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Viquez C, Rojas-Gätjens D, Mesén-Porras E, Avendaño R, Sasa M, Lomonte B, Chavarría M. Venom-microbiomics of eight species of Neotropical spiders from the Theraphosidae family. J Appl Microbiol 2024; 135:lxae113. [PMID: 38692848 DOI: 10.1093/jambio/lxae113] [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: 01/11/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/03/2024]
Abstract
AIM Tarantulas are one of the largest predatory arthropods in tropical regions. Tarantulas though not lethal to humans, their venomous bite kills small animals and insect upon which they prey. To understand the abiotic and biotic components involved in Neotropical tarantula bites, we conducted a venom-microbiomics study in eight species from Costa Rica. METHODS AND RESULTS We determined that the toxin profiles of tarantula venom are highly diverse using shotgun proteomics; the most frequently encountered toxins were ω-Ap2 toxin, neprilysin-1, and several teraphotoxins. Through culture-independent and culture-dependent methods, we determined the microbiota present in the venom and excreta to evaluate the presence of pathogens that could contribute to primary infections in animals, including humans. The presence of opportunistic pathogens with hemolytic activity was observed, with a prominence of Stenotrophomonas in the venoms. Other bacteria found in venoms and excreta with hemolytic activity included members of the genera Serratia, Bacillus, Acinetobacter, Microbacterium, and Morganella. CONCLUSIONS Our data shed light on the venom- and gut-microbiome associated with Neotropical tarantulas. This information may be useful for treating bites from these arthropods in both humans and farm animals, while also providing insight into the toxins and biodiversity of this little-explored microenvironment.
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Affiliation(s)
- Carlos Viquez
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Oficina subregional de Alajuela, Sistema Nacional de Áreas de Conservación (SINAC), Ministerio Ambiente y Energía (MINAE), Alajuela 20101, Costa Rica
| | - Diego Rojas-Gätjens
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Esteve Mesén-Porras
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Roberto Avendaño
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
| | - Mahmood Sasa
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Museo de Zoología, Centro de Investigación de Biodiversidad y Ecología Tropical, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Max Chavarría
- Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José 1174-1200, Costa Rica
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José 11501-2060, Costa Rica
- Escuela de Química, Universidad de Costa Rica, San José 11501-2060, Costa Rica
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2
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Mowery MA, Rosenwald LC, Chapman E, Lubin Y, Segoli M, Khoza T, Lyle R, White JA. Endosymbiont diversity across native and invasive brown widow spider populations. Sci Rep 2024; 14:8556. [PMID: 38609398 PMCID: PMC11014918 DOI: 10.1038/s41598-024-58723-2] [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: 09/15/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
The invasive brown widow spider, Latrodectus geometricus (Araneae: Theridiidae), has spread in multiple locations around the world and, along with it, brought associated organisms such as endosymbionts. We investigated endosymbiont diversity and prevalence across putative native and invasive populations of this spider, predicting lower endosymbiont diversity across the invasive range compared to the native range. First, we characterized the microbial community in the putative native (South Africa) and invasive (Israel and the United States) ranges via high throughput 16S sequencing of 103 adult females. All specimens were dominated by reads from only 1-3 amplicon sequence variants (ASV), and most individuals were infected with an apparently uniform strain of Rhabdochlamydia. We also found Rhabdochlamydia in spider eggs, indicating that it is a maternally-inherited endosymbiont. Relatively few other ASV were detected, but included two variant Rhabdochlamydia strains and several Wolbachia, Spiroplasma and Enterobacteriaceae strains. We then diagnostically screened 118 adult female spiders from native and invasive populations specifically for Rhabdochlamydia and Wolbachia. We found Rhabdochlamydia in 86% of individuals and represented in all populations, which suggests that it is a consistent and potentially important associate of L. geometricus. Wolbachia was found at lower overall prevalence (14%) and was represented in all countries, but not all populations. In addition, we found evidence for geographic variation in endosymbiont prevalence: spiders from Israel were more likely to carry Rhabdochlamydia than those from the US and South Africa, and Wolbachia was geographically clustered in both Israel and South Africa. Characterizing endosymbiont prevalence and diversity is a first step in understanding their function inside the host and may shed light on the process of spread and population variability in cosmopolitan invasive species.
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Affiliation(s)
- Monica A Mowery
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel.
- Department of Biology, York College, The City University of New York, Jamaica, NY, USA.
| | - Laura C Rosenwald
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Eric Chapman
- Department of Entomology, University of Kentucky, Lexington, KY, USA
| | - Yael Lubin
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Michal Segoli
- Mitrani Department of Desert Ecology, Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion, Israel
| | - Thembile Khoza
- South African National Biodiversity Institute, Biosystematics Division, Pretoria, South Africa
| | - Robin Lyle
- Agricultural Research Council-Plant Health and Protection, Biosystematics Division, Queenswood, South Africa
| | - Jennifer A White
- Department of Entomology, University of Kentucky, Lexington, KY, USA
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3
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Konecka E, Szymkowiak P. Wolbachia supergroup A in Enoplognatha latimana (Araneae: Theridiidae) in Poland as an example of possible horizontal transfer of bacteria. Sci Rep 2024; 14:7486. [PMID: 38553514 PMCID: PMC10980700 DOI: 10.1038/s41598-024-57701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Wolbachia (phylum Pseudomonadota, class Alfaproteobacteria, order Rickettsiales, family Ehrlichiaceae) is a maternally inherited bacterial symbiont infecting more than half of arthropod species worldwide and constituting an important force in the evolution, biology, and ecology of invertebrate hosts. Our study contributes to the limited knowledge regarding the presence of intracellular symbiotic bacteria in spiders. Specifically, we investigated the occurrence of Wolbachia infection in the spider species Enoplognatha latimana Hippa and Oksala, 1982 (Araneae: Theridiidae) using a sample collected in north-western Poland. To the best of our knowledge, this is the first report of Wolbachia infection in E. latimana. A phylogeny based on the sequence analysis of multiple genes, including 16S rRNA, coxA, fbpA, ftsZ, gatB, gltA, groEL, hcpA, and wsp revealed that Wolbachia from the spider represented supergroup A and was related to bacterial endosymbionts discovered in other spider hosts, as well as insects of the orders Diptera and Hymenoptera. A sequence unique for Wolbachia supergroup A was detected for the ftsZ gene. The sequences of Wolbachia housekeeping genes have been deposited in publicly available databases and are an important source of molecular data for comparative studies. The etiology of Wolbachia infection in E. latimana is discussed.
