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.
This is a preview of subscription content, log in to check access.
We thank J. Harwood and J. Dryer for providing and collecting specimens, and three anonymous reviewers for comments on an earlier draft of this manuscript.
This research work was supported by grants from the Kentucky Science and Engineering Foundation as per Grant/Award Agreements 148-502-10-261 and 148-502-16-377 with the Kentucky Science and Technology Corporation, and the National Institute of Food and Agriculture, U.S. Department of Agriculture (Hatch No. 0224651).
Online Resource 1Individual spider specimens, diagnostic results, and sequences. Tab1 includes metadata, diagnostic results, COI haplotypes and bacterial strain types associated with each specimen. Tab 2 provides the Genbank accession number and sequences associated with each COI haplotype and bacterial strain type. (XLSX 62 kb)
Online Resource 4Figs. S1 & S2 Microbiome profile of starved versus unstarved specimens of (Fig. S1) Idionella rugosa and (Fig. S2) Glenognatha foxi. Each profile was generated from a rarified sample of 3000 Illumina MiSeq reads of the V4 region of bacterial 16S rRNA. The 7-8 most common genera are presented in the key for each figure; in Fig. S1, Cardinium, Wolbachia and Rickettsia each encompass two distinct strain type OTUs. In Fig. S2, many of these OTUs could only be placed at the family or order level. (PDF 260 kb)
Huigens ME, de Almeida RP, Boons PAH, Luck RF, Stouthamer R (2004) Natural interspecific and intraspecific horizontal transfer of parthenogenesis-inducing Wolbachia in Trichogramma wasps. Proc R Soc Lond B Biol 271(1538):509–515. https://doi.org/10.1098/rspb.2003.2640Google Scholar
Caspi-Fluger A, Inbar M, Mozes-Daube N, Katzir N, Portnoy V, Belausov E, Hunter MS, Zchori-Fein E (2012) Horizontal transmission of the insect symbiont Rickettsia is plant-mediated. Proc R Soc B-Biol Sci 279(1734):1791–1796. https://doi.org/10.1098/rspb.2011.2095Google Scholar
Himler AG, Adachi-Hagimori T, Bergen JE, Kozuch A, Kelly SE, Tabashnik BE, Chiel E, Duckworth VE, Dennehy TJ, Zchori-Fein E, Hunter MS (2011) Rapid spread of a bacterial symbiont in an invasive whitefly is driven by fitness benefits and female bias. Science 332(6026):254–256. https://doi.org/10.1126/science.1199410Google Scholar
Russell JA, Weldon S, Smith AH, Kim KL, Hu Y, Łukasik P, Doll S, Anastopoulos I, Novin M, Oliver KM (2013) Uncovering symbiont-driven genetic diversity across North American pea aphids. Mol Ecol 22:2045–2059. https://doi.org/10.1111/mec.12211Google Scholar
Baldo L, Ayoub NA, Hayashi CY, Russell JA, Stahlhut JK, Werren JH (2008) Insight into the routes of Wolbachia invasion: high levels of horizontal transfer in the spider genus Agelenopsis revealed by Wolbachia strain and mitochondrial DNA diversity. Mol Ecol 17:557–569. https://doi.org/10.1111/j.1365-294X.2007.03608.xGoogle Scholar
Baldo L, Hotopp J, Jolley K, Bordenstein SR, Biber S, Choudhury R, Hayashi CY, Maiden M, Tettelin H, Werren J (2006) Multilocus sequence typing system for the endosymbiont Wolbachia pipientis. Appl Environ Microbiol 72:7098–7110. https://doi.org/10.1128/AEM.00731-06Google Scholar
Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD (2013) Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 79(17):5112–5120. https://doi.org/10.1128/AEM.01043-13Google Scholar
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336. https://doi.org/10.1038/nmeth.f.303Google Scholar
Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG (2012) Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods 10:57–59. https://doi.org/10.1038/nmeth.2276Google Scholar
Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Xu ZZ, Kightley EP, Thompson LR, Hyde ER, Gonzalez A (2017) Deblur rapidly resolves single-nucleotide community sequence patterns. MSystems 2(2):e00191–e00116. https://doi.org/10.1128/mSystems.00191-16Google Scholar
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72(7):5069–5072. https://doi.org/10.1128/AEM.03006-05Google Scholar
Zwickl DJ (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD Thesis, The University of Texas at Austin. https://code.google.com/archive/p/garli/. Accessed 10 Feb 2014
Takano S-i, Tuda M, Takasu K, Furuya N, Imamura Y, Kim S, Tashiro K, Iiyama K, Tavares M, Amaral AC (2017) Unique clade of alphaproteobacterial endosymbionts induces complete cytoplasmic incompatibility in the coconut beetle. Proc Natl Acad Sci U S A 114(23):6110–6115. https://doi.org/10.1073/pnas.1618094114Google Scholar