-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/12/2018] [Indexed: 11/08/2022] Open
Abstract
Soybean cyst nematode (SCN) Heterodera glycines is an obligate parasite that relies on the secretion of effector proteins to manipulate host cellular processes that favor the formation of a feeding site within host roots to ensure its survival. The sequence complexity and co-evolutionary forces acting upon these effectors remain unknown. Here we generated a de novo transcriptome assembly representing the early life stages of SCN in both a compatible and an incompatible host interaction to facilitate global effector mining efforts in the absence of an available annotated SCN genome. We then employed a dual effector prediction strategy coupling a newly developed nematode effector prediction tool, N-Preffector, with a traditional secreted protein prediction pipeline to uncover a suite of novel effector candidates. Our analysis distinguished between effectors that co-evolve with the host genotype and those conserved by the pathogen to maintain a core function in parasitism and demonstrated that alternative splicing is one mechanism used to diversify the effector pool. In addition, we confirmed the presence of viral and microbial inhabitants with molecular sequence information. This transcriptome represents the most comprehensive whole-nematode sequence currently available for SCN and can be used as a tool for annotation of expected genome assemblies.
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Affiliation(s)
- Michael Gardner
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Nathan Johnson
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA
| | - Eric L Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, USA
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, USA.
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, USA.
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Santos-Garcia D, Juravel K, Freilich S, Zchori-Fein E, Latorre A, Moya A, Morin S, Silva FJ. To B or Not to B: Comparative Genomics Suggests Arsenophonus as a Source of B Vitamins in Whiteflies. Front Microbiol 2018; 9:2254. [PMID: 30319574 PMCID: PMC6167482 DOI: 10.3389/fmicb.2018.02254] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/04/2018] [Indexed: 02/05/2023] Open
Abstract
Insect lineages feeding on nutritionally restricted diets such as phloem sap, xylem sap, or blood, were able to diversify by acquiring bacterial species that complement lacking nutrients. These bacteria, considered obligate/primary endosymbionts, share a long evolutionary history with their hosts. In some cases, however, these endosymbionts are not able to fulfill all of their host's nutritional requirements, driving the acquisition of additional symbiotic species. Phloem-feeding members of the insect family Aleyrodidae (whiteflies) established an obligate relationship with Candidatus Portiera aleyrodidarum, which provides its hots with essential amino acids and carotenoids. In addition, many whitefly species harbor additional endosymbionts which may potentially further supplement their host's diet. To test this hypothesis, genomes of several endosymbionts of the whiteflies Aleurodicus dispersus, Aleurodicus floccissimus and Trialeurodes vaporariorum were analyzed. In addition to Portiera, all three species were found to harbor one Arsenophonus and one Wolbachia endosymbiont. A comparative analysis of Arsenophonus genomes revealed that although all three are capable of synthesizing B vitamins and cofactors, such as pyridoxal, riboflavin, or folate, their genomes and phylogenetic relationship vary greatly. Arsenophonus of A. floccissimus and T. vaporariorum belong to the same clade, and display characteristics of facultative endosymbionts, such as large genomes (3 Mb) with thousands of genes and pseudogenes, intermediate GC content, and mobile genetic elements. In contrast, Arsenophonus of A. dispersus belongs to a different lineage and displays the characteristics of a primary endosymbiont-a reduced genome (670 kb) with ~400 genes, 32% GC content, and no mobile genetic elements. However, the presence of 274 pseudogenes suggests that this symbiotic association is more recent than other reported primary endosymbionts of hemipterans. The gene repertoire of Arsenophonus of A. dispersus is completely integrated in the symbiotic consortia, and the biosynthesis of most vitamins occurs in shared pathways with its host. In addition, Wolbachia endosymbionts have also retained the ability to produce riboflavin, flavin adenine dinucleotide, and folate, and may make a nutritional contribution. Taken together, our results show that Arsenophonus hold a pivotal place in whitefly nutrition by their ability to produce B vitamins.
