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The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807 bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.

Reef‐building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA‐seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai‘i Island with contrasting environmental conditions. We found that transcriptome‐wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site‐related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

Loss of live coral and declines in the structural complexity of reef habitats affects ecosystem-level processes such as energy flow, nutrient cycling, and community dynamics. Scleractinian corals are the primary contributor to the biological and physical three-dimensional (3D) structure of coral reef ecosystems. Disturbance events that induce coral mortality can alter the 3D structure of reefs habitats and lead to disruptions in trophic structure and organismal relationships that drive ecological processes. The coral reef ecosystem at Wai‘ōpae, southeast Hawai‘i Island, experienced several acute disturbance events in 2014, including a hurricane, tropical storms, and a severe coral bleaching event. This study utilized innovative 3D reconstruction techniques to create high-resolution models of the coral reef habitat and quantify structural metrics known to affect the biodiversity and abundance of associated reef organisms. A volumetric analysis was applied to the reconstructed 3D point clouds to determine the precise loss of habitat that occurred throughout the surveyed reef area. Conducting a temporal analysis using 3D reconstructions enabled us to test the hypothesis that volume and 3D architectural complexity of the coral community at Wai‘ōpae was significantly impacted by the acute disturbance events.

The structural complexity of coral reefs profoundly affects the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional survey techniques utilize 2-dimensional metrics that are inadequate for accurately capturing and quantifying the intricate structural complexity of scleractinian corals. A 3-dimensional (3D) approach improves the capacity to accurately measure architectural complexity, topography, rugosity, volume, and other structural characteristics that play a significant role in habitat facilitation and ecosystem processes. This study utilized Structure-from-Motion (SfM) photogrammetry techniques to create 3D mesh models for several Hawaiian corals that represent distinct morphological phenotypes. The orthophotos and digital elevation models generated from the SfM process were imported into geospatial analysis software in order to quantify several metrics pertaining to 3D complexity that are known to affect ecosystem biodiversity and productivity. The 3D structural properties of the reconstructed coral colonies were statistically analyzed to determine if the each species represents a unique morpho-functional group. The SfM reconstruction techniques described in this paper can be utilized for an array of research purposes to improve our understanding of how changes in coral composition affect habitat structure and ecological processes in coral reef ecosystems.

The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807 bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.

Growth anomaly (GA) is a coral disease characterized by enlarged skeletal lesions. Although negative effects of GA on several of coral's biological functions have been determined, the etiology and molecular pathology of this disease is very poorly understood. We studied the expression of 5 genes suspected to play a role in pathological development of GA in the endemic Hawaiian coral Montipora capitata, which is particularly susceptible to this disease. Transcript abundances of the 5 target genes in healthy tissue, GA-affected tissue, and unaffected tissue (apparently healthy tissue adjacent to GA) relative to 3 internal control genes (actin, NADH, and rpS3) were compared using quantitative reverse transcriptase PCR. Galaxin, which codes for a protein suspected to be involved in calcification and thus hypothesized to be differentially expressed in GA, was up-regulated in unaffected tissue but remained at baseline levels in GA tissue. The gene expressions of murine double minute 2 (MDM2) and tumor necrosis factor (TNF) remained unchanged in GA tissue. The expression of tyrosine protein kinase (TPK) and βγ-crystallin (BGC) were both down-regulated. These expression patterns were all inconsistent with the expression patterns of homologous genes in neoplastic diseases featuring similar morphological symptoms in humans. These expression data therefore suggest that the calcification mechanism is likely not enhanced in coral GA and that coral GA is not a malignant neoplasia.

Marine dinoflagellates in the genus Symbiodinium are primarily known for their symbiotic associations with invertebrates and protists, although they are also found free-living in nanoplankton and microphytobenthic communities. Free-living Symbiodinium are necessary for hosts that must acquire their symbionts anew each generation and for the possible reestablishment of endosymbiosis in bleached adults. The diversity and ecology of free-living Symbiodinium are not well studied by comparison with their endosymbiotic counterparts, and as a result, our understanding of the linkages between free-living and endosymbiotic Symbiodinium is poor. Here, we begin to address this knowledge gap by describing the genetic diversity of Symbiodinium in the surface water and reef sediments of Hawai‘i and Florida using Symbiodinium-specific primers for the hypervariable region of the chloroplast 23S domain V (cp23S-HVR). In total, 29 Symbiodinium sequence types were detected, 16 of which were novel. The majority of Symbiodinium sequence types in free-living environments belonged to clades A and B, but smaller numbers of sequence types belonging to clades C, D, and G were also detected. The majority of sequences recovered from Hawai‘i belonged to clades A and C and those from Florida to clade B. Such distribution patterns are consistent with the endosymbiotic diversity previously reported for these two regions. The ancestral sequence types in each clade were typically recovered from surface water and sediments both in Hawai‘i and Florida and have been previously reported as endosymbionts of a range of invertebrates, suggesting that these types have the capacity to exploit a range of very different habitats. More derived sequence types in clades A, B, C, and G were not recovered here, suggesting they are potentially restricted to endosymbiotic environments.

