New Results

Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral

Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
doi: https://doi.org/10.1101/173591

Abstract

Determining the extent to which Symbiodinium communities in corals are inherited versus environmentally-acquired is fundamental to understanding coral resilience and to predicting coral responses to stressors like warming oceans that disrupt this critical endosymbiosis. We examined the fidelity with which Symbiodinium communities in the brooding coral Seriatopora hystrix are vertically transmitted and the extent to which communities are genetically regulated, by genotyping 60 larvae and their parents (9 maternal and 45 paternal colonies) using high throughput sequencing of the ITS-2 locus. Unexpectedly, Symbiodinium communities associated with brooded larvae were distinct from those within parent colonies, including the presence of types not detected in adults. Bayesian heritability (h2) analysis revealed that 33% of variability in larval Symbiodinium communities was genetically controlled. Results highlight flexibility in the establishment of larval communities and overturn the paradigm that symbiont transmission is exclusively vertical in brooding corals. Instead, we show that Symbiodinium transmission in S. hystrix involves a mixed-mode strategy, similar to many terrestrial invertebrate symbioses. Also, variation in the abundances of common Symbiodinium types among adult communities suggests that microhabitat differences influence the structure of in hospite Symbiodinium communities. Partial genetic regulation coupled with flexibility in the environmentally-acquired component of larval Symbiodinium communities implies that corals with vertical transmission, like S. hystrix, may be more resilient to environmental change than previously thought.

Introduction

Symbiosis is fundamental to life on Earth, underpinning the existence of numerous prokaryotic and eukaryotic species and shaping the physiology and health of many organisms [1–3]. Microbial symbionts also enable hosts to expand their niche breadth to survive in environments otherwise unsuited to their physiology [4]. For example, symbiosis with photosynthetic dinoflagellates of the genus Symbiodinium has allowed corals to thrive in oligotrophic tropical seas through the utilization of symbiont photosynthates. Similar nutritional facilitation has been described for sap-sucking insects that rely on microbial partners to supplement their diets [5] and legumes that rely on rhizobia to fix nitrogen [6]. Unlike these well-characterized systems, coral endosymbioses are poorly described at the Symbiodinium type level during early ontogeny.

Nutritional symbioses can drive diversification of host and symbiont lineages [7–9], with eukaryotic symbionts like Symbiodinium having gone through multiple cycles of diversification and expansion [10]. Such sources of genetic variation provide new material upon which selection may operate [11,12], facilitating coevolution between hosts and symbionts or among symbionts [3,11,13]. Understanding the fidelity (exactness of transfer of symbionts from parent to offspring) of Symbiodinium community inheritance is key to determining the degree to which endosymbiotic Symbiodinium communities have coevolved with their coral hosts and is central to coral nutrition and health. Despite this, little is known about genetic regulation underpinning this symbiosis.

Symbionts may be acquired from the environment (horizontal transmission) or passed maternally into eggs or larvae (vertical transmission), with the latter thought to be the most prevalent mode of transmission in brooding scleractinian corals [14]. Maternally-derived symbionts may involve the transmission of one or multiple symbionts (superinfections) and, at least in well-studied insect vertical symbioses, may strongly impact host reproduction, behaviour and co-evolution [12,15]. Transmission of insect symbionts may be exclusively vertical or may occur initially as vertical transfer followed later by horizontal transmission [9,15–19]. Although similar mixed-mode transmission has been hypothesized for corals [20], the absence of experimental data means that it is not yet clear if transmission is exclusively vertical in brooding corals or if mixed-mode transmission also occurs in this group. Given recent evidence of differences in the diversity of symbiont communities transmitted from parents to offspring in two broadcast spawning corals [21,22], Symbiodinium transmission dynamics may be as complex as those observed in the Arthropoda.

In general, symbiont-host specificity is theorized to be much greater when symbionts are transmitted vertically compared to horizontally [23,24]. In corals, hosts may form strict associations with only one Symbiodinium type (and vice versa) or associate with multiple partners, but in general, superinfections of multiple Symbiodinium types and subtypes of varying abundances are common [20,25–29]. Although maternal transfer of Symbiodinium and bacteria is less well-characterized in corals than in terrestrial invertebrates [20–22,30,31], the presence of superinfections raises the possibility that Symbiodinium dynamics are similar to the mixed-mode transmission dynamics characteristic of superinfections described in terrestrial invertebrates like aphids and sharpshooter cicada [9,11]. However, unlike studies of insect symbiont specificity, no studies have used high throughput sequencing to examine maternally-transmitted Symbiodinium communities in brooding corals or the diversity of low abundance Symbiodinium types in detail. Similarly, the genetic component of parental contributions to the maturation of coral-Symbiodinium symbioses remains unquantified.

It is clear that different Symbiodinium types vary in their impact on holobiont physiology because of variation in their stress tolerance and ability to produce and transfer photosynthates to the coral host under differing light, temperature and nutrient regimes [28,32–36]. Moreover, environmental stressors may bring about shifts in the dominance of different Symbiodinium types, in some cases benefiting the host under the altered conditions [37,38]. The extent of a coral’s flexibility to acquire resilient types or shuffle symbionts may be genetically regulated, for example by heritable host immune responses, similar to those that shape symbiont diversity in Drosophila [39]. Complete inheritance results in complete fidelity of symbiont transmission, and, hence, little scope for flexibility in coral-Symbiodinium symbioses. However, the extent of such potential regulation of symbiont transmission and its underlying basis are unknown for corals.

Increasingly, studies are revealing that the genetic architecture behind traits and pathologies can be complex [40]. For example, both the diversity and abundance of microbial symbionts in the human gut are complex traits under partial genetic control [41–46]. Narrow-sense heritability (h2) is the parameter typically used to describe the degree to which variability in a trait is explained by genetic factors. Assuming that the Symbiodinium community associated with a coral can be represented as a complex trait, then an h2 value of 1 would imply that variability of the community is mostly due to host genetics. Conversely, an h2 value estimated at 0 would imply no genetic basis for variability in the community, thus the community would not be under selection and could not evolve [no evolvability; 47]. Although an h2 estimate close to 1 does not necessarily guarantee absolute genetic determination as a result of gene segregation [48], a large heritability estimate of the Symbiodinium community would imply that changes in host genotypes are required for shifts in symbiont communities. Conversely, changes in the environmental availability of Symbiodinium or in environmental conditions would have limited influence on in hospite communities. Understanding the relative contributions that host genetics versus environmental conditions make to the composition of Symbiodinium communities through estimations of h2 will improve the accuracy with which the potential, direction and speed of changes in Symbiodinium communities can be predicted.

To examine Symbiodinium community transfer between adults and their offspring in a brooding coral and quantify the narrow-sense heritability (h2) of this trait, we quantified the in hospite Symbiodinium communities of individual planula larvae and their parents across a spectrum of relatedness using high throughput sequencing. Relatedness was based on a population genetic parentage analysis that assigned the likely paternal identity of each larva. In light of results on heritability and fidelity of symbiont transfer, we discuss the potential of larvae from brooding corals like S. hystrix to acclimate to novel environments.

Results

Symbiodinium communities differ between parents and brooded larvae

Symbiodinium communities differed between adults and their larvae in the brooding coral Seriatopora hystrix (ShA) (Figure 1A, B). Overall, the composition of Symbiodinium communities was similar among adult corals, but more variable among larvae. On average, adults contained 29.9±0.6 (SE) OTUs and larvae had 22±0.4 OTUs. However, the number of unique OTUs recovered was more than five times greater from larvae than from adults (93 vs. 17 OTUs, respectively; Figure 1C). Of the 17 unique adult OTUs, ten belonged to clade C (C1, C15 and other variants), three from clade A (A1 and variants), three from D (including D1 and D1a), and one was a putative C type (Figure 1B, sequences most highly similar to mixed S. hystrix/Symbiodinium libraries– see Supporting Information). Unique to larvae were 17 OTUs from clade C (likely C1 variants), four from clade E, one from each of A3, B1, and G6, and 69 that were of putative Symbiodinium identity (Figure 1B). Of the 93 larval-specific OTUs, only the abundance of C1_OTU136 (type followed by OTU designation) and two putative clade D OTUs (OTU148 and OTU149) were significantly different from zero with the Bejamini-Hochberg correction (Figure 1B). Although raw read counts were low, C1_OTU136 was present in larvae from every dam but dam 3.

Figure 1.
Figure 1.