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Affiliation(s)
- Edyta Konecka
- Department of Microbiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Paweł Szymkowiak
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
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4
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Liu Y, Liu J, Zhang X, Yun Y. Diversity of Bacteria Associated with Guts and Gonads in Three Spider Species and Potential Transmission Pathways of Microbes within the Same Spider Host. INSECTS 2023; 14:792. [PMID: 37887804 PMCID: PMC10607309 DOI: 10.3390/insects14100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Microbial symbiosis plays a crucial role in the ecological and evolutionary processes of animals. It is well known that spiders, with their unique and diverse predatory adaptations, assume an indispensable role in maintaining ecological balance and the food chain. However, our current understanding of spider microbiomes remains relatively limited. The gut microbiota and gonad microbiota of spiders can both potentially influence their physiology, ecology, and behavior, including aspects such as digestion, immunity, reproductive health, and reproductive behavior. In the current study, based on high-throughput sequencing of the 16S rRNA V3 and V4 regions, we detected the gut and gonad microbiota communities of three spider species captured from the same habitat, namely, Eriovixia cavaleriei, Larinioides cornutus, and Pardosa pseudoannulata. In these three species, we observed that, at the phylum level classification, the gut and gonad of E. cavaleriei are primarily composed of Proteobacteria, while those of L. cornutus and P. pseudoannulata are primarily composed of Firmicutes. At the genus level of classification, we identified 372 and 360 genera from the gut and gonad bacterial communities. It is noteworthy that the gut and gonad bacterial flora of E. cavaleriei and L. cornutus were dominated by Wolbachia and Spiroplasma. Results show that there were no differences in microbial communities between females and males of the same spider species. Furthermore, there is similarity between the gut and ovary microbial communities of female spiders, implying a potential avenue for microbial transmission between the gut and gonad within female spiders. By comprehensively studying these two microbial communities, we can establish the theoretical foundation for exploring the relationship between gut and gonad microbiota and their host, as well as the mechanisms through which microbes exert their effects.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jia Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaopan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
- Centre for Behavioral Ecology & Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
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5
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Saqib HSA, Sun L, Pozsgai G, Liang P, Goraya MU, Akutse KS, You M, Gurr GM, You S. Gut microbiota assemblages of generalist predators are driven by local- and landscape-scale factors. Front Microbiol 2023; 14:1172184. [PMID: 37256058 PMCID: PMC10225636 DOI: 10.3389/fmicb.2023.1172184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/17/2023] [Indexed: 06/01/2023] Open
Abstract
The gut microbiomes of arthropods have significant impact on key physiological functions such as nutrition, reproduction, behavior, and health. Spiders are diverse and numerically dominant predators in crop fields where they are potentially important regulators of pests. Harnessing spiders to control agricultural pests is likely to be supported by an understanding of their gut microbiomes, and the environmental drivers shaping microbiome assemblages. This study aimed to deciphering the gut microbiome assembly of these invertebrate predators and elucidating potential implications of key environmental constraints in this process. Here, we used high-throughput sequencing to examine for the first time how the assemblages of bacteria in the gut of spiders are shaped by environmental variables. Local drivers of microbiome composition were globally-relevant input use system (organic production vs. conventional practice), and crop identity (Chinese cabbage vs. cauliflower). Landscape-scale factors, proportion of forest and grassland, compositional diversity, and habitat edge density, also strongly affected gut microbiota. Specific bacterial taxa were enriched in gut of spiders sampled from different settings and seasons. These findings provide a comprehensive insight into composition and plasticity of spider gut microbiota. Understanding the temporal responses of specific microbiota could lead to innovative strategies development for boosting biological control services of predators.
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Affiliation(s)
- Hafiz Sohaib Ahmed Saqib
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangdong Provincial Key Laboratory of Marine Biology, College of Science, Shantou University, Shantou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Linyang Sun
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gabor Pozsgai
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Ce3C - Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group, CHANGE – Global Change and Sustainability Institute, University of the Azores, Faculty of Agricultural Sciences and Environment, Angra do Heroísmo, Açores, Portugal
| | - Pingping Liang
- Center for Infection and Immunity, Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Imaging, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong, China
| | - Mohsan Ullah Goraya
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
| | - Komivi Senyo Akutse
- Plant Health Theme, International Centre of Insect Physiology and Ecology, Nairobi, Kenya
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Geoff M. Gurr
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- Gulbali Institute, Charles Sturt University, Orange, NSW, Australia
| | - Shijun You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, China
- Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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6
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Řezáč M, Řezáčová V, Gloríková N, Némethová E, Heneberg P. Food provisioning to Pardosa spiders decreases the levels of tissue-resident endosymbiotic bacteria. Sci Rep 2023; 13:6943. [PMID: 37117271 PMCID: PMC10147729 DOI: 10.1038/s41598-023-34229-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/26/2023] [Indexed: 04/30/2023] Open
Abstract
The diversity, host specificity, and physiological effects of endosymbiotic bacteria in spiders (Araneae) are poorly characterized. We used 16S rDNA sequencing to evaluate endosymbionts in the cephalothorax and legs of a wolf spider Pardosa agrestis. We tested the effects of feeding once or twice daily with fruit flies, aphids, or starved and compared them to those of syntopically occurring Pardosa palustris. The feeding increased traveled distance up to five times in some of the groups provisioned with food relative to the starved control. The Shannon diversity t-test revealed significant differences between these component communities of the two spider species. The increased frequency of feeding with fruit flies, but not aphids, increased the dominance and decreased the alpha diversity of OTUs. The obligate or facultative endosymbionts were present in all analyzed spider individuals and were represented mostly by Rickettsiella, Rhabdochlamydia, Spiroplasma, and the facultative intracellular parasite Legionella. Vertically transmitted endosymbionts were less common, represented by Wolbachia pipientis and Rickettsia sp. H820. The relative abundance of Mycoplasma spp. was negatively correlated with provisioned or killed aphids. In conclusion, the tissues of Pardosa spiders host tremendously diverse assemblages of bacteria, including obligate or facultative endosymbionts, with yet unknown phenotypic effects.
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Affiliation(s)
- Milan Řezáč
- Crop Research Institute, Drnovská 507, 160 00, Prague, Czech Republic
| | - Veronika Řezáčová
- Crop Research Institute, Drnovská 507, 160 00, Prague, Czech Republic.
| | - Nela Gloríková
- Crop Research Institute, Drnovská 507, 160 00, Prague, Czech Republic
| | - Ema Némethová
- Crop Research Institute, Drnovská 507, 160 00, Prague, Czech Republic
| | - Petr Heneberg
- Crop Research Institute, Drnovská 507, 160 00, Prague, Czech Republic.
- Charles University, Third Faculty of Medicine, Ruská 87, 100 00, Prague, Czech Republic.
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7
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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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8
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Halter T, Köstlbacher S, Collingro A, Sixt BS, Tönshoff ER, Hendrickx F, Kostanjšek R, Horn M. Ecology and evolution of chlamydial symbionts of arthropods. ISME COMMUNICATIONS 2022; 2:45. [PMID: 37938728 PMCID: PMC9723776 DOI: 10.1038/s43705-022-00124-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 05/08/2023]
Abstract
The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.
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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
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Barbara S Sixt
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Elena R Tönshoff
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich (ETH), Zurich, Switzerland
| | | | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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9
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Millar EN, Surette MG, Kidd KA. Altered microbiomes of aquatic macroinvertebrates and riparian spiders downstream of municipal wastewater effluents. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:151156. [PMID: 34687704 DOI: 10.1016/j.scitotenv.2021.151156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/17/2021] [Accepted: 10/18/2021] [Indexed: 05/15/2023]
Abstract
Municipal wastewater treatment plants (WWTPs) contain numerous contaminants, including antimicrobials, that could affect the composition of the beneficial bacterial communities associated with host aquatic organisms. There is also potential for these effects to transfer to terrestrial predators. Riparian spiders and five families of aquatic macroinvertebrates were collected from sites upstream and downstream of two WWTPs, Waterloo and Kitchener, discharging to the Grand River, Ontario, Canada. Whole-body microbiota were analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16S rRNA genetic barcode. Changes in the relative abundance of major microbiome phyla were observed in all downstream aquatic insects except Hydropsychidae caddisflies, which exhibited little site variation. Shannon alpha diversity differed among sites for Tetragnathidae spiders, Perlidae, Hydropsychidae, and Heptageniidae. Downstream of the Waterloo WWTP alpha diversity decreased in spiders, while downstream of the Kitchener WWTP this measure decreased in Perlidae and increased in spiders. Bray-Curtis beta diversity was dissimilar among sites in all invertebrate taxa; upstream sites differed from those downstream of Waterloo in spiders, Perlidae, and Hydropsychidae, and from those downstream of Kitchener in spiders, Perlidae, and Hydropsychidae. Finally, effluent-derived bacteria were found in the microbiomes of downstream spiders and aquatic insects and not upstream. Overall, results indicated that the microbiomes of invertebrates collected downstream differed from those collected upstream of WWTPs, which has implications for altered host health and transport of WWTP-derived bacteria through aquatic ecosystems.
