PCR and phylogenetic analysis of 16S rRNA sequence.
By using a combination of universal and symbiont-specific 16S rRNA primers, we obtained 1,474 bp of sequence from B. simplex larval DNA. An annealing temperature of 60°C provided the necessary specificity for amplification. The sequence most closely matched “Candidatus E. sertula” in the BLAST and RDP-II databases.
Phylogenetic analysis showed that the symbiont of
B. simplex clustered with “
Candidatus E. sertula” by all phylogenetic methods implemented (Fig.
1). NJ and MP bootstrap values and the Bayesian posterior probability of this clade were 100%, 99%, and 1.00, respectively. The
B. simplex symbiont shows a 95% similarity to “
Candidatus E. sertula” over 1,395 bp, corresponding to
E. coli positions 45 to 1477, and the
Endobugula cluster is nested within the
Teredinibacter clade, a group of bacterial symbionts in shipworms. These intracellular cellulolytic nitrogen-fixing symbionts are found in the gills, gonads, and eggs of shipworms, allowing shipworms to survive on a cellulose diet (
33). The close relationship between bryozoan and shipworm symbionts is intriguing, since the hosts are phylogenetically unrelated and have different diets.
The close similarity between “
Candidatus E. glebosa” and “
Candidatus E. sertula” suggests that either the acquisition of symbiont occurred before the speciation of ancestral
Bugula sp. or that
B. neritina and
B. simplex independently adopted similar bacterial symbionts. The first scenario is more parsimonious, especially taken together with the presumed vertical mode of symbiont transmission, since the symbionts are found in host larvae (
14). The investigation of cospeciation in more
Bugula-bacteria associations (three out of five
Bugula species are known to harbor symbiotic bacteria [
38]) should shed light on the evolutionary history of the symbiosis.
FISH.
Figure
2a shows the location of the circular pallial sinus in a
B. simplex larva. The symbiont-specific Endo1253R probe hybridized to long rod-shaped cells in the pallial sinuses of
B. simplex larvae (Fig.
2d and f). The universal eubacterial probe also hybridized to similar cells with similar distribution and density (Fig.
2c and e). The negative control probe, Endo1253Mis, did not bind to any cells (Fig.
2b). This probe is a “
Candidatus E. sertula”-specific probe (
14), demonstrating that “
Candidatus E. sertula”, the symbiont of
B. neritina, is not present in
B. simplex larvae. The symbiont in
B. simplex has a different morphology and distribution in the pallial sinus of the larva compared to “
Candidatus E. sertula,” unlike in previous reports (
38). The
B. simplex symbionts were elongated (with lengths ranging from 1 to 10 μm), whereas “
Candidatus E. sertula” were short rods. “
Candidatus E. sertula” cells were evenly distributed, whereas the
B. simplex symbionts are concentrated in discontinuous patches around the pallial sinus (Fig.
2c and d).
Transmission electron microscopy analysis has shown that B. simplex also harbors bacteria in its pallial sinus, but the phylogenetic affiliation of the bacteria was previously unknown. We performed these FISH experiments on B. simplex larvae to verify that the 16S sequence obtained by PCR, and sequencing arose from the symbiont in the pallial sinus. Although 16S rRNA analysis shows that “Candidatus E. sertula” and “Candidatus E. glebosa” are closely related, their cell morphologies and distribution around the larval pallial sinus are different.
The name “
Candidatus Endobugula glebosa” (“glebosa” meaning clumpy in Latin) is proposed for the
B. simplex symbiont with the following description (
24): “
Candidatus Endobugula glebosa” [(γ-
Proteobacteria) NC; G−; R; NAS (GenBank no. AY532642 ), oligonucleotide sequence complementary to the unique region of 16S rRNA 5′-CAT CAC TGC TTC GCA ACC C-3′; S (
Bugula simplex, pallial sinus of larvae); M].
PKS genes.
We obtained a PCR product of approximately 300 bp by using degenerate primers in a touchdown PCR and cloned it into a plasmid library. Colonies were picked and sequenced with primers flanking the cloning site. One sequence, EgleKSa, made up 9 out of 12 clones sequenced. The other clones did not share homology with anything in BLAST searches. EgleKSa closely matches KSa from “
Candidatus E. sertula,” the gene fragment believed to be part of the bryostatin-synthesizing cluster (
8). It has 80% amino acid identity and 85% similarity with KSa in a 103-amino-acid span. The G+C content of the fragment from
B. simplex is 48%, which is close to that of KSa (47%). This similarity is consistent with the possibility of a homologous PKS cluster in “
Candidatus E. glebosa.” The next-closest match after KSa was the fourth module of PedI of the pederin cluster in the symbiont of
Paederus fuscipes (
29) with 56% identity and 71% similarity. The amino acid alignment for these three sequences is shown in Fig.