Nonmetric multidimensional scaling (NMDS) plots, based on a Bray-Curtis distance matrix of variance-normalized OTU abundances and sequence similarity between OTUs (pairwise percent identities), illustrating differences between Symbiodinium communities associated with adult colonies and larvae of the brooding coral Seriatopora hystrix (ShA). Ellipses encircling symbols of the corresponding colour represent 95% probability regions for adults (black) and larval broods (coloured), where each brood represents all larvae sharing the same dam (colour-coded). A) Each point represents the Symbiodinium community associated with a unique coral adult or larval sample. B) Each point represents an OTU coloured by type level (see Supporting Information table S5 for full names). Outlining around each point represents the origin of the OTU, i.e., those found uniquely in adult (grey outline) or larval (broken grey outline) samples, or retrieved from both (black outline). Samples presented in (A) and OTUs presented in (B) share the same ordination space but were separated for clarity. C) Venn diagram, illustrating the number of Symbiodinium OTU’s that were unique to larvae (dark grey text) versus adults (light grey text). The number of OTUs that were significant after p-adjustments are in parentheses. Ellipses corresponding to dams 3 and 10 are not represented, as only one larva per dam was collected and sequenced.

Fifty-one OTUs were shared by adult colonies and planula larvae (43 of known Symbiodinium taxonomy, 8 putative Symbiodinium, Figure 2B), and the abundances of 28 of these OTUs differed significantly between the two groups at the adjusted p-level (Table S4, Supporting Information). Of these 28 OTUs, 23 were from clade C (including C1, C3w, C120 amongst others), three from clade D (D1, D1a), and two from clade A (A1, A3). Adult Symbiodinium communities were characterised by up to 1.3 times more D-types (D1_OTU3, D1_OTU597, D1a_OTU6), and A-types (A1_OTU10 and A3_OTU8) compared to larvae (Bejamini-Hochberg corrections, Table S4). Nine of the 23 C-types had up to 1.7 times significantly higher abundances in adults (including multiple C1 types, C120/C120a_OTU1, C1m_OTU5/105, C1v6/C22_OTU228, C15_OTU46, C31_OTU733, and C3W_OTU165) and the remaining C1 types had between 1.5 – 2.4 times significantly lower abundances in adults (Table S4).

Figure 2.
Figure 2.

A) Log2 fold change in abundances of Symbiodinium OTU’s that differed significantly between communities associated with adults versus larvae of Seriatopora hystrix (ShA). Grey-scale in the bar plot identify Symbiodinium clades. A positive change indicates the OTU is more abundant in adults. B) Boxplots showing medians, quartiles and minimum/maximum values of Symbiodinium community diversity (Leinster and Cobbold metric) in relation to individual larval relatedness. On the x-axis, 0.25 denotes half sibs, 0.5 full sibs, and 1.0 denotes larvae produced from selfing. Each larva is coloured by its respective dam. C) Network analysis of planula larvae showing OTUs present in 50% or more of larvae per brood. White diamonds correspond to maternal broods, where each brood sharing the same dam is colour-coded. Line thickness denotes relative abundance of the Symbiodinium type per brood.

Larval Symbiodinium communities vary among broods

Planula larvae that shared the same maternal parent generally clustered when Symbiodinium OTU richness, abundance, and DNA distance between OTUs were incorporated into analyses (Figure 1A, B). Thirty-one OTUs (including multiple C1 variants, D1, D1a, A1, and A3) were found in greater than 50% of larvae per brood and were generally present across all broods (Figure 2C). However, differences in the abundance of OTUs amongst larval broods were detected for symbiont types A1, A3, C1, D1, and D1a, amongst others. Briefly, larvae from dam 2 displayed higher abundances of A1 and A3. Larvae from dams 3, 7 and 10 had significantly less of C1_OTU2, whilst broods from dams 4, 6, 13, 14, and 18 had significantly different abundances of many C-types, including C120/C120a, C1, C1v1e, C1m, and C31. The abundances of D1_OTU3 and D1a_OTU6 also varied significantly among larval broods, particularly among those from dams 2, 4, and 18 vs. dam 13 (for a full description see Supporting Information and Table S4).

Heritability

Leinster and Cobbold estimates of Symbiodinium community diversity varied across the 60 larvae. Notably, variance around median estimates decreased as relatedness between individual larvae increased (Figure 2B). The posterior mean heritability of the Symbiodinium community in S. hystrix (ShA) larvae was 0.43 ± 0.21 SD, with a posterior mode of 0.33 (95% Bayesian credibility interval (BCI) 0.1 - 0.8; Figure S2, Supporting Information). Adding maternal identity as a random effect did not improve the model (Deviance Information Criterion < 2 units) but decreased the posterior mean and mode of heritability slightly (mean = 0.37 ± 0.21 SD and mode = 0.19; BCI: 0.1 - 0.8).

Patterns in adult Symbiodinium communities with colony size and spatial distribution

Of the 68 Symbiodinium OTUs found in adults, the abundance of only four C-type OTUs differed significantly among the five coral size classes. Two C-types (OTU228 and OTU105) had two times greater abundances in the 26 – 32 cm class compared to corals in each of the other four size classes (all p’s>0.05; Table S4). Similarly, C31_OTU733 was found at significantly lower abundance in corals from the 8 – 14 cm class compared to the single colony in the largest size class (p>0.05; Table S4). Colonies from the 8 – 14 cm class also had 1.7 times lower abundances of C1_OTU4 compared to corals in the 14 – 20 cm class (p>0.05; Table S4).

The distributions of three of the ten most abundant OTUs in adult corals varied significantly across the sampling area (p > 0.05; Figure 3), although not in a consistent manner with distance either along or down the sampling area. For example, although abundances of Symbiodinium C120/C120a were greatest in the lower left of the sampling area (Gradient Boosted Model (GBM): p = 0.019), consistent with a gradual increase in distance down the reef slope, this pattern was not consistent along the reef slope (GBM: p = 0.00841). The abundance of D1 was significantly higher in the top-right and lower left side of the sampling area than in other aspects (x and y interaction, GBM: p = 0.0393). D1a was least abundant in the top left and inner portion of the sampling area (GBM: p = 0.0405). Finally, although the variance normalized abundances of all three OTUs were significantly positively correlated overall (Spearman’s rank correlation rho: 0.42 – 0.77, all p < 0.004), extremely low abundances of C120/C120a at x-coordinates >15 contrast markedly with high abundances of the two D-types in the same region (Figure 3).

Figure 3.
Figure 3.

Spatial patterns in the normalised abundance of three Symbiodinium OTU’s associated with adult colonies of Seriatopora hystrix (ShA) that differed significantly in their abundances across a portion of the 16 m × 40 m sampling area at Lizard Island: A) C120/C120a, B) D1, and C) D1a. Grey scale represents changes in the normalized abundance of each OTU across sampling site coordinates. Sizes of the black circles represent size classes of coral colonies in cm (drawn to scale).

Discussion

Mixed mode transmission structures larval Symbiodinium communities in a brooding coral

The availability of a full larval pedigree for Seriatopora hystrix (ShA) [49] provided a unique opportunity to evaluate the relative contributions of heritability (i.e., the degree to which variability in a trait is explained by genetic factors) versus maternal environmental effects (the effect of larvae sharing a common maternal environment) to the composition of larval Symbiodinium communities in a brooding coral. Here we show that Symbiodinium communities associated with larvae of S. hystrix (ShA) differ from those associated with their parents, providing experimental evidence that at least a portion of the Symbiodinium community is horizontally transmitted in a brooding coral. Such paradigm-changing knowledge on symbiont transmission is important as it realigns the cnidarian literature with well-characterized models of invertebrate symbioses. Overall, Symbiodinium communities were found to be moderately heritable, with only 33% of variability in larval symbiont communities under genetic regulation. Model selection also showed that maternal environmental effects did not significantly explain variability in Symbiodinium communities found among larvae. This result, combined with the moderate heritability estimate, indicates that similarities in Symbiodinium communities among larvae of the same maternal brood were due to gene(s) inherited by these larvae.