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Affiliation(s)
- Diego Santos-Garcia
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
- *Correspondence: Diego Santos-Garcia
| | - Ksenia Juravel
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shiri Freilich
- Institute of Plant Sciences, Newe-Ya'ar Research Center, Agricultural Research Organization, Ramat-Yishai, Israel
| | - Einat Zchori-Fein
- Department of Entomology, Newe-Ya'ar Research Center, Agricultural Research Organization, Volcani Center, Ramat-Yishai, Israel
| | - Amparo Latorre
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
| | - Shai Morin
- Department of Entomology, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Francisco J. Silva
- Institute for Integrative Systems Biology, Universitat de València-CSIC, València, Spain
- Unidad Mixta de Investigación en Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO) and Institute for Integrative Systems Biology, Universitat de València, València, Spain
- Francisco J. Silva
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Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii-Caused Cytoplasmic Incompatibility and Host-Cell Interaction. mSystems 2017; 2:mSystems00141-17. [PMID: 29181449 PMCID: PMC5698495 DOI: 10.1128/msystems.00141-17] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 10/23/2017] [Indexed: 11/29/2022] Open
Abstract
The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes. Cytoplasmic incompatibility (CI) is an intriguing, widespread, symbiont-induced reproductive failure that decreases offspring production of arthropods through crossing incompatibility of infected males with uninfected females or with females infected with a distinct symbiont genotype. For years, the molecular mechanism of CI remained unknown. Recent genomic, proteomic, biochemical, and cell biological studies have contributed to understanding of CI in the alphaproteobacterium Wolbachia and implicate genes associated with the WO prophage. Besides a recently discovered additional lineage of alphaproteobacterial symbionts only moderately related to Wolbachia, Cardinium (Bacteroidetes) is the only other symbiont known to cause CI, and genomic evidence suggests that it has very little homology with Wolbachia and evolved this phenotype independently. Here, we present the first transcriptomic study of the CI Cardinium strain cEper1, in its natural host, Encarsia suzannae, to detect important CI candidates and genes involved in the insect-Cardinium symbiosis. Highly expressed transcripts included genes involved in manipulating ubiquitination, apoptosis, and host DNA. Female-biased genes encoding ribosomal proteins suggest an increase in general translational activity of Cardinium in female wasps. The results confirm previous genomic analyses that indicated that Wolbachia and Cardinium utilize different genes to induce CI, and transcriptome patterns further highlight expression of some common pathways that these bacteria use to interact with the host and potentially cause this enigmatic and fundamental manipulation of host reproduction. IMPORTANCE The majority of insects carry maternally inherited intracellular bacteria that are important in their hosts’ biology, ecology, and evolution. Some of these bacterial symbionts cause a reproductive failure known as cytoplasmic incompatibility (CI). In CI, the mating of symbiont-infected males and uninfected females produces few or no daughters. The CI symbiont then spreads and can have a significant impact on the insect host population. Cardinium, a bacterial endosymbiont of the parasitoid wasp Encarsia in the Bacteroidetes, is the only bacterial lineage known to cause CI outside the Alphaproteobacteria, where Wolbachia and another recently discovered CI symbiont reside. Here, we sought insight into the gene expression of a CI-inducing Cardinium strain in its natural host, Encarsia suzannae. Our study provides the first insights into the Cardinium transcriptome and provides support for the hypothesis that Wolbachia and Cardinium target similar host pathways with distinct and largely unrelated sets of genes.