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Affiliation(s)
- Elise N Millar
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
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10
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Armstrong EE, Perez-Lamarque B, Bi K, Chen C, Becking LE, Lim JY, Linderoth T, Krehenwinkel H, Gillespie RG. A holobiont view of island biogeography: Unravelling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates. Mol Ecol 2021; 31:1299-1316. [PMID: 34861071 DOI: 10.1111/mec.16301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 12/24/2022]
Abstract
The diversification of a host lineage can be influenced by both the external environment and its assemblage of microbes. Here, we use a young lineage of spiders, distributed along a chronologically arranged series of volcanic mountains, to investigate how their associated microbial communities have changed as the spiders colonized new locations. Using the stick spider Ariamnes waikula (Araneae, Theridiidae) on the island of Hawai'i, and outgroup taxa on older islands, we tested whether each component of the "holobiont" (spider hosts, intracellular endosymbionts and gut microbial communities) showed correlated signatures of diversity due to sequential colonization from older to younger volcanoes. To investigate this, we generated ddRAD data for the host spiders and 16S rRNA gene amplicon data from their microbiota. We expected sequential colonizations to result in a (phylo)genetic structuring of the host spiders and in a diversity gradient in microbial communities. The results showed that the host A. waikula is indeed structured by geographical isolation, suggesting sequential colonization from older to younger volcanoes. Similarly, the endosymbiont communities were markedly different between Ariamnes species on different islands, but more homogeneous among A. waikula populations on the island of Hawai'i. Conversely, the gut microbiota, which we suspect is generally environmentally derived, was largely conserved across all populations and species. Our results show that different components of the holobiont respond in distinct ways to the dynamic environment of the volcanic archipelago. This highlights the necessity of understanding the interplay between different components of the holobiont, to properly characterize its evolution.
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Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, California, USA
| | - Benoît Perez-Lamarque
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Ke Bi
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA.,Museum of Vertebrate Zoology, University of California, Berkeley, California, USA.,Ancestry, San Francisco, California, USA
| | - Cerise Chen
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA.,Long Marine Laboratory, University of California, Santa Cruz, California, USA
| | - Leontine E Becking
- Marine Animal Ecology Group, Wageningen University & Research, Wageningen, The Netherlands.,Wageningen Marine Research, Den Helder, The Netherlands
| | - Jun Ying Lim
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Tyler Linderoth
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Henrik Krehenwinkel
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA.,Department of Biogeography, Trier University, Trier, Germany
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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11
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Tyagi K, Tyagi I, Kumar V. Insights into the gut bacterial communities of spider from wild with no evidence of phylosymbiosis. Saudi J Biol Sci 2021; 28:5913-5924. [PMID: 34588907 PMCID: PMC8459122 DOI: 10.1016/j.sjbs.2021.06.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 12/13/2022] Open
Abstract
In the present study, an effort has been made to elucidate the gut bacterial diversity of twelve species of the family Araneidae under three subfamilies collected from 5 states of India along with their predicted metabolic role in functional metabolism. Further, we also compared the host species phylogeny based on partial cytochrome c oxidase subunit I (COI) sequences with the gut bacteria composition dendrogram to decipher the phylosymbiotic relationships. Analysis revealed the presence of 22 bacterial phyla, 145 families, and 364 genera in the gut, with Proteobacteria, Firmicutes, Actinobacteria, and Deinococcus-Thermus as the highest abundant phyla. Moreover, phylum Bacteriodetes was dominated only in Cyclosa mulmeinensis and Chlamydiae in Neoscona bengalensis. At the genus level, Bacillus, Acinetobacter, Cutibacterium, Pseudomonas, and Staphylococcus were the most dominant genera. Furthermore, the genus Prevotella was observed only in Cyclosa mulmeinensis, and endosymbiont Wolbachia only in Eriovixia laglaizei. The differential abundance analysis (DeSeq2) revealed the 19 significant ASVs represented by the genera like Acinetobacter, Vagoccoccus, Prevotella, Staphylococcus, Curvibacter, Corynebacterium, Paracoccus, Streptococcus, Microbacterium, and Pseudocitrobacter. The inter- and intra-subfamilies comparison based on diversity indices (alpha and beta diversity) revealed that the subfamily Araneinae have high richness and diversity than Argiopinae and Gasteracanthinae. The phylosymbiotic analysis revealed that there is no congruence between the gut bacteria composition dendrogram with their host phylogeny.
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Affiliation(s)
| | | | - Vikas Kumar
- Centre for DNA Taxonomy, Molecular Systematics Division, Zoological Survey of India, Kolkata 700053, India
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12
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Collingro A, Köstlbacher S, Horn M. Chlamydiae in the Environment. Trends Microbiol 2020; 28:877-888. [PMID: 32591108 DOI: 10.1016/j.tim.2020.05.020] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 12/19/2022]
Abstract
Chlamydiae have been known for more than a century as major pathogens of humans. Yet they are also found ubiquitously in the environment where they thrive within protists and in an unmatched wide range of animals. This review summarizes recent advances in understanding chlamydial diversity and distribution in nature. Studying these environmental chlamydiae provides a novel perspective on basic chlamydial biology and evolution. A picture is beginning to emerge with chlamydiae representing one of the evolutionarily most ancient and successful groups of obligate intracellular bacteria.
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Affiliation(s)
- Astrid Collingro
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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13
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Dunaj SJ, Bettencourt BR, Garb JE, Brucker RM. Spider phylosymbiosis: divergence of widow spider species and their tissues' microbiomes. BMC Evol Biol 2020; 20:104. [PMID: 32811423 PMCID: PMC7433143 DOI: 10.1186/s12862-020-01664-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Microbiomes can have profound impacts on host biology and evolution, but to date, remain vastly understudied in spiders despite their unique and diverse predatory adaptations. This study evaluates closely related species of spiders and their host-microbe relationships in the context of phylosymbiosis, an eco-evolutionary pattern where the microbial community profile parallels the phylogeny of closely related host species. Using 16S rRNA gene amplicon sequencing, we characterized the microbiomes of five species with known phylogenetic relationships from the family Theridiidae, including multiple closely related widow spiders (L. hesperus, L. mactans, L. geometricus, S. grossa, and P. tepidariorum). RESULTS We compared whole animal and tissue-specific microbiomes (cephalothorax, fat bodies, venom glands, silk glands, and ovary) in the five species to better understand the relationship between spiders and their microbial symbionts. This showed a strong congruence of the microbiome beta-diversity of the whole spiders, cephalothorax, venom glands, and silk glands when compared to their host phylogeny. Our results support phylosymbiosis in these species and across their specialized tissues. The ovary tissue microbial dendrograms also parallel the widow phylogeny, suggesting vertical transfer of species-specific bacterial symbionts. By cross-validating with RNA sequencing data obtained from the venom glands, silk glands and ovaries of L. hesperus, L. geometricus, S. grossa, and P. tepidariorum we confirmed that several microbial symbionts of interest are viably active in the host. CONCLUSION Together these results provide evidence that supports the importance of host-microbe interactions and the significant role microbial communities may play in the evolution and adaptation of their hosts.
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Affiliation(s)
- Sara J Dunaj
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | | | - Jessica E Garb
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Robert M Brucker
- The Rowland Institute of Harvard University, Cambridge, MA, USA.