Heritability estimates reveal important information about the evolvability of a trait, such as the capacity of brooding corals to vary their symbiont communities in response to changing environmental conditions. If levels of heritability and genetic variance are low, then responses to natural or artificial selection (evolvability) would be limited [48]. Conversely, high heritability and high genetic variance of a trait would enable greater responses to selection pressures. On the other hand, highly heritable symbiont communities with low genotypic variation could be problematic for vertically-transmitting coral populations if adult communities are thermally sensitive [50]. We found moderate heritability of Symbiodinium communities in S. hystrix (ShA). Much greater heritability of the Symbiodinium community was expected in this vertically-transmitting coral, especially in comparison with what is known of other important reproductive and fitness traits. For example, fertilization success, larval heat tolerance, protein content, settlement success, settlement substrate preferences, and juvenile growth and survivorship are all heritable traits [51–55]. Although the distribution of posteriors was skewed towards values greater than that of our heritability estimate, it is unlikely that heritability (i.e., genetic regulation) for this trait will resolve to be much greater with increased sampling effort (~0.5-0.6, Figure S2). The moderate levels of genetic regulation (i.e., heritability) found here suggest that S. hystrix (ShA) has some capacity to respond to changing environmental conditions. Thus, intervention efforts to facilitate such phenotypic change may be possible [48]. Given that assisted evolution efforts involving heat-selected Symbiodinium types show promise in horizontally-transmitting corals [56, but see 57], it may be that vertically-transmitting, brooding species with moderate fidelity like S. hystrix (ShA) could also be candidates for assisted Symbiodinium uptake.

Combined maternal and environmental uptake produces locally adapted but flexible Symbiodinium communities

Detection of 93 larval-specific OTUs in this study demonstrates that brooding corals like S. hystrix (ShA) have a mixed-mode transmission strategy, in which dominant symbionts are transmitted vertically but additional background strains are acquired from environmental sources. Although adult diversity may have been under-sampled by only sequencing one branch of each parental colony, unique larval OTUs were not detected in any of the 45 adult colonies that were genotyped. Environmental uptake of novel Symbiodinium by larvae of this species is further supported by the appreciable amount of variation in the composition of larval Symbiodinium communities that was not under genetic control, according to our heritability model. These results validate the hypothesis of potential mixed-mode transmission initially raised by Byler et al. [20]. However, although juveniles hosted multiple symbionts in their study, they did not find differences in diversity between S. pistillata adults and larvae [20]. Evidence of mixed-mode transmission in S. hystrix (ShA) contradicts previous assumptions that maternally-transmitted symbiont communities are transferred to offspring with high fidelity in corals [23–25]. Our findings are consistent with transmission patterns documented in other symbiotic systems, such as wild Drosophilia hydei populations [9], Acromyrmex ants [15,16], and paramecium [17,18], and aligns symbiotic transmission ecology in corals with terrestrial invertebrate symbioses. Additionally, the novel diversity found in S. hystrix (ShA) larvae mirrors increased diversity of Symbiodinium communities detected in eggs of Montipora capitata and M. digitata compared to adults [21,22] and of bacterial communities in larvae of the brooding coral Porites astreoides, as well as of various bacterial communities associated with larvae of sponge species with supposed vertical transmission [31,58].

Mounting evidence for mixed-mode transmission across phyla suggests that it may be evolutionarily advantageous to compromise between completely vertically- and horizontally-acquired symbiont communities, as both strategies provide distinct advantages and disadvantages [14,20]. In S. hystrix (ShA), vertical transmission of Symbiodinium that are locally adapted to the parental environment is likely to provide benefits for a species that is able to self-fertilize [49,59] and has highly localised larval dispersal (e.g., 60–62]. However, a locally adapted community might become a liability if environmental conditions change or if larval dispersal distances are long. Negative effects include deregulation or disruption of symbiont abundances, which may have harmful physiological effects on the host, like bleaching in corals [38] or wasp parasitism in insects [9,63]. Thus, a mixed-mode strategy that results in superinfections of multiple symbionts can be beneficial [e.g., parasitoid protection in aphid hosts, 9,19] and may provide more flexibility for adjusting to variable environmental conditions. Similarly, a mixed mating strategy of selfing and outcrossing in S. hystrix (ShA), combined with a functional nutritional symbiosis upon release, may facilitate both local and long-distance dispersal [49]. Our findings confirm that diversity and flexibility in Symbiodinium transmission are greater than previously thought, highlighting the potential for evolvability that may confer greater resilience than coral species with strict vertical transmission.

Additional to environmental uptake of Symbiodinium during early ontogeny, processes like competitive exclusion may contribute to differences between larval and adult communities in S. hystrix (ShA). Theory suggests that competition among symbionts may preclude transmission of an exact replica of the parental symbiont community because conditions promoting growth for some symbionts may differ between life stages [11]. The novel symbiont diversity found in S. hystrix (ShA) larvae may provide benefits similar to those observed in insect symbioses, for example to provide larvae with the flexibility to host optimal symbiont types for the changing conditions through ontogeny [20,27]. For example, Symbiodinium C1_OTU136, which was uniquely identified in larvae, may represent an adaptive advantage for this early life stage. Clade C types are taxonomically and physiologically diverse [10,64], and exhibit a range of tolerances for light and temperature, which are also reflected in their in hospite distributions across individual adult colonies and species [65]. Larval settlement and early juvenile survival are generally highest in cryptic, low-light areas that offer protection from predation [66,67]. Given that optimal settlement environments differ substantially from light environments experienced by adults, potentially by as much as 10-fold [67], it is possible that variation in Symbiodinium communities between larvae and adults observed here relates to different selective pressures associated with differing light environments [68–70]. Other potentially numerous, uncharacterized differences between larval and adult microhabitats may also contribute to differences in selective pressures between life stages. The potential ecological roles for the larval-specific OTUs recorded here are unknown. Indeed, it is possible that they represent non-symbiotic, free-living types [71] that may have attached to the exterior of the larvae following release or that may have entered brooded larvae without engaging in symbiosis. Further work is needed to determine how many of these OTUs represent physiologically important versus transient Symbiodinium.

Potential mechanisms shaping larval Symbiodinium communities

The immune system is an obvious mechanism by which the host could exert control over the symbiotic community by regulating the establishment of individual Symbiodinium types [72] or of either whole clades or functional units (i.e., clades or types with similar metabolic roles) [44]. The symbioses of Wolbachia and Spiroplasma bacteria among Drosophila and lepidopteran genera, for example, are highly specific and exclude other bacterial lineages through a dynamic and mature immune response, to the extent that specific Drosophila species host novel and specific Wolbachia and/or Spiroplasma strains [12,39]. Mechanisms of immunity that could be transmitted through inheritance of parental genes include components of both the innate and adaptive immune response, including some that have been implicated in shaping invertebrate symbiont communities, such as T-cells, Nod2, defensins, and antimicrobial peptides [as reviewed in 73,74]. These mechanisms have been documented during Symbiodinium establishment in corals [72,75,76] and observed in the Hydra/bacteria symbiosis [73,77].

Conversely, the greater variation and diversity found in larval compared to adult Symbiodinium communities may be a function of an immature immune response that is not yet able to differentiate appropriate Symbiodinium types, rather than an adaptive response. As the coral immune system matures over time [78,79], it is possible that a winnowing process eliminates symbionts that are not physiologically beneficial to the coral host [20,27]. If true, then the ubiquitous presence of Symbiodinium C1_OTU136 in larvae may be a consequence of an opportunistic Symbiodinium type taking advantage of immature host immunity. Further work is needed to identify the role that the immune response has in shaping Symbiodinium communities; in particular what (if any) immune-related genes are being transmitted from parents to offspring and whether novel symbionts are a function of an under-developed immune response.

Winnowing and microhabitat variation may shape adult Symbiodinium communities

The disparate Symbiodinium communities in larvae versus adults found here further indicate that the re-shaping of the Symbiodinium community through ontogeny is an important developmental process in corals. Ontogenetic variability in microbial communities (both Symbiodinium and bacteria) is common in both vertically- and horizontally-transmitting cnidarian species [20,21,26,27,29–31,80–84]. The low level of variation in Symbiodinium communities associated with corals ranging in diameter from 8 cm to >30 cm [3-10 years; 85] suggests that the end of the winnowing process likely occurs earlier in the development of the brooding coral S. hystrix (ShA)(i.e., before 3 years) than in broadcast-spawning corals [~3.5 years; 26,27]. Although evidence for switching of symbiont communities in adults corals exists [86], the pre-winnowing period may be the most flexible time for hosts to associate with a diversity of microbes. Therefore, identifying at what stage winnowing occurs in brooding corals will provide crucial insights into when the flexibility to associate with environmentally-acquired and potentially stress-tolerant types diminishes and specialisation of the Symbiodinium community begins.