This study investigated the morphology, severity, and distribution of growth anomalies (GAs) in the coral, Montipora capitata, from Wai‘ōpae tide pools, southeast Hawai‘i Island. A macro-image analysis of skeletal microstructure placed GAs into two definable categories; Type A and Type B. Type A GAs had polyp density reduced by 43.05 ± 0.80% (mean ± SE) compared to healthy M. capitata tissue, with many fused and protrusive tuberculae. Type B GAs had no discernable polyps or calices and fused protuberant coenosteum. The prevalence of Type A and Type B GAs among all M. capitata colonies (n = 1,093) in 8 tide pools at Wai‘ōpae was 22.1% (range 2.8–33.7%) and 8.2% (range 0.0–16.9%), respectively. The proportion of colony surface area occupied by GA (relative GA cover) was quantified to assess the severity of this disease among all surveyed colonies. The relative GA cover was significantly greater on colonies larger than 1 m in diameter than smaller colonies and in the central portion of colonies than in the periphery. Furthermore, relative GA cover was negatively related to water motion (R 2 = 0.748, P

Many scleractinian corals must acquire their endosymbiotic dinoflagellates (genus Symbiodinium) anew each generation from environmental pools, and exchange between endosymbiotic and environmental pools of Symbiodinium (reef waters and sediments) has been proposed as a mechanism for optimizing coral physiology in the face of environmental change. Our understanding of the diversity of Symbiodinium spp. in environmental pools is poor by comparison to that engaged in endosymbiosis, which reflects the challenges of visualizing the genus against the backdrop of the complex and diverse micro-eukaryotic communities found free-living in the environment. Here, the molecular diversity of Symbiodinium living in the waters and sediments of a reef near Coconut Island, O‘ahu, Hawai‘i, sampled at four hourly intervals over a period of 5 d was characterized using a Symbiodinium-specific hypervariable region of the chloroplast 23S. A comparison of Symbiodinium spp. diversity recovered from environmental samples with the endosymbiotic diversity in coral species that dominate the adjacent reef revealed limited overlap between these communities. These data suggest that the potential for infection, exchange, and/or repopulation of corals with Symbiodinium derived from the environment is limited at this location, a finding that is perhaps consistent with the high proportion of coral species in this geographic region that transmit endosymbionts from generation to generation.

The primary productivity of coral–dinoflagellate symbiosis is classically viewed as nitrogen (N)-limited. However, the recent discovery of N-fixing bacteria residing within coral tissues challenges this view. This study investigated the diversity and abundance of N-fixing bacteria associated with Hawaiian corals of the genus Montipora. Phylogenetic analysis of a partial sequence of the nitrogenase gene (nifH), revealed a diverse group of N-fixing bacteria in association with Montipora capitata and Montipora flabellata. These nifH sequences were closely affiliated with known taxa in α-, β-, γ-, and δ-proteobacteria, as well as cyanobacteria. Gamma-proteobacteria were the dominant bacterial class represented, and bacteria closely related to the genus Vibrio were the prevailing group within this class. Quantitative PCR was used to evaluate the abundance of the dominant class of N-fixing bacteria from different parts of four M. capitata colonies. The abundance of the dominant γ-proteobacteria was positively correlated (p = 0.001) with the abundance of symbiotic dinoflagellates, suggesting a physiological relationship between the two coral symbionts. The evidence obtained in this study suggests that N-limitation may not be a major regulator of the productivity of dinoflagellate symbionts of corals, but provides impetus for renewed investigation into N-cycling in this multi-partner symbiosis.

Many symbiotic marine invertebrates acquire free-living Symbiodinium from the envi- ronment. Abundance and diversity of free-living Symbiodinium could influence recovery from bleaching, resilience, and the long-term adaptation of host organisms. Although free-living Symbio- dinium have been detected in the water column and substrates of coral reefs, their diversity and availability to the hosts are poorly understood. Tank experiments were conducted to test whether asymbiotic coral larvae of Acropora monticulosa acquired free-living Symbiodinium from the water column or sediment to become symbiotic. Treatments included filtered (0.22 µm) seawater (FSW), unfiltered seawater (SW), FSW and sediment, and SW and sediment. Our results showed that greater proportions of larvae in sediment-containing treatments acquired Symbiodinium earlier and had greater in hospite Symbiodinium densities when compared to seawater-only treatments. Addition- ally, clade A Symbiodinium was only recovered in the larvae from the sediment-containing treat- ments, whereas clades B and C were recovered from all treatments. Differences in distribution, abun- dance, replication and motility patterns of Symbiodinium, as well as larval behavior, may have contributed to the observed differences between uptake from the sediment and the water column. However, our results suggest that the sediment may represent an important source of free-living Symbiodinium available for uptake during primary acquisition by coral larvae.

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems.