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14
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Friel AD, Neiswenter SA, Seymour CO, Bali LR, McNamara G, Leija F, Jewell J, Hedlund BP. Microbiome Shifts Associated With the Introduction of Wild Atlantic Horseshoe Crabs ( Limulus polyphemus) Into a Touch-Tank Exhibit. Front Microbiol 2020; 11:1398. [PMID: 32765431 PMCID: PMC7381184 DOI: 10.3389/fmicb.2020.01398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 05/29/2020] [Indexed: 12/18/2022] Open
Abstract
The Atlantic horseshoe crab (Limulus polyphemus) is a common marine aquarium species and model organism for research. There is potential monetary and conservation value in developing a stable captive population of horseshoe crabs, however, one major impediment to achieving captivity is a lack of knowledge regarding captive diseases. We utilized 16S rRNA gene amplicon sequencing to track changes in the microbiomes of four body locations in three wild-caught (tracked over 14 months in captivity) and three tank-acclimated (>2 years in captivity) adult L. polyphemus in a touch tank at Shark Reef Aquarium at Mandalay Bay in Las Vegas, NV. The wild population hosted diverse and distinct microbiomes on the carapace (260 ± 96 amplicon sequence variants or ASVs), cloaca (345 ± 77 ASVs), gills (309 ± 36 ASVs), and oral cavity (359 ± 37 ASVs), which were dominated by classes Gammaproteobacteria, Bacteroidia, and Alphaproteobacteria. A rapid decline in richness across all body locations was observed within 1 month of captivity, with tank-acclimated (>2 years) animals having <5% of the initial microbiome richness and a nearly completely restructured microbial community. Tank-acclimated horseshoe crabs possessed distinct microbiomes that were highly uneven and low in species richness on the carapace (31 ± 7 ASVs), cloaca (53 ± 19 ASVs), gills (17 ± 2 ASVs), and oral cavity (31 ± 13 ASVs). The carapace, oral cavity, and gills of the tank-acclimated animals hosted abundant populations of Aeromonas (>60%) and Pseudomonas (>20%), both of which are known opportunistic pathogens of aquatic animals and can express chitinases, providing a plausible mechanism for the development of the carapace lesion pathology observed in this and other studies. The cloaca of the tank-acclimated animals was slightly more diverse than the other body locations with Aeromonas, Enterococcus, Shewanella, and Vagococcus dominating the community. These results provide an important baseline on the microbiomes of both wild and tank-acclimated horseshoe crabs and underscore the need to continue to investigate how native microbial populations may protect animals from pathogens.
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Affiliation(s)
- Ariel D Friel
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Sean A Neiswenter
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Cale O Seymour
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Lauren Rose Bali
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Ginger McNamara
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Fabian Leija
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States
| | - Jack Jewell
- Shark Reef Aquarium at Mandalay Bay, Las Vegas, NV, United States
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, United States.,Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, United States
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15
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Kennedy SR, Tsau S, Gillespie R, Krehenwinkel H. Are you what you eat? A highly transient and prey-influenced gut microbiome in the grey house spider Badumna longinqua. Mol Ecol 2020; 29:1001-1015. [PMID: 32011756 DOI: 10.1111/mec.15370] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2020] [Accepted: 01/29/2020] [Indexed: 01/01/2023]
Abstract
Stable core microbial communities have been described in numerous animal species and are commonly associated with fitness benefits for their hosts. Recent research, however, highlights examples of species whose microbiota are transient and environmentally derived. Here, we test the effect of diet on gut microbial community assembly in the spider Badumna longinqua. Using 16S rRNA gene amplicon sequencing combined with quantitative PCR, we analyzed diversity and abundance of the spider's gut microbes, and simultaneously characterized its prey communities using nuclear rRNA markers. We found a clear correlation between community similarity of the spider's insect prey and gut microbial DNA, suggesting that microbiome assembly is primarily diet-driven. This assumption is supported by a feeding experiment, in which two types of prey-crickets and fruit flies-both substantially altered microbial diversity and community similarity between spiders, but did so in different ways. After cricket consumption, numerous cricket-derived microbes appeared in the spider's gut, resulting in a rapid homogenization of microbial communities among spiders. In contrast, few prey-associated bacteria were detected after consumption of fruit flies; instead, the microbial community was remodelled by environmentally sourced microbes, or abundance shifts of rare taxa in the spider's gut. The reshaping of the microbiota by both prey taxa mimicked a stable core microbiome in the spiders for several weeks post feeding. Our results suggest that the spider's gut microbiome undergoes pronounced temporal fluctuations, that its assembly is dictated by the consumed prey, and that different prey taxa may remodel the microbiota in drastically different ways.
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Affiliation(s)
- Susan R Kennedy
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany.,Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Sophia Tsau
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Rosemary Gillespie
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
| | - Henrik Krehenwinkel
- Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA.,Universität Trier Biogeographie, Trier, Germany
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16
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White JA, Styer A, Rosenwald LC, Curry MM, Welch KD, Athey KJ, Chapman EG. Endosymbiotic Bacteria Are Prevalent and Diverse in Agricultural Spiders. MICROBIAL ECOLOGY 2020; 79:472-481. [PMID: 31300838 DOI: 10.1007/s00248-019-01411-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 07/02/2019] [Indexed: 05/15/2023]
Abstract
Maternally inherited bacterial endosymbionts are common in arthropods, but their distribution and prevalence are poorly characterized in many host taxa. Initial surveys have suggested that vertically transmitted symbionts may be particularly common in spiders (Araneae). Here, we used diagnostic PCR and high-throughput sequencing to evaluate symbiont infection in 267 individual spiders representing 14 species (3 families) of agricultural spiders. We found 27 operational taxonomic units (OTUs) that are likely endosymbiotic, including multiple strains of Wolbachia, Rickettsia, and Cardinium, which are all vertically transmitted and frequently associated with reproductive manipulation of arthropod hosts. Additional strains included Rickettsiella, Spiroplasma, Rhabdochlamydia, and a novel Rickettsiales, all of which could range from pathogenic to mutualistic in their effects upon their hosts. Seventy percent of spider species had individuals that tested positive for one or more endosymbiotic OTUs, and specimens frequently contained multiple symbiotic strain types. The most symbiont-rich species, Idionella rugosa, had eight endosymbiotic OTUs, with as many as five present in the same specimen. Individual specimens within infected spider species had a variety of symbiotypes, differing from one another in the presence or absence of symbiotic strains. Our sample included both starved and unstarved specimens, and dominant bacterial OTUs were consistent per host species, regardless of feeding status. We conclude that spiders contain a remarkably diverse symbiotic microbiota. Spiders would be an informative group for investigating endosymbiont population dynamics in time and space, and unstarved specimens collected for other purposes (e.g., food web studies) could be used, with caution, for such investigations.
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Affiliation(s)
- Jennifer A White
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA.
| | - Alexander Styer
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Laura C Rosenwald
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
| | - Meghan M Curry
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
| | - Kelton D Welch
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
| | - Kacie J Athey
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
- Tree Fruit Research and Extension Center, Washington State University, Wenatchee, WA, 98801, USA
| | - Eric G Chapman
- Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA
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17
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Sheffer MM, Uhl G, Prost S, Lueders T, Urich T, Bengtsson MM. Tissue- and Population-Level Microbiome Analysis of the Wasp Spider Argiope bruennichi Identified a Novel Dominant Bacterial Symbiont. Microorganisms 2019; 8:E8. [PMID: 31861544 PMCID: PMC7023434 DOI: 10.3390/microorganisms8010008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Many ecological and evolutionary processes in animals depend upon microbial symbioses. In spiders, the role of the microbiome in these processes remains mostly unknown. We compared the microbiome between populations, individuals, and tissue types of a range-expanding spider, using 16S rRNA gene sequencing. Our study is one of the first to go beyond targeting known endosymbionts in spiders and characterizes the total microbiome across different body compartments (leg, prosoma, hemolymph, book lungs, ovaries, silk glands, midgut, and fecal pellets). Overall, the microbiome differed significantly between populations and individuals, but not between tissue types. The microbiome of the wasp spider Argiope bruennichi features a novel dominant bacterial symbiont, which is abundant in every tissue type in spiders from geographically distinct populations and that is also present in offspring. The novel symbiont is affiliated with the Tenericutes, but has low sequence identity (<85%) to all previously named taxa, suggesting that the novel symbiont represents a new bacterial clade. Its presence in offspring implies that it is vertically transmitted. Our results shed light on the processes that shape microbiome differentiation in this species and raise several questions about the implications of the novel dominant bacterial symbiont on the biology and evolution of its host.