Spatial patterns in the abundances of Symbiodinium C120, D1, and D1a in adult corals were not consistent along or down the reef slope at Lizard Island, but may reflect variable temperature and light regimes at the microhabitat level that interact with differing photo-physiologies among symbiont types [87,88]. Variation in benthic light regimes at cm-level scales down the vertical faces of individual colonies and variation in irradiance within coral tissues have been shown to drive symbiont communities in other coral species [69,70,89,90]. Thus differences at the meter-level scales found in this study could be important for structuring in hospite Symbiodinium diversity, and may be partly responsible for the variability found at the level of individual larvae and broods. These small scale differences in symbiont abundances within adults may subsequently influence variability in Symbiodinium types among larvae. However, further work is needed to understand how fine-scale environmental variables impact Symbiodinium presence and abundance at the type and OTU level in this species.

Conclusion

Based on novel heritability and paternity analyses, we show that Symbiodinium communities associated with the brooding coral S. hystrix (ShA) are only partially genetically regulated by their host and that larvae retain the flexibility to associate with novel symbionts across generations. Unexpectedly, our results reveal a mixed-mode transmission strategy for establishing Symbiodinium communities in larvae of a brooding coral, based on demonstrations that novel and unique Symbiodinium types are found in brooded larvae but not in adults. Importantly, this information aligns symbiosis transmission ecology in corals with well-known terrestrial invertebrate symbioses that typically exhibit mixed-mode transmission strategies. Advances in the understanding of heritable genetic mechanisms quantified here provide important insights into how Symbiodinium communities may be targeted for intervention strategies to increase reef resilience.

Materials and Methods

Study species and sampling design

The common, hermaphroditic coral Seriatopora hystrix broods sexually-produced larvae following internal fertilization of eggs by sperm from surrounding colonies [49,91]. DNA extracts of planula larvae for the present study were selected from samples that were collected in an earlier study to assess sperm dispersal distances and larval parentage of a cryptic species within the S. hystrix species complex, specified as S. hystrix (ShA) [49,92]. In Warner et al.’s study, colonies were tagged and sampled for molecular analyses within a 16 m x 16 m sampling area, with additional colonies sampled from two adjacent transects (totalling 16 m x 40 m area) in the Lizard Island lagoon [S14°41.248, E145°26.606; 49,92]. Microsatellite genotypes and paternity assigned to individual larvae in this earlier study [49] enabled us to examine the effect of both maternal and paternal identity on larval Symbiodinium communities across a full pedigree of larval relatedness. Hence, our study included full-sib and half-sib larvae, and four individuals produced by selfing (further details in Supporting information and Table S1).

Symbiodinium community genotyping

Symbiodinium communities of adults and larvae were quantified with amplicon sequencing of the ITS-2 locus using the same DNA extractions that had been used to assign microsatellite genotypes and paternity in Warner et al. (2016). Nine maternal and 45 assigned paternal colonies (which included the nine maternal colonies), plus all larvae whose paternity was designated with a confidence level of Very High, High, or Medium by Warner et al. (2016) (n=60 larvae) were sequenced with the primers ITS2alg-F and ITS2alg-R [93] using paired-end Illumina Miseq technology. Library preparation and sequencing were performed at the University of Texas at Austin’s Genomics Sequencing and Analysis Facility (USA) using their standard protocols, including Bioanalyzer (Agilent)-based DNA standardization and pooled triplicate PCR before library preparation.

Raw reads (total = 6,875,177) were analysed using the USEARCH and UPARSE pipelines [v.7; 94], as outlined in Quigley et al. [95; further details in Supporting Information]. Because there is currently no single copy marker for Symbiodinium genotyping [96], the ITS-2 marker was selected for the broadest comparisons to the vast literature that has used this marker to describe Symbiodinium diversity, including some using next generation sequencing (e.g., [22,95,97–100]. Additional steps were taken to assess the presence and impact of intragenomic variants (further explained below). Briefly, reads were filtered, clustered into OTUs at 97% similarity, annotated with NCBI nt database and Symbiodinium-specific searches (further details in Supporting Information Table S2). Using these methods, the majority of the OTUs were re-assigned to a clade/type level, leaving only 0.03% of cleaned reads (1459 reads, 78 OTUs) that could not be classified, and which may represent new Symbiodinium types (Table S3, Figure S1, Supporting Information).

To account for variable read-depth across all samples, sample reads were normalized using ‘DESeq2’ and ‘Phyloseq’ implemented in R [101–103]. Nonmetric multidimensional scaling (NMDS) was performed and plotted using the normalized counts matrix using ‘Phyloseq’, ‘vegan’, and ‘ggplot’ [104,105]. Genetic distances between OTUs were calculated in ‘Ape’ [106]. Statistical testing of variation in OTU abundance was performed on raw reads in ‘DESeq2’, which incorporates variance normalization of OTU abundance, and interpreted using the Bejamini-Hochberg correction for multiple-inferences of p-adjusted alpha at 0.05. ‘DESeq2’ outputs are expressed in multiplicative (log2 fold) terms between or among treatments [107]. Network analysis on planula larvae was performed using the ‘igraph’ package [108] and custom scripts from [109].

Estimating the diversity and heritability of Symbiodinium communities

To describe the Symbiodinium community in coral samples, we used a diversity measure (qDZ ij(p)) that incorporates OTU richness, evenness and sequence similarity [110]. Sequence similarity was calculated using pairwise percent similarities between OTU sequences using the ‘Ape’ package with a “raw” model of molecular evolution. Heritability of Symbiodinium diversity associated with the 60 larvae was calculated using the package ‘MCMCglmm’ [111] utilizing the diversity metrics described above, where the coefficient of relatedness between individuals was set as a random effect. Models were run with 1.5 × 106 iterations, a thinning of 50, and burn-in of 10% of the total iterations. A non-informative flat prior specification was used following an inverse gamma distribution [112]. Assumptions of chain mixing, normality of posterior distributions, and autocorrelation were met. The posterior heritability was calculated by dividing the model variance attributed to relatedness by the sum of additive and residual variance. Deviance Information Criterion was used to test if adding a maternal random effect had a statistically significant effect on heritability estimates.

Multiple ITS-2 copies and intragenomic variation

Intragenomic variation within and between Symbiodinium types makes classifying type-level diversity in Symbiodinium based on sequence data difficult [99,113–115]. However, comparisons between single-cell and next-generation sequencing suggests that clustering across samples at 97% similarity sufficiently collapses intragenomic variants to the type level [99], as has been used in this study. Furthermore, a recent study suggests that clustering across samples at 97% identity underestimates diversity instead of overestimating it [109]. Intragenomic variation and generation of false-positives is therefore substantially minimized by using across-sample clustering at 97% similarity, as we have employed. Single cell sequencing is currently financially and logistically outside the scope of studies that examine communities of hundreds of different Symbiodinium types (as with coral juveniles), with a majority of these types not yet existing in culture. It is questionable if microsatellite flanking regions provide superior taxonomic resolution [116], and as no known single-copy marker exists, using other markers in tandem with ITS-2 will only result in data representing multiple, multi-copy markers. We addressed intragenomic variation by clustering across samples at 97% similarity and also provided two additional analyses to test for their presence and potential impact on the heritability estimate; and both confirm the robust nature of our conclusions in regards to this issue. Overall, we undertook a three-step approach, as outlined in [95], to assess if multiple copies and intragenomic variation of ITS-2 genes could potentially bias abundance and heritability estimates across Symbiodinium types after clustering at 97% identity. Briefly, OTUs were first divided by clade and inspected for co-occurrence across samples using the tree function in ‘Phyloseq’ and grouped into subsets of co-occurring OTUs. Secondly, OTUs that increased proportionally and with high percent pairwise similarity were inspected. Finally, pairwise percent identities were calculated for these latter subsets of OTUs using the package ‘Ape’ [106], and correlations of variance-normalized abundances were calculated for pairs that had greater than 85% similarity with the function ggpairs in the package ‘GGally’ [104]. The diversity metric was calculated taking into account possible intragenomic variation by pooling the raw abundances of potential intragenomic variants (OTUs: 8/10, 12/22/24, 28/223, 3/6, 588/848), and heritability was calculated using the parameters described above. As we found little evidence of intragenomic variation amongst OTUs, these results and their impact on heritability estimates are only discussed in the Supporting Information.

Colony size and spatial distribution of adult S. hystrix (ShA) colonies

To determine if Symbiodinium communities varied with colony size (as a proxy for colony age), adult colonies were divided into five size classes based on their mean diameter [49]: < 8 cm (n = 1 colony), 8 – < 14 cm (n = 19), 14 – < 20 cm (n = 13), 20 – < 26 cm (n = 11), and 26 – 32 cm (n = 1). Differential abundance testing of Symbiodinium OTUs was among size classes was performed as for larval communities.