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Driscoll TP, Verhoeve VI, Guillotte ML, Lehman SS, Rennoll SA, Beier-Sexton M, Rahman MS, Azad AF, Gillespie JJ. Wholly Rickettsia! Reconstructed Metabolic Profile of the Quintessential Bacterial Parasite of Eukaryotic Cells. mBio 2017; 8:e00859-17. [PMID: 28951473 PMCID: PMC5615194 DOI: 10.1128/mbio.00859-17] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 08/15/2017] [Indexed: 02/02/2023] Open
Abstract
Reductive genome evolution has purged many metabolic pathways from obligate intracellular Rickettsia (Alphaproteobacteria; Rickettsiaceae). While some aspects of host-dependent rickettsial metabolism have been characterized, the array of host-acquired metabolites and their cognate transporters remains unknown. This dearth of information has thwarted efforts to obtain an axenic Rickettsia culture, a major impediment to conventional genetic approaches. Using phylogenomics and computational pathway analysis, we reconstructed the Rickettsia metabolic and transport network, identifying 51 host-acquired metabolites (only 21 previously characterized) needed to compensate for degraded biosynthesis pathways. In the absence of glycolysis and the pentose phosphate pathway, cell envelope glycoconjugates are synthesized from three imported host sugars, with a range of additional host-acquired metabolites fueling the tricarboxylic acid cycle. Fatty acid and glycerophospholipid pathways also initiate from host precursors, and import of both isoprenes and terpenoids is required for the synthesis of ubiquinone and the lipid carrier of lipid I and O-antigen. Unlike metabolite-provisioning bacterial symbionts of arthropods, rickettsiae cannot synthesize B vitamins or most other cofactors, accentuating their parasitic nature. Six biosynthesis pathways contain holes (missing enzymes); similar patterns in taxonomically diverse bacteria suggest alternative enzymes that await discovery. A paucity of characterized and predicted transporters emphasizes the knowledge gap concerning how rickettsiae import host metabolites, some of which are large and not known to be transported by bacteria. Collectively, our reconstructed metabolic network offers clues to how rickettsiae hijack host metabolic pathways. This blueprint for growth determinants is an important step toward the design of axenic media to rescue rickettsiae from the eukaryotic cell.IMPORTANCE A hallmark of obligate intracellular bacteria is the tradeoff of metabolic genes for the ability to acquire host metabolites. For species of Rickettsia, arthropod-borne parasites with the potential to cause serious human disease, the range of pilfered host metabolites is unknown. This information is critical for dissociating rickettsiae from eukaryotic cells to facilitate rickettsial genetic manipulation. In this study, we reconstructed the Rickettsia metabolic network and identified 51 host metabolites required to compensate patchwork Rickettsia biosynthesis pathways. Remarkably, some metabolites are not known to be transported by any bacteria, and overall, few cognate transporters were identified. Several pathways contain missing enzymes, yet similar pathways in unrelated bacteria indicate convergence and possible novel enzymes awaiting characterization. Our work illuminates the parasitic nature by which rickettsiae hijack host metabolism to counterbalance numerous disintegrated biosynthesis pathways that have arisen through evolution within the eukaryotic cell. This metabolic blueprint reveals what a Rickettsia axenic medium might entail.
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Affiliation(s)
- Timothy P Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Victoria I Verhoeve
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Mark L Guillotte
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Stephanie S Lehman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sherri A Rennoll
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Magda Beier-Sexton
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - M Sayeedur Rahman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Abdu F Azad
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Hubert J, Kopecky J, Nesvorna M, Alejandra Perotti M, Erban T. Detection and localization of Solitalea-like and Cardinium bacteria in three Acarus siro populations (Astigmata: Acaridae). EXPERIMENTAL & APPLIED ACAROLOGY 2016; 70:309-327. [PMID: 27502113 DOI: 10.1007/s10493-016-0080-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/26/2016] [Indexed: 05/09/2023]
Abstract
Bacteria associated with mites influence their fitness, nutrition and reproduction. Previously, we found Solitalea-like (Sphingobacteriales) and Candidatus Cardinium (Cytophagales) bacteria in the stored product mite Acarus siro L. by cloning and using pyrosequencing. In this study, taxon-specific primers targeting 16S rRNA gene were used to detect and quantify the bacteria in mites and eggs of three A. siro populations. The specific probes for fluorescent in situ hybridization (FISH) were used to localize Solitalea-like and Cardinium bacteria in mite bodies. The population growth as an indirect estimator of fitness was used to describe the mite-bacteria interactions on (1) control diet; (2) rifampicin supplemented diet; (3) tetracycline supplemented diet; (4) rifampicin pretreated mites; (5) tetracycline pretreated mites. Solitalea-like 16S rRNA gene sequences from A. siro formed a separate cluster together with sequences from Tyrophagus putrescentiae. qPCR analysis indicated that number of Solitalea-like bacteria 16S rRNA gene copies was ca. 100× higher than that of Cardinium and the numbers differed between populations. FISH analysis localized Solitalea-like bacteria in the parenchymal tissues, mesodeum and food bolus of larvae, nymphs and adults. Solitalea-like, but not Cardinium bacteria were detected by taxon-specific primers in mites and eggs of all three investigated populations. None of the antibiotic treatments eliminated Solitalea-like bacteria in the A. siro populations tested. Rifampicin pretreatment significantly decreased the population growth. The numbers of Solitalea-like bacteria did not correlate with the population growth as a fitness indicator. This study demonstrated that A. siro can host Solitalea-like bacteria either alone or together with Cardinium. We suggest that Solitalea-like bacteria are shared by vertical transfer in A. siro populations.
