APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Aug. 2009, p. 5328–5335 Vol. 75, No. 16 0099-2240/09/$08.00ϩ0 doi:10.1128/AEM.00717-09 Copyright © 2009, American Society for Microbiology. All Rights Reserved. Evolution and Diversity of Facultative Symbionts from the Aphid Subfamily Lachninaeᰔ† Gaelen R. Burke,1* Benjamin B. Normark,2 Colin Favret,3 and Nancy A. Moran1 Department of Ecology and Evolutionary Biology, University of Arizona, 1041 East Lowell Street, Tucson, Arizona 85721-00881; Department of Plant, Soil, and Insect Sciences, University of Massachusetts, 270 Stockbridge Road, Amherst, Massachusetts 010032; and AphidNet, LLC, 18901 Tributary Lane, Gaithersburg, Maryland 208793 Received 27 March 2009/Accepted 11 June 2009 Many aphids harbor a variety of endosymbiotic bacteria. The functions of these symbionts can range from an obligate nutritional role to a facultative role in protecting their hosts against environmental stresses. One such symbiont is “Candidatus Serratia symbiotica,” which is involved in defense against heat and potentially also in aphid nutrition. Lachnid aphids have been the focus of several recent studies investigating the transition of this symbiont from a facultative symbiont to an obligate symbiont. In a phylogenetic analysis of Serratia symbionts from 51 lachnid hosts, we found that diversity in symbiont morphology, distribution, and function is due to multiple independent origins of symbiosis from ancestors belonging to Serratia and possibly also to evolution within distinct symbiont clades. Our results do not support cocladogenesis of “Ca. Serratia symbiotica” with Cinara subgenus Cinara species and weigh against an obligate nutritional role. Finally, we show that species belonging to the subfamily Lachninae have a high incidence of facultative symbiont infection. Many insect species harbor heritable endosymbiotic bacte- (10, 15, 16, 26). In contrast to most Buchnera strains, Buchnera ria. Among the best studied of these species are aphids. Almost strains from Cinara cedri (Lachnini) have lost the genes for all aphids are infected with the obligate nutritional symbiont biosynthesis of the essential amino acid tryptophan, while “Ca. Buchnera aphidicola, which is generally required for the sur- Serratia symbiotica” in the same host possesses at least part of vival of aphids and provides essential amino acids that are rare the pathway, suggesting that it has a mutualistic role in the in their phloem sap diet (32). Many aphids also possess addi- nutrition of aphids (26). tional symbionts that may be facultative from the host’s per- In A. pisum,“Ca. Serratia symbiotica” cells are rod-shaped spective and that coexist with Buchnera (20). bacteria that are present in the sheath cells, hemolymph, and Three lineages of facultative symbionts that are prevalent in bacteriocytes of some individuals. In contrast, in C. cedri “Ca. aphids belong to the Enterobacteriaceae. Two of these lineages Serratia symbiotica” occurs in all individuals, and its cells are (“Candidatus Hamiltonella defensa” and “Candidatus Regiella large, round, and pleomorphic, similar to the cells of many insecticola”) form well-defined clades distinct from free-living obligate bacterial aphid endosymbionts, including Buchnera bacterial species (4, 20) and confer clear advantages to their (10, 26). Furthermore, “Ca. Serratia symbiotica” has consis- hosts by protecting them against natural enemies. “Ca. Ham- tently been present in other Cinara species sampled (28). Both iltonella defensa” prevents wasp parasitism by arresting devel- the rod-shaped and pleomorphic forms are assigned to “Ca. opment of wasp larvae in pea aphids, and “Ca. Regiella insec- Serratia symbiotica” based on phylogenetic analyses of several ticola” provides resistance against the fungal pathogen gene sequences, but they fall into two distinct sister clades of Pandora neoaphidis (24, 31). The third lineage, “Candidatus symbiont lineages that seem to coincide with bacterial mor- Serratia symbiotica,” is closely related to free-living members phology (17, 20). of the genus Serratia. This symbiont is distributed sporadically This diversity in “Ca. Serratia symbiotica” morphology, dis- among aphid species and has been proposed to have a variety tribution, and functions may represent evolution of different of effects on hosts. In pea aphids (Acyrthosiphon pisum; Mac- features within lineages of a single symbiont clade. If “Ca. rosiphini), “Ca. Serratia symbiotica” ameliorates the deleteri- Serratia symbiotica” is an obligate nutritional symbiont in ous fitness effects of heat shock by protecting symbiont-har- Cinara hosts, it is expected that Cinara-associated symbionts boring bacteriocyte cells (2, 19, 29). Additionally, a strain of would form a clade in which