Sitepainter [117] and Inkscape [118] were used to test for spatial patterns in the distribution of Symbiodinium OTUs associated with the 45 adult colonies of S. hystrix (ShA) that were genotyped across the 16 m x 40 m sampling area. Gradient Boosted Models and linear models were run in the package ‘gbm’ [119] to examine spatial distributions of the ten most abundant OTUs. Linear models were checked for assumptions of linearity, normality, and homogeneity of variance. Square-root transformations were used to correct for issues of normality or heterogeneity. Latitude and longitude coordinates were centered before fitting models. The package ‘Spatstat’ [120] was used to visualize spatial variability in abundances of the three most significantly heterogeneous OTUs across the sampling area (OTUs: 1, 3, and 6). Spearman’s Rho rank correlation coefficients were calculated to test for competitive exclusion amongst the three OTUs that varied significantly across the sampling area. Pairwise p-values were generated for all OTU comparisons using the base ‘stats’ package in R.

Data Accessibility

DNA sequences: All sequencing data will be made available through NCBI SRA.

Author contributions

K.M.Q. and B.L.W. conceived of the experiment. K.M.Q. and P.A.W. designed the sampling scheme and performed the experiment, collected and analysed the data. L.K.B. provided reagents and materials. K.M.Q. wrote and B.L.W., L.K.B., and P.A.W. edited and critically reviewed the manuscript. All authors read and approved the final version.

Acknowledgments

This study was carried out with permission and in accordance with the recommendations from the Great Barrier Reef Marine Park Authority.