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Affiliation(s)
- Monica M. Sheffer
- Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany;
| | - Gabriele Uhl
- Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany;
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany;
- South African National Biodiversity Institute, National Zoological Gardens of South Africa, Pretoria 0001, South Africa
| | - Tillmann Lueders
- Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95448 Bayreuth, Germany;
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, 174897 Greifswald, Germany;
| | - Mia M. Bengtsson
- Institute of Microbiology, University of Greifswald, 174897 Greifswald, Germany;
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18
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Hu G, Zhang L, Yun Y, Peng Y. Taking insight into the gut microbiota of three spider species: No characteristic symbiont was found corresponding to the special feeding style of spiders. Ecol Evol 2019; 9:8146-8156. [PMID: 31380078 PMCID: PMC6662400 DOI: 10.1002/ece3.5382] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/19/2022] Open
Abstract
Microorganisms in insect guts have been recognized as having a great impact on their hosts' nutrition, health, and behavior. Spiders are important natural enemies of pests, and the composition of the gut microbiota of spiders remains unclear. Will the bacterial taxa in spiders be same as the bacterial taxa in insects, and what are the potential functions of the gut bacteria in spiders? To gain insight into the composition of the gut bacteria in spiders and their potential function, we collected three spider species, Pardosa laura, Pardosa astrigera, and Nurscia albofasciata, in the field, and high-throughput sequencing of the 16S rRNA V3 and V4 regions was used to investigate the diversity of gut microbiota across the three spider species. A total of 23 phyla and 150 families were identified in these three spider species. The dominant bacterial phylum across all samples was Proteobacteria. Burkholderia, Ralstonia, Ochrobactrum, Providencia, Acinetobacter, Proteus, and Rhodoplanes were the dominant genera in the guts of the three spider species. The relative abundances of Wolbachia and Rickettsiella detected in N. albofasciata were significantly higher than those in the other two spider species. The relative abundance of Thermus, Amycolatopsis, Lactococcus, Acinetobacter Microbacterium, and Koribacter detected in spider gut was different among the three spider species. Biomolecular interaction networks indicated that the microbiota in the guts had complex interactions. The results of this study also suggested that at the genus level, some of the gut bacteria taxa in the three spider species were the same as the bacteria in insect guts.
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Affiliation(s)
- Guowen Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
| | - Lihua Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
- Centre for Behavioral Ecology & Evolution, School of Life SciencesHubei UniversityWuhanChina
| | - Yu Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio‐Resources, School of Life SciencesHubei UniversityWuhanChina
- Centre for Behavioral Ecology & Evolution, School of Life SciencesHubei UniversityWuhanChina
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19
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Zhang YK, Yu ZJ, Wang D, Bronislava V, Branislav P, Liu JZ. The bacterial microbiome of field-collected Dermacentor marginatus and Dermacentor reticulatus from Slovakia. Parasit Vectors 2019; 12:325. [PMID: 31248443 PMCID: PMC6598266 DOI: 10.1186/s13071-019-3582-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/21/2019] [Indexed: 11/10/2022] Open
Abstract
Background The important roles of microbial flora in tick biology and ecology have received much attention. Dermacentor marginatus and Dermacentor reticulatus are known vectors of various pathogens across Europe, including Slovakia. However, their bacterial microbiomes are poorly explored. Methods In this study, bacterial microbiomes of field-collected D. marginatus and D. reticulatus from Slovakia were characterized using 16S rRNA high-throughput sequencing. Results Different analyses demonstrated that the D. marginatus and D. reticulatus microbiomes differ in their diversity and taxonomic structures. Furthermore, species- and sex-specific bacteria were detected in the two species. A possible bacterial pathogen “Candidatus Rhabdochlamydia sp.” was detected from D. marginatus males. Among the observed bacteria, Rickettsia showed high abundance in the two species. Several maternally inherited bacteria such as Coxiella, Arsenophonus, Spiroplasma, Francisella and Rickettsiella, were abundant, and their relative abundance varied depending on tick species and sex, suggesting their biological roles in the two species. Conclusions The bacterial microbiomes of field-collected D. marginatus and D. reticulatus were shaped by tick phylogeny and sex. Maternally inherited bacteria were abundant in the two species. These findings are valuable for understanding tick-bacteria interactions, biology and vector competence of ticks. Electronic supplementary material The online version of this article (10.1186/s13071-019-3582-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan-Kai Zhang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Zhi-Jun Yu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Duo Wang
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Víchová Bronislava
- Institute of Parasitology, Slovak Academy of Sciences, 04001, Kosice, Slovak Republic
| | - Peťko Branislav
- Institute of Parasitology, Slovak Academy of Sciences, 04001, Kosice, Slovak Republic.,University of Veterinary Medicine and Pharmacy in Kosice, 04185, Kosice, Slovak Republic
| | - Jing-Ze Liu
- Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, Hebei, China.
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20
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Pillonel T, Bertelli C, Aeby S, de Barsy M, Jacquier N, Kebbi-Beghdadi C, Mueller L, Vouga M, Greub G. Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. Genome Biol Evol 2019; 11:1334-1344. [PMID: 30949677 PMCID: PMC6490308 DOI: 10.1093/gbe/evz072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2019] [Indexed: 12/15/2022] Open
Abstract
The Rhabdochlamydiaceae family is one of the most widely distributed within the phylum Chlamydiae, but most of its members remain uncultivable. Rhabdochlamydia 16S rRNA was recently reported in more than 2% of 8,534 pools of ticks from Switzerland. Shotgun metagenomics was performed on a pool of five female Ixodes ricinus ticks presenting a high concentration of chlamydial DNA, allowing the assembly of a high-quality draft genome. About 60% of sequence reads originated from a single bacterial population that was named "Candidatus Rhabdochlamydia helvetica" whereas only few thousand reads mapped to the genome of "Candidatus Midichloria mitochondrii," a symbiont normally observed in all I. ricinus females. The 1.8 Mbp genome of R. helvetica is smaller than other Chlamydia-related bacteria. Comparative analyses with other chlamydial genomes identified transposases of the PD-(D/E)XK nuclease family that are unique to this new genome. These transposases show evidence of interphylum horizontal gene transfers between multiple arthropod endosymbionts, including Cardinium spp. (Bacteroidetes) and diverse proteobacteria such as Wolbachia, Rickettsia spp. (Rickettsiales), and Caedimonas varicaedens (Holosporales). Bacterial symbionts were previously suggested to provide B-vitamins to hematophagous hosts. However, incomplete metabolic capacities including for B-vitamin biosynthesis, high bacterial density and limited prevalence suggest that R. helvetica is parasitic rather than symbiotic to its host. The identification of novel Rhabdochlamydia strains in different hosts and their sequencing will help understanding if members of this genus have become highly specialized parasites with reduced genomes, like the Chlamydiaceae, or if they could be pathogenic to humans using ticks as a transmission vector.