the intraclade relationships mirror “Ca. Serratia symbiotica” provided some resistance to parasi- those of the hosts (cocladogenesis), as observed for Buchnera Ca. toid wasp attack (24). “ Serratia symbiotica” has been pro- and other obligate nutritional symbionts of insects (13, 21, 38). posed to play a role in nutrition by producing amino acids for Indeed, Lamelas et al. postulated that, based on their similar its aphid host and by decreasing its host’s reliance on Buchnera phylogenies, Serratia symbionts from aphids belonging to the subgenus Cinara have had a long-term relationship with their * Corresponding author. Mailing address: Department of Ecology hosts (17). and Evolutionary Biology, University of Arizona, 1041 E. Lowell St., In addition to the three most common facultative symbiont Tucson, AZ 85721-0088. Phone: (520) 626-8344. Fax: (520) 621-9190. types found in aphids described above, several other symbiont E-mail: [email protected]. lineages with unknown functions have been identified by am- † Supplemental material for this article may be found at http://aem .asm.org/. plification of bacterial 16S rRNA gene sequences from various ᰔ Published ahead of print on 19 June 2009. aphid species (10, 28, 39). Here we examine the diversity of 5328 VOL. 75, 2009 FACULTATIVE SYMBIONTS OF THE APHID SUBFAMILY LACHNINAE 5329 Serratia and other facultative symbionts in aphids belonging to rRNA gene of these taxa resulted in a gene tree showing the the subfamily Lachninae. We investigated the distribution of evolutionary relationships among symbionts and free-living symbionts in aphid species and geographic locations and species in the genus Serratia (Fig. 1). looked for coevolutionary patterns that may correspond to the Most aphid symbionts belonging to the genus Serratia fall functions of facultative symbionts within their hosts. into two sister clades corresponding to clusters A and B, as described by Lamelas et al. (17). These symbionts include MATERIALS AND METHODS almost all of the Serratia symbionts from the aphid family Aphididae, including the Lachninae. Extraction, PCR analysis, cloning, and sequencing of DNA from aphid sam- ples. A panel of aphids belonging to the aphid subfamily Lachninae (with a focus Cluster A contains symbionts from members of both the on species of the genus Cinara) were screened for bacterial endosymbionts Aphididae and the Lachninae, including Cinara. The majority (Table 1; see Table S1 in the supplemental material). In most cases, screening of the symbionts belonging to cluster A show little diversity; was based on a single individual per aphid species or population, unless indicated the greatest pairwise distance is 0.064 substitution per site. otherwise (Table 1). Cluster B contains symbionts solely from the Lachninae. These DNA extraction was performed with single aphids using a DNeasy kit (Qia- gen). PCR was used to amplify 16S rRNA using primers 10F (5Ј-AGTTTGAT symbionts show greater diversity than those in cluster A (the CATGGCTCAGATTG-3Ј), 35R (5Ј-CCTTCATCGCCTCTGACTGC-3Ј), and greatest pairwise distance is 0.096 substitution per site), and 1507R (5Ј-TACCTTGTTACGACTTCACCCCAG-3Ј). Each reaction mixture lineages from closely related aphid hosts are generally more ␮ (50 l) contained 10 mM Tris-HCl (pH 9.0), 50 mM KCl, 0.1% Triton X-100, 1.5 closely related to each other than to other symbiont lineages in mM MgCl2, 1 mM deoxynucleoside triphosphates (Eppendorf), 250 pmol of each primer, and 2 U Taq polymerase (Eppendorf). PCR amplification was carried the clade (Fig. 1). “Ca. Serratia symbiotica” lineages from C. out with a Mastercycler Gradient (Eppendorf) as follows: 94°C for 2 min, fol- cedri and Pterochloroides persicae cluster with high levels of lowed by 35 cycles of 94°C for 1 min, 55°C for 1 min, and 72°C for 3 min and then support. a final incubation at 72°C for 10 min. Amplified products were examined using A third group of Serratia strains from aphids does not branch standard 1% agarose gel electrophoresis and staining with ethidium bromide. with clusters A and B. The 16S rRNA gene tree indicates that Single, discrete bands were cleaned using Agencourt AMPure PCR purification (Agencourt, Beverly, MA). these strains are more closely related to Serratia marcescens In order to separate Buchnera and facultative symbiont 16S rRNA gene se- than to other symbiotic clades. quences, cloning was performed using a pGEM-T Easy kit (Promega), and Phylogenetic reconstruction of Buchnera lineages. 16S rRNA pGEM-T Easy with its insert was transformed into Escherichia coli competent gene sequences were obtained from all bacterial strains from cells (Promega). The insert size for eight colonies was checked using colony PCR performed with primers M13F (5Ј-GTAAAACGACGGCCAG-3Ј) and M13R Lachninae