References

  1. 1.↵
    Lewis ZT, Totten SM, Smilowitz JT, Popovic M, Parker E, Lemay DG, et al. Maternal fucosyltransferase 2 status affects the gut bifidobacterial communities of breastfed infants. Microbiome. BioMed Central; 2015;3: 1.
    OpenUrl
  2. 2.
    Gilbert SF, Sapp J, Tauber AI. A symbiotic view of life: we have never been individuals. Q Rev Biol. JSTOR; 2012;87: 325–341.
    OpenUrlCrossRefPubMedWeb of Science
  3. 3.↵
    Moya A, Peretó, J, Gil R, Latorre A. Learning how to live together: genomic insights into prokaryote–animal symbioses. Nat Rev Genet. Nature Publishing Group; 2008;9: 218–229.
    OpenUrlCrossRefPubMedWeb of Science
  4. 4.↵
    Goffredi SK, Johnson SB, Vrijenhoek RC. Genetic diversity and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Appl Environ Microbiol. Am Soc Microbiol; 2007;73: 2314–2323.
    OpenUrlAbstract/FREE Full Text
  5. 5.↵
    Baumann P. Biology of bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol. Annual Reviews; 2005;59: 155–189.
    OpenUrlCrossRefPubMedWeb of Science
  6. 6.↵
    Oldroyd GED, Murray JD, Poole PS, Downie JA. The rules of engagement in the legume-rhizobial symbiosis. Annu Rev Genet. Annual Reviews; 2011;45: 119–144.
    OpenUrlCrossRefPubMedWeb of Science
  7. 7.↵
    Brucker RM, Bordenstein SR. Speciation by symbiosis. Trends Ecol Evol. Elsevier; 2012;27: 443–451.
    OpenUrlCrossRefPubMedWeb of Science
  8. 8.
    Douglas AE. Mycetocyte symbiosis in insects. Biol Rev. Wiley Online Library; 1989;64: 409–434.
    OpenUrlCrossRefPubMedWeb of Science
  9. 9.↵
    Oliver KM, Smith AH, Russell JA. Defensive symbiosis in the real world–advancing ecological studies of heritable, protective bacteria in aphids and beyond. Funct Ecol. Wiley Online Library; 2014;28: 341–355.
    OpenUrl
  10. 10.↵
    Thornhill DJ, Lewis AM, Wham DC, LaJeunesse TC. Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts. Evolution (NY). Wiley Online Library; 2014;68: 352–367.
    OpenUrl
  11. 11.↵
    Moran NA, McCutcheon JP, Nakabachi A. Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet. Annual Reviews; 2008;42: 165–190.
    OpenUrlCrossRefPubMedWeb of Science
  12. 12.↵
    Russell JA, Funaro CF, Giraldo YM, Goldman-Huertas B, Suh D, Kronauer DJC, et al. A veritable menagerie of heritable bacteria from ants, butterflies, and beyond: broad molecular surveys and a systematic review. PLoS One. Public Library of Science; 2012;7: e51027.
    OpenUrlCrossRefPubMed
  13. 13.↵
    Moran NA, Dunbar HE. Sexual acquisition of beneficial symbionts in aphids. Proc Natl Acad Sci. National Acad Sciences; 2006;103: 12803–12806.
    OpenUrlAbstract/FREE Full Text
  14. 14.↵
    Baird AH, Guest JR, Willis BL. Systematic and biogeographical patterns in the reproductive biology of scleractinian corals. Annu Rev Ecol Evol Syst. 2009;40: 551–571.
    OpenUrlCrossRefWeb of Science
  15. 15.↵
    Andersen SB, Hansen LH, Sapountzis P, Sørensen SJ, Boomsma JJ. Specificity and stability of the Acromyrmex–Pseudonocardia symbiosis. Mol Ecol. 2013;22: 4307–4321.
    OpenUrlCrossRefWeb of Science
  16. 16.↵
    Scheuring I, Yu DW. How to assemble a beneficial microbiome in three easy steps. Ecol Lett. Wiley Online Library; 2012;15: 1300–1307.
    OpenUrlCrossRefPubMed
  17. 17.↵
    Fujishima M, Fujita M. Infection and maintenance of Holospora obtusa, a macronucleus-specific bacterium of the ciliate Paramecium caudatum. J Cell Sci. 1985;76: 179–187.
    OpenUrlAbstract/FREE Full Text
  18. 18.↵
    Kaltz O, Koella JC, Poulin R. Host growth conditions regulate the plasticity of horizontal and vertical transmission in Holospora undulata, a bacterial parasite of the protozoan Paramecium caudatum. Evolution (NY). BioOne; 2003;57: 1535–1542.
    OpenUrl
  19. 19.↵
    Sandström JP, Russell JA, White JP, Moran NA. Independent origins and horizontal transfer of bacterial symbionts of aphids. Mol Ecol. Wiley Online Library; 2001;10: 217–228.
    OpenUrlCrossRefPubMedWeb of Science
  20. 20.↵
    Byler KA, Carmi-Veal M, Fine M, Goulet TL. Multiple symbiont acquisition strategies as an adaptive mechanism in the coral Stylophora pistillata. PLoS One. Public Library of Science; 2013;8: e59596.
    OpenUrlCrossRefPubMed
  21. 21.↵
    Padilla-Gamiño JL, Pochon X, Bird C, Concepcion GT, Gates RD. From parent to gamete: vertical transmission of Symbiodinium (Dinophyceae) ITS2 sequence assemblages in the reef building coral Montipora capitata. PLoS One. 2012;7: e38440.
    OpenUrlPubMed
  22. 22.↵
    Quigley K, Willis B, Bay L. Heritability of the Symbiodinium community in vertically-and horizontally-transmitting broadcast spawning corals. bioRxiv. Cold Spring Harbor Labs Journals; 2017; 100453.
  23. 23.↵
    Baker AC. Flexibility and specificity in coral-algal symbiosis: Diversity, ecology, and biogeography of Symbiodinium. Annu Rev Ecol Evol Syst. 2003;34: 661–689. doi:10.1146/annurev.ecolsys.34.011802.132417
    OpenUrlCrossRefWeb of Science
  24. 24.↵
    Douglas AE. Host benefit and the evolution of specialization in symbiosis Heredity (Edinb). 1998;81: 599–603.
    OpenUrlCrossRef
  25. 25.↵
    Fabina NS, Putnam HM, Franklin EC, Stat M, Gates RD. Transmission mode predicts specificity and interaction patterns in coral-Symbiodinium networks. PLoS One. 2012;7: e44970.
    OpenUrlCrossRefPubMed
  26. 26.↵
    Abrego D, van Oppen MJH, Willis BL. Highly infectious symbiont dominates initial uptake in coral juveniles. Mol Ecol. 2009;18: 3518–3531. doi:10.1111/j.1365-294X.2009.04275.x
    OpenUrlCrossRefPubMed
  27. 27.↵
    Abrego D, van Oppen MJH, Willis BL. Onset of algal endosymbiont specificity varies among closely related species of Acropora corals during early ontogeny. Mol Ecol. Wiley Online Library; 2009;18: 3532–3543.
    OpenUrlCrossRefPubMedWeb of Science
  28. 28.↵
    Little AF, van Oppen MJH, Willis BL. Flexibility in algal endosymbioses shapes growth in reef corals. Science (80-). 2004;304: 1492–1494. doi:10.1126/science.1095733
    OpenUrlAbstract/FREE Full Text
  29. 29.↵
    Poland DM, Coffroth MA. Trans-generational specificity within a cnidarian–algal symbiosis. Coral Reefs. 2017; 1–11. doi:10.1007/s00338-016-1514-0
    OpenUrlCrossRef
  30. 30.↵
    Apprill A, Marlow HQ, Martindale MQ, Rappé MS. The onset of microbial associations in the coral Pocillopora meandrina. ISME J. Nature Publishing Group; 2009;3: 685–699.
    OpenUrlCrossRefPubMedWeb of Science
  31. 31.↵
    Sharp KH, Distel D, Paul VJ. Diversity and dynamics of bacterial communities in early life stages of the Caribbean coral Porites astreoides. ISME J. Nature Publishing Group; 2012;6: 790–801.
    OpenUrlCrossRefPubMedWeb of Science
  32. 32.↵
    Reynolds JM, Bruns BU, Fitt WK, Schmidt GW. Enhanced photoprotection pathways in symbiotic dinoflagellates of shallow-water corals and other cnidarians. Proc Natl Acad Sci U S A. 2008;105: 13674–13678. doi:10.1073/pnas.0805187105
    OpenUrlAbstract/FREE Full Text
  33. 33.
    Cantin N, van Oppen M, Willis B, Mieog J, Negri A. Juvenile corals can acquire more carbon from high-performance algal symbionts. Coral Reefs. Springer Berlin / Heidelberg; 2009;28: 405–414. doi:10.1007/s00338-009-0478-8
    OpenUrlCrossRefWeb of Science
  34. 34.
    Berkelmans R, van Oppen MJH. The role of zooxanthellae in the thermal tolerance of corals: a “nugget of hope” for coral reefs in an era of climate change. Proc R Soc B Biol Sci. 2006;273: 2305–2312. doi:10.1098/rspb.2006.3567
    OpenUrlCrossRefPubMedWeb of Science
  35. 35.
    Hume BCC, D’Angelo C, Smith EG, Stevens JR, Burt J, Wiedenmann J. Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world’s hottest sea, the Persian/Arabian Gulf. Sci Rep. Nature Publishing Group; 2015;5: 1–8.
    OpenUrlCrossRefPubMed
  36. 36.↵
    LaJeunesse TC, Lee SY, Gil-Agudelo DL, Knowlton N, Jeong HJ. Symbiodinium necroappetens sp. nov.(Dinophyceae): an opportunist “zooxanthella”found in bleached and diseased tissues of Caribbean reef corals. Eur J Phycol. Taylor & Francis; 2015;50: 223–238.
    OpenUrlCrossRef
  37. 37.↵
    Jones AM, Berkelmans R, van Oppen MJH, Mieog JC, Sinclair W. A community change in the algal endosymbionts of a scleractinian coral following a natural bleaching event: field evidence of acclimatization. Proc R Soc B Biol Sci. 2008;275: 1359–1365. doi:10.1098/rspb.2008.0069
    OpenUrlCrossRefPubMedWeb of Science
  38. 38.↵
    Cunning R, Silverstein RN, Baker AC. Investigating the causes and consequences of symbiont shuffling in a multi-partner reef coral symbiosis under environmental change. Proc R Soc B. 2015;282: 20141725.
    OpenUrlCrossRefPubMed
  39. 39.↵
    Mateos M, Castrezana SJ, Nankivell BJ, Estes AM, Markow TA, Moran NA. Heritable endosymbionts of Drosophila. Genetics. Genetics Soc America; 2006;174: 363–376.
    OpenUrlAbstract/FREE Full Text
  40. 40.↵