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Affiliation(s)
- Jan Hubert
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, 16106, Czech Republic.
| | - Jan Kopecky
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, 16106, Czech Republic
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, 16106, Czech Republic
| | - M Alejandra Perotti
- Ecology and Evolutionary Biology Section, School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AS, UK
| | - Tomas Erban
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, 16106, Czech Republic
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Zhu DT, Xia WQ, Rao Q, Liu SS, Ghanim M, Wang XW. Sequencing and comparison of the Rickettsia genomes from the whitefly Bemisia tabaci Middle East Asia Minor I. INSECT SCIENCE 2016; 23:531-542. [PMID: 27273750 DOI: 10.1111/1744-7917.12367] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
The whitefly, Bemisia tabaci, harbors the primary symbiont 'Candidatus Portiera aleyrodidarum' and a variety of secondary symbionts. Among these secondary symbionts, Rickettsia is the only one that can be detected both inside and outside the bacteriomes. Infection with Rickettsia has been reported to influence several aspects of the whitefly biology, such as fitness, sex ratio, virus transmission and resistance to pesticides. However, mechanisms underlying these differences remain unclear, largely due to the lack of genomic information of Rickettsia. In this study, we sequenced the genome of two Rickettsia strains isolated from the Middle East Asia Minor 1 (MEAM1) species of the B. tabaci complex in China and Israel. Both Rickettsia genomes were of high coding density and AT-rich, containing more than 1000 coding sequences, much larger than that of the coexisted primary symbiont, Portiera. Moreover, the two Rickettsia strains isolated from China and Israel shared most of the genes with 100% identity and only nine genes showed sequence differences. The phylogenetic analysis using orthologs shared in the genus, inferred the proximity of Rickettsia in MEAM1 and Rickettsia bellii. Functional analysis revealed that Rickettsia was unable to synthesize amino acids required for complementing the whitefly nutrition. Besides, a type IV secretion system and a number of virulence-related genes were detected in the Rickettsia genome. The presence of virulence-related genes might benefit the symbiotic life of the bacteria, and hint on potential effects of Rickettsia on whiteflies. The genome sequences of Rickettsia provided a basis for further understanding the function of Rickettsia in whiteflies.