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Affiliation(s)
- Trestan Pillonel
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Claire Bertelli
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Sébastien Aeby
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Marie de Barsy
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Nicolas Jacquier
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Linda Mueller
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Manon Vouga
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
| | - Gilbert Greub
- Center for Research on Intracellular Bacteria, Institute of Microbiology, Lausanne University Hospital, University of Lausanne, Switzerland
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21
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Babczyńska A, Sułowicz S, Talik E, Hermyt M, Bednarek A, Sawadro M, Molenda A. Sterile Capsule-Egg Cocoon Covering Constitutes an Antibacterial Barrier for Spider Parasteatoda tepidariorum Embryos. Physiol Biochem Zool 2019; 92:115-124. [PMID: 30601104 DOI: 10.1086/701390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Coexistence of organisms and pathogens has resulted in the evolution of efficient antimicrobial defense, especially at the embryonic stage. This investigation aimed to substantiate the hypothesis that the layers of silk in a spider cocoon play a role in the immunity of the embryos against microorganisms present in the external environment. A two-step interdisciplinary attempt has been made. First, the eggs and empty cocoons of the spider Parasteatoda tepidariorum were incubated on lysogeny broth agar media for 3 d. In the samples of eggs, no growth of bacteria was detected. This indicated that the eggs inside cocoons were sterile. Therefore, in the second step, the cocoons and egg surface were analyzed using SEM, TEM, and LM. The obtained images demonstrated that both inner and outer layers of the silk are built of threads of the same diameter, set in an irregular manner, and randomly clustered into groups. The threads in the outer layer were packed more densely than in the inner one. TEM analysis revealed threads of two types of fibrils and their arrangement. The resultant thread tangle of the cocoon, possibly correlated with the ultrastructure of the fibers, seems to be an example of a structure-function relationship playing a crucial ecoimmunological role in spider embryonic development.
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22
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Novel Cardinium strains in non-marine ostracod (Crustacea) hosts from natural populations. Mol Phylogenet Evol 2018; 130:406-415. [PMID: 30244151 DOI: 10.1016/j.ympev.2018.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 09/06/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
Abstract
Endosymbiotic bacteria are known from many metazoan taxa, where they manipulate host biology and reproduction. Here, we used classic PCR amplification and direct DNA sequencing with universal primers for four different endosymbionts to test for their presence in more than 300 specimens of three recent non-marine ostracod superfamilies from different geographic areas and aquatic habitats. We verified these results with "high throughput" amplicon sequencing of 16S of nine selected specimens and evolutionary placement algorithms. The phylogenetic position of endosymbionts detected in ostracod hosts was compared to known endosymbionts from other metazoans. While Wolbachia, Spiroplasma and Rickettsia are absent, we find evidence for the general presence of Cardinium bacteria in natural populations of various non-marine ostracod species. Phylogenetic reconstructions based on Cardinium 16S data and estimates of genetic distances both indicate that Cardinium from ostracods are distantly related to Cardinium from Diptera and Nematoda but represent novel strains with a monophyletic origin. Cardinium bacteria from different ostracod hosts have genetic distances of up to 3.8%, providing evidence against recent and frequent horizontal transmissions amongst the three ostracod superfamilies. High throughput sequencing reveals more than 400 different 16S amplicon sequence variants in the investigated ostracods as well as the presence of different Cardinium strains within individual Eucypris virens and Heterocypris hosts. These results call for future, more in-depth investigations. Mapping Cardinium infections on COI trees of non-marine ostracod hosts shows that the occurrence of these endosymbionts is not linked to genetic species identity or phylogenetic host groups and, except for one ostracod morphospecies, prevalence never reaches 100%.
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23
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Zhang L, Yun Y, Hu G, Peng Y. Insights into the bacterial symbiont diversity in spiders. Ecol Evol 2018; 8:4899-4906. [PMID: 29876068 PMCID: PMC5980269 DOI: 10.1002/ece3.4051] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 11/11/2022] Open
Abstract
Most spiders are natural enemies of pests, and it is beneficial for the biological control of pests to learn the relationships between symbionts and their spider hosts. Research on the bacterial communities of insects has been conducted recently, but only a few studies have addressed the bacterial communities of spiders. To obtain a complete overview of the microbial communities of spiders, we examined eight species of spider (Pirata subpiraticus, Agelena difficilis, Artema atlanta, Nurscia albofasciata, Agelena labyrinthica, Ummeliata insecticeps, Dictis striatipes, and Hylyphantes graminicola) with high-throughput sequencing based on the V3 and V4 regions of the 16S rRNA gene. The bacterial communities of the spider samples were dominated by five types of endosymbionts, Wolbachia, Cardinium, Rickettsia, Spiroplasma, and Rickettsiella. The dominant OTUs (operational taxonomic units) from each of the five endosymbionts were analyzed, and the results showed that different spider species were usually dominated by special OTUs. In addition to endosymbionts, Pseudomonas, Sphingomonas, Acinetobacter, Novosphingobium, Aquabacterium, Methylobacterium, Brevundimonas, Rhizobium, Bradyrhizobium, Citrobacter, Arthrobacter, Pseudonocardia, Microbacterium, Lactobacillus, and Lactococcus were detected in spider samples in our study. Moreover, the abundance of Sphingomonas, Methylobacterium, Brevundimonas, and Rhizobium in the spider D. striatipes was significantly higher (p < .05) than the bacterial abundance of these species in seven other spider species. These findings suggest that same as in insects, co-infection of multiple types of endosymbionts is common in the hosts of the Araneae order, and other bacterial taxa also exist in spiders besides the endosymbionts.
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Affiliation(s)
- Lihua Zhang
- Centre for Behavioral Ecology and EvolutionCollege of Life SciencesHubei UniversityWuhanChina
| | - Yueli Yun
- Centre for Behavioral Ecology and EvolutionCollege of Life SciencesHubei UniversityWuhanChina
| | - Guowen Hu
- Centre for Behavioral Ecology and EvolutionCollege of Life SciencesHubei UniversityWuhanChina
| | - Yu Peng
- Centre for Behavioral Ecology and EvolutionCollege of Life SciencesHubei UniversityWuhanChina
- Hubei Collaborative Innovation Center for Green Transformation of Bio‐ResourcesCollege of Life SciencesHubei UniversityWuhanChina
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24
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Gardiner M, Weldon A, Poindexter SA, Gibson N, Nekaris KAI. Survey of practitioners handling slow lorises (Primates: Nycticebus): an assessment of the harmful effects of slow loris bites. JOURNAL OF VENOM RESEARCH 2018; 9:1-7. [PMID: 30090322 PMCID: PMC6055083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 11/22/2022]
Abstract
Slow lorises (Nycticebus spp.) are one of six venomous mammals, and the only known venomous primate. In the wild envenomation occurs mainly during conspecific competition for mates and territory, but may also be used as an application against parasites or for predator defense. Envenomation in humans is documented, with the most extreme accounts detailing near-fatal anaphylactic shock. From September 2016 - August 2017, we received questionnaire responses from 80 wild animal practitioners working with Nycticebus spp. in zoos, rescue centres and in the wild. We identified 54 practitioners who had experience of being bitten or were otherwise affected by slow loris venom, and an additional 26 incomplete entries. No fatalities were reported. Fifteen respondents noted that medical intervention was required, 12 respondents indicated no reaction to being bitten (9 of these indicated they were wearing gloves). Symptoms for those affected included: anaphylactic shock, paraesthesia, haematuria, dyspnoea, extreme pain, infection and general malaise. Impact of slow loris bites ranged from instantaneous to long-persisting complications, and healing time ranged from 1 day to >8 months. Extremities, including hands and arms, were mostly affected from the bites. Six of nine species of slow loris were reported to bite, with N. pygmaeus being the most common in our sample. We make suggestions regarding the use of these highly threatened yet dangerous primates as unsuitable tourist photo props and zoo animal ambassadors. We discuss the medical complications experienced in relation to protein sensitisation, and bacterial pathogenesis. We recommend future work to ascertain the protein content of slow loris venom to aid in enabling mitigation of risks posed.