    Cho J. The heritable immune system. Nat Biotechnol. Nature Publishing Group; 2015;33: 608–609.
    OpenUrl
  41. 41.↵
    Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, et al. Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. Proc Natl Acad Sci. 2010;107: 18933–18938.
    OpenUrlAbstract/FREE Full Text
  42. 42.
    Campbell JH, Foster CM, Vishnivetskaya T, Campbell AG, Yang ZK, Wymore A, et al. Host genetic and environmental effects on mouse intestinal microbiota. ISME J. Nature Publishing Group; 2012;6: 2033–2044.
    OpenUrlCrossRefPubMedWeb of Science
  43. 43.
    Turnbaugh PJ, Quince C, Faith JJ, McHardy AC, Yatsunenko T, Niazi F, et al. Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci. National Acad Sciences; 2010;107: 7503–7508.
    OpenUrlAbstract/FREE Full Text
  44. 44.↵
    Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell. Elsevier; 2006;124: 837–848.
    OpenUrlCrossRefPubMedWeb of Science
  45. 45.
    Zoetendal EG, Akkermans ADL, Akkermans-van Vliet WM, de Visser JAGM, de Vos WM. The host genotype affects the bacterial community in the human gastronintestinal tract. Microb Ecol Health Dis. Taylor & Francis; 2001;13: 129–134.
    OpenUrlCrossRef
  46. 46.↵
    Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Sci Adv. American Association for the Advancement of Science; 2015;1: e1400216.
    OpenUrlFREE Full Text
  47. 47.↵
    Lynch M, Walsh B. Genetics and analysis of quantitative traits. 1998;
  48. 48.↵
    Visscher PM, Hill WG, Wray NR. Heritability in the genomics era— concepts and misconceptions. Nat Rev Genet. 2008;9: 255–266.
    OpenUrlCrossRefPubMedWeb of Science
  49. 49.↵
    Warner PA, Willis BL, van Oppen MJH. Sperm dispersal distances estimated by parentage analysis in a brooding scleractinian coral. Mol Ecol. 2016;25: 1398–1415.
    OpenUrl
  50. 50.↵
    Matz M V, Treml EA, Aglyamova G V, van Oppen MJH, Bay LK. Adaptive pathways of coral populations on the Great Barrier Reef. bioRxiv. Cold Spring Harbor Labs Journals; 2017; 114173.
  51. 51.↵
    Baums IB, Devlin-Durante MK, Polato NR, Xu D, Giri S, Altman NS, et al. Genotypic variation influences reproductive success and thermal stress tolerance in the reef building coral, Acropora palmata. Coral Reefs. Springer; 2013;32: 703–717.
    OpenUrlCrossRefWeb of Science
  52. 52.
    Dixon GB, Davies SW, Aglyamova G V, Meyer E, Bay LK, Matz M V. Genomic determinants of coral heat tolerance across latitudes. Science (80-). 2015;348: 1460–1462. Available: http://science.sciencemag.org/content/348/6242/1460.abstract
    OpenUrlAbstract/FREE Full Text
  53. 53.
    Meyer E, Davies S, Wang S, Willis BL, Abrego D, Juenger TE, et al. Genetic variation in responses to a settlement cue and elevated temperature in the reef-building coral Acropora millepora. . Mar Ecol Prog Ser. 2009;392: 81–92.
    OpenUrlCrossRefWeb of Science
  54. 54.
    Kenkel CD, Traylor MR, Wiedenmann J, Salih A, Matz M V. Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress. Proc R Soc B Biol Sci. 2011; doi:10.1098/rspb.2010.2344
    OpenUrlCrossRefPubMed
  55. 55.↵
    Kenkel CD, Setta SP, Matz M V. Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides. Heredity (Edinb). The Genetics Society; 2015;115: 509–516. Available: http://dx.doi.org/10.1038/hdy.2015.52
    OpenUrl
  56. 56.↵
    Levin RA, Beltran VH, Hill R, Kjelleberg S, McDougald D, Steinberg PD, et al. Sex, scavengers, and chaperones: transcriptome secrets of divergent Symbiodinium thermal tolerances. Mol Biol Evol. SMBE; 2016; msw119.
  57. 57.↵
    Chakravarti LJ, Beltran VH, Oppen MJH. Rapid thermal adaptation in photosymbionts of reef-building corals. Glob Chang Biol. 2017;
  58. 58.↵
    Schmitt S, Angermeier H, Schiller R, Lindquist N, Hentschel U. Molecular microbial diversity survey of sponge reproductive stages and mechanistic insights into vertical transmission of microbial symbionts. Appl Environ Microbiol. Am Soc Microbiol; 2008;74: 7694–7708.
    OpenUrlAbstract/FREE Full Text
  59. 59.↵
    Sherman CDH. Mating system variation in the hermaphroditic brooding coral, Seriatopora hystrix. Heredity (Edinb). Nature Publishing Group; 2008;100: 296–303.
    OpenUrl
  60. 60.
    Underwood JN, Smith LD, Van Oppen MJH, Gilmour JP. Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol Ecol. Wiley Online Library; 2007;16: 771–784.
    OpenUrlPubMedWeb of Science
  61. 61.
    van Oppen MJH, Lutz A, De’ath G, Peplow L, Kininmonth S. Genetic traces of recent long-distance dispersal in a predominantly self-recruiting coral. PLoS One. Public Library of Science; 2008;3: e3401.
    OpenUrlCrossRefPubMed
  62. 62.
    Noreen AME, Harrison PL, van Oppen MJH. Genetic diversity and connectivity in a brooding reef coral at the limit of its distribution. Proc R Soc London B Biol Sci. The Royal Society; 2009;276: 3927–3935.
    OpenUrlCrossRefPubMed
  63. 63.↵
    Xie J, Vilchez I, Mateos M. Spiroplasma bacteria enhance survival of Drosophila hydei attacked by the parasitic wasp Leptopilina heterotoma. PLoS One. Public Library of Science; 2010;5: e12149.
    OpenUrlCrossRefPubMed
  64. 64.↵
    LaJeunesse TC. “Species” radiations of symbiotic dinoflagellates in the atlantic and Indo-Pacific since the Miocene-Pliocene Transition. Mol Biol Evol. 2005;22: 570–581. doi:10.1093/molbev/msi042
    OpenUrlCrossRefPubMedWeb of Science
  65. 65.↵
    Sampayo EM, Ridgway T, Bongaerts P, Hoegh-Guldberg O. Bleaching susceptibility and mortality of corals are determined by fine-scale differences in symbiont type. Proc Natl Acad Sci. 2008;105: 10444–10449. doi:10.1073/pnas.0708049105
    OpenUrlAbstract/FREE Full Text
  66. 66.↵
    Maida M, Coll JC, Sammarco PW. Shedding new light on scleractinian coral recruitment. J Exp Mar Bio Ecol. Elsevier; 1994;180: 189–202.
    OpenUrl
  67. 67.↵
    Suzuki G, Yamashita H, Kai S, Hayashibara T, Suzuki K, Iehisa Y, et al. Early uptake of specific symbionts enhances the post-settlement survival of Acropora corals. Mar Ecol Prog Ser. Inter-Research; 2013;494: 149–158.
    OpenUrlCrossRefWeb of Science
  68. 68.↵
    Gómez-Cabrera M del C, Ortiz JC, Loh WKW, Ward S, Hoegh-Guldberg O. Acquisition of symbiotic dinoflagellates (Symbiodinium) by juveniles of the coral Acropora longicyathus. Coral Reefs. Springer; 2008;27: 219–226.
    OpenUrlCrossRefWeb of Science
  69. 69.↵
    Kemp DW, Fitt WK, Schmidt GW. A microsampling method for genotyping coral symbionts. Coral Reefs. 2008;27: 289–293. doi:10.1007/s00338-007-0333-8
    OpenUrlCrossRef
  70. 70.↵
    Rowan R, Knowlton N, Baker A, Jara J. Landscape ecology of algal symbionts creates variation in episodes of coral bleaching. Nature. 1997;388: 265–269.
    OpenUrlCrossRefGeoRefPubMedWeb of Science
  71. 71.↵
    Lee MJ, Jeong HJ, Jang SH, Lee SY, Kang NS, Lee KH, et al. Most low-abundance “background” Symbiodinium spp. are transitory and have minimal functional significance for symbiotic corals. Microb Ecol. 2016; 1–13. doi:10.1007/s00248-015-0724-2
    OpenUrlCrossRef
  72. 72.↵
    Bay LK, Cumbo VR, Abrego D, Kool JT, Ainsworth TD, Willis BL. Infection dynamics vary between Symbiodinium types and cell surface treatments during establishment of endosymbiosis with coral larvae. Diversity. 2011;3: 356–374. Available: http://www.mdpi.com/1424-2818/3/3/356
    OpenUrlCrossRef
  73. 73.↵
    Franzenburg S, Walter J, Künzel S, Wang J, Baines JF, Bosch TCG, et al. Distinct antimicrobial peptide expression determines host species-specific bacterial associations. Proc Natl Acad Sci. National Acad Sciences; 2013;110: E3730–E3738.
    OpenUrlAbstract/FREE Full Text
  74. 74.↵
    Raina J-B, Tapiolas D, Motti CA, Foret S, Seemann T, Tebben J, et al. Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ. PeerJ Inc.; 2016;4: e2275.
    OpenUrlCrossRef
  75. 75.↵
    Wood-Charlson EM, Hollingsworth LL, Krupp DA, Weis VM. Lectin/glycan interactions play a role in recognition in a coral/dinoflagellate symbiosis. Cell Microbiol. 2006;8: 1985–1993.
    OpenUrlCrossRefPubMedWeb of Science
  76. 76.↵
    Davy SK, Allemand D, Weis VM. Cell biology of cnidarian-dinoflagellate symbiosis. Microbiol Mol Biol Rev. 2012;76: 229–261. doi:10.1128/mmbr.05014-11
    OpenUrlAbstract/FREE Full Text
  77. 77.↵
    Fraune S, Augustin R, Anton-Erxleben F, Wittlieb J, Gelhaus C, Klimovich VB, et al. In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides. Proc Natl Acad Sci. National Acad Sciences; 2010;107: 18067–18072.
    OpenUrlAbstract/FREE Full Text
  78. 78.↵
    Frank U, Oren U, Loya Y, Rinkevich B. Alloimmune maturation in the coral Stylophora pistillata is achieved through three distinctive stages, 4 months post–metamorphosis. Proc R Soc London B Biol Sci. The Royal Society; 1997;264: 99–104.
    OpenUrlCrossRefWeb of Science
  79. 79.↵