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Affiliation(s)
- Dan-Tong Zhu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Qiang Xia
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qiong Rao
- School of Agriculture and Food Science, Zhejiang Agriculture and Forestry University, Lin'an, Hangzhou, China
| | - Shu-Sheng Liu
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Murad Ghanim
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Xiao-Wei Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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40
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Sahoo RK. Why Antagonistic Traits against Cytoplasmic Incompatibility Are So Elusive. Front Microbiol 2016; 7:392. [PMID: 27065360 PMCID: PMC4814451 DOI: 10.3389/fmicb.2016.00392] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/14/2016] [Indexed: 11/21/2022] Open
Affiliation(s)
- Ranjit Kumar Sahoo
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram Thiruvananthapuram, India
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Gonella E, Pajoro M, Marzorati M, Crotti E, Mandrioli M, Pontini M, Bulgari D, Negri I, Sacchi L, Chouaia B, Daffonchio D, Alma A. Plant-mediated interspecific horizontal transmission of an intracellular symbiont in insects. Sci Rep 2015; 5:15811. [PMID: 26563507 PMCID: PMC4643326 DOI: 10.1038/srep15811] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/24/2015] [Indexed: 11/09/2022] Open
Abstract
Intracellular reproductive manipulators, such as Candidatus Cardinium and Wolbachia are vertically transmitted to progeny but rarely show co-speciation with the host. In sap-feeding insects, plant tissues have been proposed as alternative horizontal routes of interspecific transmission, but experimental evidence is limited. Here we report results from experiments that show that Cardinium is horizontally transmitted between different phloem sap-feeding insect species through plants. Quantitative PCR and in situ hybridization experiments indicated that the leafhopper Scaphoideus titanus releases Cardinium from its salivary glands during feeding on both artificial media and grapevine leaves. Successional time-course feeding experiments with S. titanus initially fed sugar solutions or small areas of grapevine leaves followed by feeding by the phytoplasma vector Macrosteles quadripunctulatus or the grapevine feeder Empoasca vitis revealed that the symbionts were transmitted to both species. Explaining interspecific horizontal transmission through plants improves our understanding of how symbionts spread, their lifestyle and the symbiont-host intermixed evolutionary pattern.
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Affiliation(s)
- Elena Gonella
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, 10095 Grugliasco
| | - Massimo Pajoro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, 10095 Grugliasco
| | - Massimo Marzorati
- Dipartimento di Scienze per gli Alimenti, la Nutrizione, l'Ambiente (DeFENS), Università degli Studi di Milano, 20133 Milan
| | - Elena Crotti
- Dipartimento di Scienze per gli Alimenti, la Nutrizione, l'Ambiente (DeFENS), Università degli Studi di Milano, 20133 Milan
| | - Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, 41100 Modena
| | - Marianna Pontini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, 10095 Grugliasco
| | - Daniela Bulgari
- Dipartimento di Scienze Agrarie e Ambientali-Produzione, Territorio, Agroenergia, Università degli Studi di Milano, 20133 Milan
| | - Ilaria Negri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, 10095 Grugliasco
| | - Luciano Sacchi
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università degli Studi di Pavia, 27100 Pavia
| | - Bessem Chouaia
- Dipartimento di Scienze per gli Alimenti, la Nutrizione, l'Ambiente (DeFENS), Università degli Studi di Milano, 20133 Milan
| | - Daniele Daffonchio
- Dipartimento di Scienze per gli Alimenti, la Nutrizione, l'Ambiente (DeFENS), Università degli Studi di Milano, 20133 Milan.,King Abdullah University of Science and Technology, BESE Division, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Alberto Alma
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Università degli Studi di Torino, 10095 Grugliasco
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42
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Brown AMV, Howe DK, Wasala SK, Peetz AB, Zasada IA, Denver DR. Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis. Genome Biol Evol 2015; 7:2727-46. [PMID: 26362082 PMCID: PMC4607532 DOI: 10.1093/gbe/evv176] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacterial mutualists can modulate the biochemical capacity of animals. Highly coevolved nutritional mutualists do this by synthesizing nutrients missing from the host’s diet. Genomics tools have advanced the study of these partnerships. Here we examined the endosymbiont Xiphinematobacter (phylum Verrucomicrobia) from the dagger nematode Xiphinema americanum, a migratory ectoparasite of numerous crops that also vectors nepovirus. Previously, this endosymbiont was identified in the gut, ovaries, and eggs, but its role was unknown. We explored the potential role of this symbiont using fluorescence in situ hybridization, genome sequencing, and comparative functional genomics. We report the first genome of an intracellular Verrucomicrobium and the first exclusively intracellular non-Wolbachia nematode symbiont. Results revealed that Xiphinematobacter had a small 0.916-Mb genome with only 817 predicted proteins, resembling genomes of other mutualist endosymbionts. Compared with free-living relatives, conserved proteins were shorter on average, and there was large-scale loss of regulatory pathways. Despite massive gene loss, more genes were retained for biosynthesis of amino acids predicted to be essential to the host. Gene ontology enrichment tests showed enrichment for biosynthesis of arginine, histidine, and aromatic amino acids, as well as thiamine and coenzyme A, diverging from the profiles of relatives Akkermansia muciniphilia (in the human colon), Methylacidiphilum infernorum, and the mutualist Wolbachia from filarial nematodes. Together, these features and the location in the gut suggest that Xiphinematobacter functions as a nutritional mutualist, supplementing essential nutrients that are depleted in the nematode diet. This pattern points to evolutionary convergence with endosymbionts found in sap-feeding insects.