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Affiliation(s)
- Matthew Gardiner
- 1Oxford Brookes University, Nocturnal Primate Research Group, Oxford, UK,3The Little Fireface Project, Cisurupan, Cipaganti, Indonesia
| | - Ariana Weldon
- 1Oxford Brookes University, Nocturnal Primate Research Group, Oxford, UK,3The Little Fireface Project, Cisurupan, Cipaganti, Indonesia
| | - Stephanie A Poindexter
- 1Oxford Brookes University, Nocturnal Primate Research Group, Oxford, UK,3The Little Fireface Project, Cisurupan, Cipaganti, Indonesia
| | | | - K Anna I Nekaris
- 1Oxford Brookes University, Nocturnal Primate Research Group, Oxford, UK,3The Little Fireface Project, Cisurupan, Cipaganti, Indonesia,*Correspondence to: Anna Nekaris, ; Tel:+44 (0)1865 483767
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25
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Zhang L, Zhang G, Yun Y, Peng Y. Bacterial community of a spider, Marpiss magister (Salticidae). 3 Biotech 2017; 7:371. [PMID: 29071168 PMCID: PMC5639805 DOI: 10.1007/s13205-017-0994-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/23/2017] [Indexed: 12/11/2022] Open
Abstract
Arthropods are associated with various microorganisms which confer benefits to their hosts. Recently, research has been conducted on bacterial communities of insects to provide an insight into the potential interactions of the symbiotic bacteria and their hosts. Spiders are interesting to study as they are perceived to be natural enemies of pests. The effect of endosymbionts on spiders has been reported, but little is known about the overall bacterial communities present in spiders. Here, we report on the characterization of bacterial communities present in the whole body of the spider Marpiss magister using Illumina sequencing of 16S rRNA amplicons. Our study shows that the most abundant phyla of bacteria included Proteobacteria, Tenericutes, Bacteroidetes and Actinobacteria. At the genus level, the most abundant genera included Rickettsia, Wolbachia, Spiroplasma, and Cardinium. Besides these dominant endosymbionts, our study also showed the existence of bacteria in the genera Arthrobacter, Novosphingobium, Acinetobacter, Pseudomonas, Aquabacterium and Sphingomonas at an abundance ranging from 0.65 to 0.84%, and the existence of bacterial in genera Lactobacillus, Sphingobium, Methylobacterium, Bradyrhizobium, Propionibacterium, Brevundimonas, Achromobacter, Microbacterium, Corynebacterium, and Flavobacterium at a slightly lower abundance ranging from 0.1 to 0.5%. Therefore, our finding indicates that endosymbionts are not the only microbiota present in the spider M. magister, and other bacterial taxa also exist in its bacterial community.
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Affiliation(s)
- Lihua Zhang
- Centre for Behavioral Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
| | - Guimin Zhang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
| | - Yueli Yun
- Centre for Behavioral Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
| | - Yu Peng
- Centre for Behavioral Ecology and Evolution, College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan, 430062 People’s Republic of China
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26
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Collingro A, Köstlbacher S, Mussmann M, Stepanauskas R, Hallam SJ, Horn M. Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. ISME JOURNAL 2017. [PMID: 28644443 PMCID: PMC5604735 DOI: 10.1038/ismej.2017.95] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chlamydiae are obligate intracellular bacteria comprising important human pathogens and symbionts of protists. Molecular evidence indicates a tremendous diversity of chlamydiae particularly in marine environments, yet our current knowledge is based mainly on terrestrial representatives. Here we provide first insights into the biology of marine chlamydiae representing three divergent clades. Our analysis of single-cell amplified genomes revealed hallmarks of the chlamydial lifestyle, supporting the ancient origin of their characteristic developmental cycle and major virulence mechanisms. Surprisingly, these chlamydial genomes encode a complete flagellar apparatus, a previously unreported feature. We show that flagella are an ancient trait that was subject to differential gene loss among extant chlamydiae. Together with a chemotaxis system, these marine chlamydiae are likely motile, with flagella potentially playing a role during host cell infection. This study broadens our view on chlamydial biology and indicates a largely underestimated potential to adapt to different hosts and environments.
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Affiliation(s)
- Astrid Collingro
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Stephan Köstlbacher
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | - Marc Mussmann
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
| | | | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthias Horn
- Department of Microbial and Ecosystems Science, Division of Microbial Ecology, University of Vienna, Vienna, Austria
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27
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Degli Esposti M, Martinez Romero E. The functional microbiome of arthropods. PLoS One 2017; 12:e0176573. [PMID: 28475624 PMCID: PMC5419562 DOI: 10.1371/journal.pone.0176573] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
Many studies on the microbiome of animals have been reported but a comprehensive analysis is lacking. Here we present a meta-analysis on the microbiomes of arthropods and their terrestrial habitat, focusing on the functional profile of bacterial communities derived from metabolic traits that are essential for microbial life. We report a detailed analysis of probably the largest set of biochemically defined functional traits ever examined in microbiome studies. This work deals with the phylum proteobacteria, which is usually dominant in marine and terrestrial environments and covers all functions associated with microbiomes. The considerable variation in the distribution and abundance of proteobacteria in microbiomes has remained fundamentally unexplained. This analysis reveals discrete functional groups characteristic for adaptation to anaerobic conditions, which appear to be defined by environmental filtering of taxonomically related taxa. The biochemical diversification of the functional groups suggests an evolutionary trajectory in the structure of arthropods' microbiome, from metabolically versatile to specialized proteobacterial organisms that are adapted to complex environments such as the gut of social insects. Bacterial distribution in arthropods' microbiomes also shows taxonomic clusters that do not correspond to functional groups and may derive from other factors, including common contaminants of soil and reagents.
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Affiliation(s)
- Mauro Degli Esposti
- Italian Institute of Technology, Genoa, Italy
- Center for Genomic Sciences, UNAM Campus of Cuernavaca, Cuernavaca, Morelos, Mexico
- * E-mail:
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28
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Hokynar K, Vesterinen EJ, Lilley TM, Pulliainen AT, Korhonen SJ, Paavonen J, Puolakkainen M. Molecular Evidence of Chlamydia-Like Organisms in the Feces of Myotis daubentonii Bats. Appl Environ Microbiol 2017; 83:e02951-16. [PMID: 27815278 PMCID: PMC5203614 DOI: 10.1128/aem.02951-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 10/31/2016] [Indexed: 11/20/2022] Open
Abstract
Chlamydia-like organisms (CLOs) are recently identified members of the Chlamydiales order. CLOs share intracellular lifestyles and biphasic developmental cycles, and they have been detected in environmental samples as well as in various hosts such as amoebae and arthropods. In this study, we screened bat feces for the presence of CLOs by molecular analysis. Using pan-Chlamydiales PCR targeting the 16S rRNA gene, Chlamydiales DNA was detected in 54% of the specimens. PCR amplification, sequencing, and phylogenetic analysis of the 16S rRNA and 23S rRNA genes were used to classify positive specimens and infer their phylogenetic relationships. Most sequences matched best with Rhabdochlamydia species or uncultured Chlamydia sequences identified in ticks. Another set of sequences matched best with sequences of the Chlamydia genus or uncultured Chlamydiales from snakes. To gain evidence of whether CLOs in bat feces are merely diet borne, we analyzed insects trapped from the same location where the bats foraged. Interestingly, the CLO sequences resembling Rhabdochlamydia spp. were detected in insect material as well, but the other set of CLO sequences was not, suggesting that this set might not originate from prey. Thus, bats represent another potential host for Chlamydiales and could harbor novel, previously unidentified members of this order. IMPORTANCE Several pathogenic viruses are known to colonize bats, and recent analyses indicate that bats are also reservoir hosts for bacterial genera. Chlamydia-like organisms (CLOs) have been detected in several animal species. CLOs have high 16S rRNA sequence similarity to Chlamydiaceae and exhibit similar intracellular lifestyles and biphasic developmental cycles. Our study describes the frequent occurrence of CLO DNA in bat feces, suggesting an expanding host species spectrum for the Chlamydiales As bats can acquire various infectious agents through their diet, prey insects were also studied. We identified CLO sequences in bats that matched best with sequences in prey insects but also CLO sequences not detected in prey insects. This suggests that a portion of CLO DNA present in bat feces is not prey borne. Furthermore, some sequences from bat droppings not originating from their diet might well represent novel, previously unidentified members of the Chlamydiales order.