    Puill-Stephan E, Willis BL, Abrego D, Raina J-B, van Oppen MJH. Allorecognition maturation in the broadcast-spawning coral Acropora millepora. Coral Reefs. Springer; 2012;31: 1019–1028.
    OpenUrl
  80. 80.↵
    Coffroth MA, Santos S, Goulet T. Early ontogenetic expression of specificity in a cnidarian-algal symbiosis. Mar Ecol Prog Ser. 2001;222: 85–96.
    OpenUrlCrossRefWeb of Science
  81. 81.
    Poland DM, Mansfield JM, Hannes AR, Lewis CLF, Shearer TL, Connelly SJ, et al. Variation in Symbiodinium communities in juvenile Briareum asbestinum (Cnidaria: Octocorallia) over temporal and spatial scales. Mar Ecol Prog Ser. 2013;476: 23–37.
    OpenUrl
  82. 82.
    Littman RA, Willis BL, Bourne DG. Bacterial communities of juvenile corals infected with different Symbiodinium (dinoflagellate) clades. Mar Ecol Prog Ser. Inter-Research; 2009;389: 45–59.
    OpenUrlCrossRefWeb of Science
  83. 83.
    Lema KA, Bourne DG, Willis BL. Onset and establishment of diazotrophs and other bacterial associates in the early life history stages of the coral Acropora millepora. Mol Ecol. Wiley Online Library; 2014;23: 4682–4695.
    OpenUrlCrossRef
  84. 84.↵
    Nyholm S V, McFall-Ngai M. The winnowing: establishing the squid–Vibrio symbiosis. Nat Rev Microbiol. Nature Publishing Group; 2004;2: 632–642.
    OpenUrlCrossRefPubMedWeb of Science
  85. 85.↵
    Babcock RC. Comparative demography of three species of scleractinian corals using age and size dependent classifications. Ecol Monogr. Wiley Online Library; 1991;61: 225–244.
    OpenUrlCrossRefWeb of Science
  86. 86.↵
    Boulotte NM, Dalton SJ, Carroll AG, Harrison PL, Putnam HM, Peplow LM, et al. Exploring the Symbiodinium rare biosphere provides evidence for symbiont switching in reef-building corals. ISME J. Nature Publishing Group; 2016;
  87. 87.↵
    LaJeunesse TC, Smith RT, Finney J, Oxenford H. Outbreak and persistence of opportunistic symbiotic dinoflagellates during the 2005 Caribbean mass coral “bleaching” event. Proc R Soc B Biol Sci. 2009;276: 4139–4148. doi:10.1098/rspb.2009.1405
    OpenUrlCrossRefPubMed
  88. 88.↵
    Baker AC, Starger CJ, McClanahan TR, Glynn PW. Coral reefs: Corals’ adaptive response to climate change. Nature. 2004;430: 741. doi:http://www.nature.com/nature/journal/v430/n7001/suppinfo/4307_41a_S1.html
    OpenUrlCrossRefPubMedWeb of Science
  89. 89.↵
    Wangpraseurt D, Larkum AWD, Ralph PJ, Kühl M. Light gradients and optical microniches in coral tissues. Frontiers in Microbiology. 2012. pp. 1–9. Available: http://www.frontiersin.org/Journal/Abstract.aspx?s=53&name=aquatic_microbiology&ART_DOI=10.3389/fmicb.2012.00316
  90. 90.↵
    Wangpraseurt D, Polerecky L, Larkum A, Ralph P, Nielsen D, Pernice M, et al. The in-situ light microenvironment of corals. Limnol Oceanogr. 2014;59: 917–926. doi:10.4319/lo.2014.59.3.0917
    OpenUrlCrossRef
  91. 91.↵
    Ayre DJ, Resing JM. Sexual and asexual production of planulae in reef corals. Mar Biol. Springer; 1986;90: 187–190.
    OpenUrlCrossRef
  92. 92.↵
    Warner PA, Oppen MJH, Willis BL. Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity. Mol Ecol. 2015;24: 2993–3008.
    OpenUrlCrossRef
  93. 93.↵
    Pochon X, Pawlowski J, Zaninetti L, Rowan R. High genetic diversity and relative specificity among Symbiodinium-like endosymbiotic dinoflagellates in soritid foraminiferans. Mar Biol. 2001;139: 1069–1078. Available: <Go to ISI>://WOS:000173168700006
    OpenUrlCrossRefWeb of Science
  94. 94.↵
    Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods. Nature Publishing Group; 2013;10: 996–998.
    OpenUrlCrossRefPubMedWeb of Science
  95. 95.↵
    Quigley KM, Willis BL, Bay LK. Maternal effects and Symbiodinium community composition drive differential patterns in juvenile survival in the coral Acropora tenuis. R Soc Open Sci. 2016;3: 1–17. Available: http://rsos.royalsocietypublishing.org/content/3/10/160471.abstract
    OpenUrl
  96. 96.↵
    Pochon X, Putnam H, Burki F, Gates R. Identifying and characterizing alternative molecular markers for the symbiotic and free-living dinoflagellate genus Symbiodinium. PLoS One. Public Library of Science; 2012;7: e29816. doi:10.1371/journal.pone.0029816
    OpenUrlCrossRefPubMed
  97. 97.↵
    Thomas L, Kendrick GA, Kennington WJ, Richards ZT, Stat M. Exploring Symbiodinium diversity and host specificity in Acropora corals from geographical extremes of Western Australia with 454 amplicon pyrosequencing. Mol Ecol. Wiley Online Library; 2014;23: 3113–3126.
    OpenUrl
  98. 98.
    Green EA, Davies SW, Matz M V, Medina M. Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ. PeerJ Inc.; 2014;2: e386.
    OpenUrlCrossRef
  99. 99.↵
    Arif C, Daniels C, Bayer T, Banguera Hinestroza E, Barbrook A, Howe CJ, et al. Assessing Symbiodinium diversity in scleractinian corals via Next Generation Sequencing based genotyping of the ITS2 rDNA region. Mol Ecol. Wiley Online Library; 2014;23: 4418–4433.
    OpenUrlCrossRef
  100. 100.↵
    Ziegler M, Arif C, Burt JA, Dobretsov S, Roder C, LaJeunesse TC, et al. Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula. J Biogeogr. Wiley Online Library; 2017;
  101. 101.↵
    Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. Springer; 2014;15: 1–21.
    OpenUrlCrossRefPubMed
  102. 102.
    McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One. Public Library of Science; 2013;8: e61217.
    OpenUrlCrossRefPubMed
  103. 103.↵
    R Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. Available: http://www.R-project.org; 2012.
  104. 104.↵
    Schloerke B, Crowley J, Cook D, Hofmann H, Wickham H, Briatte F, et al. Ggally: Extension to ggplot2. R package version 0.5. 0. 2014.
  105. 105.↵
    Wickham H. ggplot2: elegant graphics for data analysis. Springer Science & Business Media; 2009.
  106. 106.↵
    Paradis E, Claude J, Strimmer K. APE: analyses of phylogenetics and evolution in R language. Bioinformatics. Oxford Univ Press; 2004;20: 289–290.
    OpenUrlCrossRefPubMedWeb of Science
  107. 107.↵
    Love M, Anders S, Huber W. Differential analysis of count data–the DESeq2 package. Genome Biol. 2014;15: 550.
    OpenUrlCrossRefPubMed
  108. 108.↵
    Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal, Complex Syst. 2006;1695: 1–9.
    OpenUrl
  109. 109.↵
    Cunning R, Gates RD, Edmunds PJ. Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands. PeerJ Preprints; 2017.
  110. 110.↵
    Leinster T, Cobbold CA. Measuring diversity: the importance of species similarity. Ecology. Eco Soc America; 2012;93: 477–489.
    OpenUrlCrossRefPubMedWeb of Science
  111. 111.↵
    Hadfield JD. MCMC methods for multi-response generalized linear mixed models: the MCMCglmm R package. J Stat Softw. 2010;33: 1–22.
    OpenUrlCrossRefPubMedWeb of Science
  112. 112.↵
    Wilson AJ, Reale D, Clements MN, Morrissey MM, Postma E, Walling CA, et al. An ecologist’s guide to the animal model. J Anim Ecol. Wiley Online Library; 2010;79: 13–26.
    OpenUrlCrossRefPubMedWeb of Science
  113. 113.↵
    Quigley KM, Davies SW, Kenkel CD, Willis BL, Matz M V, Bay LK. Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals. PLoS One. Public Library of Science; 2014;9: e94297.
    OpenUrlCrossRefPubMed
  114. 114.
    Sampayo EM, Dove S, Lajeunesse TC. Cohesive molecular genetic data delineate species diversity in the dinoflagellate genus Symbiodinium. Mol Ecol. Blackwell Publishing Ltd; 2009;18: 500–519. doi:10.1111/j.1365-294X.2008.04037.x
    OpenUrlCrossRefPubMed
  115. 115.↵
    Thornhill DJ, Lajeunesse TC, Santos SR. Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Mol Ecol. Blackwell Publishing Ltd; 2007;16: 5326–5340. doi:10.1111/j.1365-294X.2007.03576.x
    OpenUrlCrossRefPubMedWeb of Science
  116. 116.↵
    Howells EJ, Willis BL, Bay LK, van Oppen MJH. Microsatellite allele sizes alone are insufficient to delineate species boundaries in Symbiodinium. Mol Ecol. 2016; n/a–n/a. doi:10.1111/mec.13631
    OpenUrlCrossRef
  117. 117.↵
    Gonzalez A, Stombaugh J, Lauber CL, Fierer N, Knight R. SitePainter: a tool for exploring biogeographical patterns. Bioinformatics. Oxford Univ Press; 2012;28: 436–438.
    OpenUrlCrossRefPubMed
  118. 118.↵
    Albert M, Andler J, Bah T, Barbry-Blot P, Barraud JF, Baxter B. Inkscape. 2013.
  119. 119.↵
    Ridgeway G. gbm: Generalized boosted regression models. R Packag version. 2006;1.
  120. 120.↵
    Baddeley A, Turner R. Spatstat: an R package for analyzing spatial point patterns. J Stat Softw. 2005;12: 1–42.
    OpenUrlCrossRefPubMed
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Posted August 08, 2017.
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Unexpected mixed-mode transmission and moderate genetic regulation of Symbiodinium communities in a brooding coral
Kate M. Quigley, Patricia A. Warner, Line K. Bay, Bette L. Willis
bioRxiv 173591; doi: https://doi.org/10.1101/173591
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