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Affiliation(s)
| | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | | | - Amy B Peetz
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Inga A Zasada
- USDA-ARS Horticultural Crops Research Laboratory, Corvallis, Oregon
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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43
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Wernegreen JJ. Endosymbiont evolution: predictions from theory and surprises from genomes. Ann N Y Acad Sci 2015; 1360:16-35. [PMID: 25866055 DOI: 10.1111/nyas.12740] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/27/2015] [Accepted: 02/11/2015] [Indexed: 10/23/2022]
Abstract
Genome data have created new opportunities to untangle evolutionary processes shaping microbial variation. Among bacteria, long-term mutualists of insects represent the smallest and (typically) most AT-rich genomes. Evolutionary theory provides a context to predict how an endosymbiotic lifestyle may alter fundamental evolutionary processes--mutation, selection, genetic drift, and recombination--and thus contribute to extreme genomic outcomes. These predictions can then be explored by comparing evolutionary rates, genome size and stability, and base compositional biases across endosymbiotic and free-living bacteria. Recent surprises from such comparisons include genome reduction among uncultured, free-living species. Some studies suggest that selection generally drives this streamlining, while drift drives genome reduction in endosymbionts; however, this remains an hypothesis requiring additional data. Unexpected evidence of selection acting on endosymbiont GC content hints that even weak selection may be effective in some long-term mutualists. Moving forward, intraspecific analysis offers a promising approach to distinguish underlying mechanisms, by testing the null hypothesis of neutrality and by quantifying mutational spectra. Such analyses may clarify whether endosymbionts and free-living bacteria occupy distinct evolutionary trajectories or, alternatively, represent varied outcomes of similar underlying forces.
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Affiliation(s)
- Jennifer J Wernegreen
- Nicholas School of the Environment and Center for Genomic and Computational Biology, Duke University, Durham, North Carolina
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44
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Gillespie JJ, Driscoll TP, Verhoeve VI, Utsuki T, Husseneder C, Chouljenko VN, Azad AF, Macaluso KR. Genomic diversification in strains of Rickettsia felis Isolated from different arthropods. Genome Biol Evol 2014; 7:35-56. [PMID: 25477419 PMCID: PMC4316617 DOI: 10.1093/gbe/evu262] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Rickettsia felis (Alphaproteobacteria: Rickettsiales) is the causative agent of an emerging flea-borne rickettsiosis with worldwide occurrence. Originally described from the cat flea, Ctenocephalides felis, recent reports have identified R. felis from other flea species, as well as other insects and ticks. This diverse host range for R. felis may indicate an underlying genetic variability associated with host-specific strains. Accordingly, to determine a potential genetic basis for host specialization, we sequenced the genome of R. felis str. LSU-Lb, which is an obligate mutualist of the parthenogenic booklouse Liposcelis bostrychophila (Insecta: Psocoptera). We also sequenced the genome of R. felis str. LSU, the second genome sequence for cat flea-associated strains (cf. R. felis str. URRWXCal2), which are presumably facultative parasites of fleas. Phylogenomics analysis revealed R. felis str. LSU-Lb diverged from the flea-associated strains. Unexpectedly, R. felis str. LSU was found to be divergent from R. felis str. URRWXCal2, despite sharing similar hosts. Although all three R. felis genomes contain the pRF plasmid, R. felis str. LSU-Lb carries an additional unique plasmid, pLbaR (plasmid of L. bostrychophila associated Rickettsia), nearly half of which encodes a unique 23-gene integrative conjugative element. Remarkably, pLbaR also encodes a repeats-in-toxin-like type I secretion system and associated toxin, heretofore unknown from other Rickettsiales genomes, which likely originated from lateral gene transfer with another obligate intracellular parasite of arthropods, Cardinium (Bacteroidetes). Collectively, our study reveals unexpected genomic diversity across three R. felis strains and identifies several diversifying factors that differentiate facultative parasites of fleas from obligate mutualists of booklice.