4a.
In the previous study using these degenerate KS primers on
B. neritina larvae, only one of the nine unique sequences obtained was consistently associated with all bryostatin-producing colonies, while the other eight KS sequences probably originated from environmental bacteria (
8). We did not retrieve the other KS domains in the putative bryostatin cluster in “
Candidatus E. sertula” by using this set of degenerate primers (unpublished data). Similarly, with these primers, we obtained only one KS sequence from
B. simplex/“
Candidatus E. glebosa.”
Just as the 300-bp KSa was used as a probe to isolate the 68-kbp putative bryostatin PKS cluster in “
Candidatus E. sertula” (
16), EgleKSa isolated in this study could be used to retrieve the putative PKS cluster from “
Candidatus E. glebosa.” Sequencing of the entire cluster would reveal whether the PKS cluster is intact, as well as the similarities and differences of the “
Candidatus E. glebosa” PKS to the putative bryostatin PKS, and it will provide clues into the nature of the “
Candidatus E. glebosa” metabolite, whether it is another bryostatin (possessing the known bryopyran skeleton) or if it has a novel polyketide backbone.
PCR survey.
By using specific 16S rRNA primers, the 16S rRNA gene of the symbiont “
Candidatus E. glebosa” was amplified from a number of
B. simplex adult colonies collected over 3 years (Fig.
4b). This sequence was absent in
B. neritina, as well as the cooccurring
B. stolonifera and
B. turrita. Specific primers BsimKSF and BsimKSR amplified the fragment of expected size from several populations of
B. simplex (Fig.
4c) and show the same amplification pattern as the “
Candidatus E. glebosa” 16S gene survey. The consistent presence of “
Candidatus E. glebosa” 16S rRNA and EgleKSa genes in several
B. simplex populations strongly suggests that the symbiont is not a transient bacterium. This survey does not preclude the possibility of multiple symbionts in
B. simplex, which occurs in other hosts. For example, at least four symbionts which are closely related to each other reside in the gills of shipworms (
10). The analysis of a 16S rRNA clone library made from amplifying
B. simplex DNA with universal primers, combined with FISH to localize the sequences, can help resolve this question (
10).
Bryostatin activity and LC-MS.
Various degrees of bryostatin activity have been measured using the PdBU assay on different samples of
Bugula species (Fig.
4d and e). Figure
4d shows a representative plot of percent displacement of PdBU for
B. simplex and
B. stolonifera extracts. The IC
50 is converted to bryostatin 1 equivalents using the IC
50 of bryostatin 1 (Fig.
4e). Although the PdBU assay is not necessarily specific for bryostatins, previous experiments have demonstrated that it is an accurate indication of bryostatin activity in bryozoans (
8). Extracts of adults and larvae from
B. neritina and
B. simplex can displace PdBU from PKC (Fig.
4e), while extracts of the aposymbiotic and cooccurring
B. stolonifera and
B. turrita are inactive, supporting the hypothesis that
Endobugula symbionts are involved in bryostatin production.
B. neritina and
B. simplex larval extracts have more bryostatin activity (when normalized by weight) than extracts of their respective adults (Fig.
4e), confirming the role of bryostatins in the chemical defense of larvae (
21).
LC-MS analysis of the ethyl acetate fraction of
B. neritina larval extracts showed peaks consistent with the bryostatins based on retention times, molecular masses, and UV spectra. The known bryostatins from
B. neritina are relatively nonpolar and elute between 20 to 28 min. They have masses between 766 and 932 (see review in reference
25), and chemotype M bryostatins have a UV maximum at 230 nm (
26). During the
B. neritina reference run, ions tended to form sodium adducts [M + Na]
+. Ion extraction analyses showed that chemotype O bryostatins were absent, which was expected since the larvae were collected from shallow
B. neritina populations, which contain only M bryostatins (
9).