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Affiliation(s)
- K Hokynar
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - E J Vesterinen
- Archipelago Research Institute, University of Turku, Turku, Finland
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - T M Lilley
- Biology Department, Bucknell University, Lewisburg, Pennsylvania, USA
| | - A T Pulliainen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - S J Korhonen
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - J Paavonen
- Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - M Puolakkainen
- Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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29
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Vanthournout B, Hendrickx F. Hidden suppression of sex ratio distortion suggests Red queen dynamics between Wolbachia and its dwarf spider host. J Evol Biol 2016; 29:1488-94. [PMID: 26995349 DOI: 10.1111/jeb.12861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/05/2016] [Accepted: 02/26/2016] [Indexed: 01/13/2023]
Abstract
Genetic conflict theory predicts strong selection for host nuclear factors suppressing endosymbiont effects on reproduction; however, evidence of these suppressors is currently scarce. This can either be caused by a low suppressor evolution rate, or if suppressors originate frequently, by rapid spread and concurrent masking of their activity by silencing the endosymbiont effect. To explore this, we use two populations of a dwarf spider with a similar female bias, caused by a Wolbachia infection. Using inter- and intrapopulation crosses, we determine that one of these populations demonstrates a higher suppressing capability towards Wolbachia despite having a similar population sex ratio. This suggests that spider and endosymbiont are locked in so-called red queen dynamics where, despite continuous coevolution, average fitness remains the same, hence hiding the presence of the suppressor. Finding different suppressor activity in populations that even lack phenotypic differentiation (i.e. similar sex ratio) further supports the hypothesis that suppressors originate often, but are often hidden by their own mode of action by countering endosymbiont effects.
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Affiliation(s)
- B Vanthournout
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium.,Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | - F Hendrickx
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium.,Royal Belgian Institute of Natural Sciences, Brussels, Belgium
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30
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Keiser CN, Shearer TA, DeMarco AE, Brittingham HA, Knutson KA, Kuo C, Zhao K, Pruitt JN. Cuticular bacteria appear detrimental to social spiders in mixed but not monoculture exposure. Curr Zool 2016; 62:377-384. [PMID: 29491926 PMCID: PMC5829440 DOI: 10.1093/cz/zow015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/22/2015] [Indexed: 12/15/2022] Open
Abstract
Much of an animal’s health status, life history, and behavior are dictated by
interactions with its endogenous and exogenous bacterial communities. Unfortunately,
interactions between hosts and members of their resident bacterial community are often
ignored in animal behavior and behavioral ecology. Here, we aim to identify the nature of
host–microbe interactions in a nonmodel organism, the African social spider
Stegodyphus dumicola. We collected and identified bacteria from the
cuticles of spiders in situ and then exposed spiders to bacterial
monocultures cultures via topical application or injection. We also topically inoculated
spiders with a concomitant “cocktail” of bacteria and measured the behavior of spiders
daily for 24 days after inoculation. Lastly, we collected and identified bacteria from the
cuticles of prey items in the capture webs of spiders, and then fed spiders domestic
crickets which had been injected with these bacteria. We also injected 1 species of
prey-borne bacteria into the hemolymph of spiders. Only Bacillus
thuringiensis caused increased mortality when injected into the hemolymph of
spiders, whereas no bacterial monocultures caused increased mortality when applied
topically, relative to control solutions. However, a bacterial cocktail of cuticular
bacteria caused weight loss and mortality when applied topically, yet did not detectibly
alter spider behavior. Consuming prey injected with prey-borne bacteria was associated
with an elongated lifespan in spiders. Thus, indirect evidence from multiple experiments
suggests that the effects of these bacteria on spider survivorship appear contingent on
their mode of colonization and whether they are applied in monoculture or within a mixed
cocktail. We urge that follow-up studies should test these host–microbe interactions
across different social contexts to determine the role that microbes play in colony
performance.
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Affiliation(s)
- Carl N Keiser
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Taylor A Shearer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Alexander E DeMarco
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Hayley A Brittingham
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Karen A Knutson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Candice Kuo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Katherine Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
| | - Jonathan N Pruitt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260 USA
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31
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Jousselin E, Clamens AL, Galan M, Bernard M, Maman S, Gschloessl B, Duport G, Meseguer AS, Calevro F, Coeur d'acier A. Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus. Mol Ecol Resour 2015; 16:628-40. [PMID: 26458227 DOI: 10.1111/1755-0998.12478] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 02/07/2023]
Abstract
The bacterial communities inhabiting arthropods are generally dominated by a few endosymbionts that play an important role in the ecology of their hosts. Rather than comparing bacterial species richness across samples, ecological studies on arthropod endosymbionts often seek to identify the main bacterial strains associated with each specimen studied. The filtering out of contaminants from the results and the accurate taxonomic assignment of sequences are therefore crucial in arthropod microbiome studies. We aimed here to validate an Illumina 16S rRNA gene sequencing protocol and analytical pipeline for investigating endosymbiotic bacteria associated with aphids. Using replicate DNA samples from 12 species (Aphididae: Lachninae, Cinara) and several controls, we removed individual sequences not meeting a minimum threshold number of reads in each sample and carried out taxonomic assignment for the remaining sequences. With this approach, we show that (i) contaminants accounted for a negligible proportion of the bacteria identified in our samples; (ii) the taxonomic composition of our samples and the relative abundance of reads assigned to a taxon were very similar across PCR and DNA replicates for each aphid sample; in particular, bacterial DNA concentration had no impact on the results. Furthermore, by analysing the distribution of unique sequences across samples rather than aggregating them into operational taxonomic units (OTUs), we gained insight into the specificity of endosymbionts for their hosts. Our results confirm that Serratia symbiotica is often present in Cinara species, in addition to the primary symbiont, Buchnera aphidicola. Furthermore, our findings reveal new symbiotic associations with Erwinia- and Sodalis-related bacteria. We conclude with suggestions for generating and analysing 16S rRNA gene sequences for arthropod-endosymbiont studies.
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Affiliation(s)
- E Jousselin
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - A-L Clamens
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Galan
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - M Bernard
- INRA - UMR 1313 GABI-SIGENAE, INRA de Jouy en Josas, Domaine de Vilvert, 78352, Jouy en Josas, France
| | - S Maman
- INRA, GenPhySE, Sigenae, Chemin de Borde rouge -CS 52627, 31326, Castanet Tolosan, France
| | - B Gschloessl
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - G Duport
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A S Meseguer
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
| | - F Calevro
- UMR 203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA de Lyon, Université de Lyon, 20 Avenue Einstein, F-69621, Villeurbanne, France
| | - A Coeur d'acier
- INRA - UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro), 755 avenue du Campus Agropolis CS 30016, F-34 988, Montferrier-sur-Lez, France
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