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Affiliation(s)
- Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Victoria I Verhoeve
- Department of Pathobiological Sciences, Louisiana State University, School of Veterinary Medicine
| | - Tadanobu Utsuki
- Department of Pathobiological Sciences, Louisiana State University, School of Veterinary Medicine
| | - Claudia Husseneder
- Department of Entomology, Louisiana State University Agricultural Center, Baton Rouge, Louisiana
| | - Vladimir N Chouljenko
- Department of Pathobiological Sciences, Louisiana State University, School of Veterinary Medicine
| | - Abdu F Azad
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland
| | - Kevin R Macaluso
- Department of Pathobiological Sciences, Louisiana State University, School of Veterinary Medicine
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45
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Santos-Garcia D, Silva FJ, Moya A, Latorre A. No exception to the rule: Candidatus Portiera aleyrodidarum cell wall revisited. FEMS Microbiol Lett 2014; 360:132-6. [PMID: 25196985 DOI: 10.1111/1574-6968.12595] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 09/02/2014] [Indexed: 02/05/2023] Open
Abstract
Many insect endosymbionts described so far are gram-negative bacteria. Primary endosymbionts are obligatory bacteria usually harboured by insects inside vacuoles in specialized cells called bacteriocytes. This combination produces a typical three-membrane system with one membrane derived from the insect vacuole and the other two from the bacterial gram-negative cell envelope, composed by the cell wall (the outer membrane plus the periplasmic space) and the plasma membrane (the inner membrane). For the last 21 years, the primary endosymbiont of whiteflies 'Candidatus Portiera aleyrodidarum' was considered an exception to this rule. Previous works stated that only two membranes were present, the vacuolar membrane and one of the two bacterial membranes. The absence of the cell wall was related to the special vertical transmission of the endosymbionts in whiteflies. In this work, we present electron microscopic studies showing a complete cell envelope in 'Ca. Portiera aleyrodidarum' from the whitefly Bemisia tabaci. Additionally, comparison of the inferred metabolism from the gene content did not show any difference in cell envelope biogenesis compared with the closely related three-membrane endosymbionts 'Candidatus Carsonella ruddii' and 'Candidatus Evansia muelleri' Xc1. Our results rule out the proposal that 'Ca. Portiera aleyrodidarum' is an exception to the three-membrane system.
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Affiliation(s)
- Diego Santos-Garcia
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Paterna, Spain
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46
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Martínez-Cano DJ, Reyes-Prieto M, Martínez-Romero E, Partida-Martínez LP, Latorre A, Moya A, Delaye L. Evolution of small prokaryotic genomes. Front Microbiol 2014; 5:742. [PMID: 25610432 PMCID: PMC4285135 DOI: 10.3389/fmicb.2014.00742] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 12/07/2014] [Indexed: 02/05/2023] Open
Abstract
As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.
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Affiliation(s)
| | - Mariana Reyes-Prieto
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
| | | | | | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de ValenciaValencia, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética, Cinvestav Unidad IrapuatoIrapuato, Mexico
- *Correspondence: Luis Delaye, Departamento de Ingeniería Genética, Cinvestav Unidad Irapuato, Kilometer 9.6, Libramiento Norte, Carretera Irapuato-León, Irapuato, Guanajuato 36821, Mexico e-mail:
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