The ethyl acetate fraction of
B. simplex larval extracts showed two peaks, Bs801 and Bs817, that resemble known bryostatins based on their UV spectra (Fig.
5c) but are distinct based on retention times (Fig.
5a and b) and molecular masses (Fig.
5d). Bs801, with retention time of 24.7 min, has a [M + Na]
+m/z of 801 and has a UV spectrum consistent with type M bryostatins (Fig.
5). Though the mass of 778 (M
+ − Na
+) does not match known bryostatins, it falls within the correct range of their masses. Bs817, with a retention time of 27.4 min, has a [M + Na]
+m/z of 817 and a UV spectrum consistent with type M bryostatins (Fig.
5). The molecular weight 794 (M
+ − Na
+) corresponds to either bryostatin 13 or 20, but the retention time of Bs817 does not match any peak in the
B. neritina extract. The
m/z of 817 in the
B. neritina profile (Bryo817) matches retention times 25.5 and 26.5 min (Fig.
5b), which are probably bryostatins 13 and 20. The large peak at 27.7 min in
B. neritina, Bryo831, has an
m/z of 831 and is probably either bryostatin 10 or 18. Since Bs801 and Bs817 do not exactly match any known bryostatins but have bryostatin characteristics (approximate mass and correct UV spectrum), they are potentially new bryostatin-like polyketides. There is common peak in both
B. neritina and
B. simplex extracts at 28.4 min with
m/z of 637 (Bn637 and Bs637; Fig.
5). This mass is lower than any known bryostatin, and its UV spectrum does not match that of bryostatins.
Extraction of 500 kg of
B. neritina adult colonies was required for complete structure elucidation of bryostatin 1 (
27). Thus, similar quantities of
B. simplex may be necessary to determine the structures of the bryostatin-like molecules. Since
B. simplex is less abundant than
B. neritina, it may be a formidable task to collect sufficient quantities for chemical characterization of bryostatin-like molecules. Because PdBU results demonstrate that the larvae contain a higher level of bryostatin activity (
21) (Fig.
5b), larvae may prove to be a more feasible source of novel bryostatin-like polyketides in
B. simplex.
Bacterial symbionts in invertebrates typically provide their hosts with metabolic pathways that do not exist in the host. For example, in shipworms, the symbiont
Teredinebacter turnerae digests cellulose and fixes nitrogen (
33), and sulfur-oxidizing bacteria provide reduced carbon for bivalves (
6). Another variation of this principle is that of bioactive metabolite symbiosis (
16), in which the symbiont provides bioactive metabolites to their host for chemical defense. With this principle in mind, bacterial symbionts in invertebrates are being investigated as sources of bioactive metabolites that can be potential drugs (
8,
23,
28). Since many obligate symbionts have not been cultivated, the biosynthetic gene clusters must be cloned and expressed in a heterologous host in order to produce the metabolite ex symbio (
16,
28). Modular PKS from bacterial symbionts of invertebrates present an opportunity for combinatorial biosynthesis to produce novel compounds. Further investigations are needed to characterize bioactive metabolites in
B. simplex/“
Candidatus E. glebosa” and to clone the PKS cluster. More species of
Bugula should be investigated to determine whether symbionts are present and related to the
Endobugula clade and whether the symbionts produce bioactive metabolites to contribute to the defense of host larvae. These studies will aid in addressing cospeciation and the role of symbiosis in this genus.
In the
B. neritina/“
Candidatus E. sertula” system, “
Candidatus E. sertula” resides in
B. neritina and produces bryostatins to chemically defend host larvae (
8,
21). The work presented here provides the following lines of evidence for a similar and evolutionarily related symbiosis in
B. simplex/“
Candidatus E. glebosa”: (i) “
Candidatus E. glebosa” is similarly located in the larvae as “
Candidatus E. sertula” is in
B. neritina; (ii) “
Candidatus E. glebosa” and “
Candidatus E. sertula” form a monophyletic group; (iii) the PKS fragment isolated from
B. simplex/“
Candidatus E. glebosa” closely matches KSa from “
Candidatus E. sertula”; (iv) “
Candidatus E. glebosa” and its PKS fragment are consistently associated with
B. simplex; (v)
B. simplex extracts have bryostatin activity in the PdBU assay, similar to that of
B. neritina; and (vi) compounds with retention times, masses, and UV profiles similar to those of known bryostatins are found in
B. simplex extracts.