We determined the effects of temperature and nutrients on the chain length of a diatom, Skeletonema costatum, in batch culture and enclosure experiments with estuarine water from San Francisco Bay, USA, using the recently developed CytoBuoy flow cytometer. Determination of the number of cells per diatom chain by CytoBuoy flow cytometer and associated software correlated well with but was much more precise and time efficient than microscopic quantification. Increasing temperatures (from 6, 8 to 17°C) and nutrient concentrations induced high growth rates and dominance by longer chains in a cultured S. costatum strain that was originally acclimatized to a temperature range of 11-30°C. Similarly, a positive correlation between growth rate and chain length was observed in S. costatum in batch culture and natural communities in enclosure experiments. Maximal chain lengths of S. costatum were greater in natural populations than in the batch culture. Longer chains affect sinking rates and thus likely help the diatom remain suspended in the upper part of the water column where physical and chemical parameters are more favorable for growth.

To understand the enhanced ability of marine diatoms to assimilate nitrogen (N), we measured changes in the transcript abundance and enzyme activity of glutamine synthetase (GS), one of the key enzymes that link carbon (C) and N metabolism, in the common diatom Skeletonema costatum (Greville) Cleve. Transcript abundance of glnII (the gene that encodes the GSII isoenzyme), measured by quantitative reverse transcriptase-PCR, and total GS activity increased 2 to 3.5 times above background in the cells taking up nitrate (NO 3 - ) but not the cells taking up ammonium (NH 4 + ). A background level of glnII mRNA was maintained at a steady level up to 15 days of N starvation before decreasing to below detection after 21 days. These results confirm that transcription of glnII is induced to assimilate NH 4 + derived from reduction of NO 3 - . Because of this role of GSII in diatoms assimilating NH 4 + derived from NO 3 - reduction rather than from the environmental NH 4 + , quantification of glnII mRNA promises to be a useful indication of new production by phytoplankton.

Symbiotic dinoflagellates belonging to the genus Symbiodinium (Freudenthal) are found worldwide in association with shallow-water tropical and subtropical marine invertebrates. Most phylogenetic studies of Symbiodinium have used nuclear rRNA (nrDNA) genes to infer relationships among members of the genus. In this report, we present the first phylogeny of Symbiodinium based on DNA sequences from a mitochondrial protein-coding gene (cytochrome oxidase subunit I [coxl]). Two principal groups, one comprised of Symbiodinium clade A and the second encompassing Symbiodinium clades B/C/ D/E/F, are strongly supported in the coxl phylogeny. Relationships within Symbiodinium clades B/C/D/E/ F, however, are less well resolved compared with phylogenies inferred from nrDNA and chloroplast large subunit (cp23S)-rDNA genes. Statistical tests between alternative tree topologies verified, with an exception being the position of one controversial member of Symbiodinium clade D, that relationships inferred from coxl are congruent with those inferred from nrDNA and cp23S-rDNA. Taken together, the relationships between the major Symbiodinium clades are robust, and there appears to be no evidence of hybridization or differential introgression of nuclear and plastid genomes between clades.

As the indigenous people of an island chain in the middle of the moananuiākea (the expansive ocean) surrounded by coral reefs, Native Hawaiians have profound ancestral and spiritual connections to the coral. These connections between Hawaiians and coral manifests themselves in a multitude of diverse and pragmatic ways. Yet, the primary Hawaiian wisdom information is accessed and shared through chants, dance, and other daily activities as well as such immemorial forms as dreams and thoughts. Elements of the natural world are described as having intimate kin relations to the Hawaiian people as ancestral akua, or deities. The coral is no exception. Hawaiian people consider coral to be an akua, that provides birth and death to both the people and the islands, possessing much mana, the essence of spirituality. Corals are considered the beginning of life, and are thus the most ancient ancestors of all living things in Hawai‘i. In this paper, we use oral tradition, material culture, and indigenous ecological knowledge to present some of the most salient cultural symbolisms and pragmatic uses given to corals in Hawai’i. Our main objective is to use local perspectives and narratives to emphasize the biocultural, spiritual ecological, and, social relevance of coral to the Native Hawaiian people.

Growth anomaly (GA) is a commonly observed coral disease that impairs biological functions of the affected tissue. GA is prevalent at Wai ‘ōpae tide pools, southeast Hawai ‘i Island. Here two distinct forms of this disease, Type A and Type B, affect the coral, Montipora capitata . While the effects of GA on biology and ecology of the coral host are beginning to be understood, the impact of this disease on the photophysiology of the dinoflagellate symbiont, Symbiodinium spp., has not been investigated. The GA clearly alters coral tissue structure and skeletal morphology and density. These tissue and skeletal changes are likely to modify not only the light micro-environment of the coral tissue, which has a direct impact on the photosynthetic potential of Symbiodinium spp., but also the physiological interactions within the symbiosis. This study utilized Pulse amplitude modulation fluorometry (PAM) to characterize the photophysiology of healthy and GA-affected M . capitata tissue. Overall, endosymbionts within GA-affected tissue exhibit reduced photochemical efficiency. Values of both Fv/Fm and ΔF/ Fm’ were significantly lower (p

Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.