Microsatellites from clade B Symbiodinium spp. specialized for Caribbean corals in the genus Madracis

In order to determine boundaries of genetic recombination among putative ‘species’ of endosymbiotic dinoflagellates, nine polymorphic microsatellite loci were developed and optimized for clade B Symbiodinium designated as type 7 (B7) and two related types, B13 and B13a. Together, they form a subclade in clade B that is specific to Caribbean corals in the genus Madracis. A total of 52 samples were analysed (including 43 B7, 2 B13, 7 B13a) originating from seven Caribbean locations. Diversity indices at each haploid locus ranged from 0.302 to 0.836 and four to 14 alleles were found per locus. The loci were preliminarily cross‐tested on closely related ‘ancestral’ B1 populations found in maze coral Meandrina meandrites and that of another host specialist, B5, from the lesser starlet coral Siderastrea radians.     

Correlated evolution of sex and reproductive mode in corals (Anthozoa: Scleractinia)

Sexuality and reproductive mode are two fundamental life-history traits that exhibit largely unexplained macroevolutionary patterns among the major groups of multicellular organisms. For example, the cnidarian class Anthozoa (corals and anemones) is mainly comprised of gonochoric (separate sex) brooders or spawners, while one order, Scleractinia (skeleton-forming corals), appears to be mostly hermaphroditic spawners. Here, using the most complete phylogeny of scleractinians, we reconstruct how evolutionary transitions between sexual systems (gonochorism versus hermaphrodism) and reproductive modes (brooding versus spawning) have generated large-scale taxonomic patterns in these characters. Hermaphrodites have independently evolved in three large, distantly related lineages consisting of mostly reef-building species. Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost than gained, and can only be acquired by brooders. This circuitous evolutionary pathway accounts for the prevalence of hermaphroditic spawners among reef-forming scleractinians, despite their ancient gonochoric heritage.     

Improvement of photosynthesis in zooxanthellate corals by autofluorescent chromatophores

Autofluorescent chromatophores were detected in 17 out of 71 zooxanthellate coral species studied. Chromatophores are localized either in the oral gastrodermic (endoderm) or oral epidermis (ectoderm). The pigment granules within the chromatophores (0.5–1.0 m in diameter) show a brilliant light-blue/turquoise autofluorescence (emission between 430 and 500 nm) after excitation with light of 365–410 nm. All species where the autofluorescent gastrodermal chromatophores form a compact layer, embedding the zooxanthellae, belong to the family Agariciidae. In contrast, some species of the Faviidae (2), Pectiniidae (1) and Mussidae (1) were found to have distinct, autofluorescent chromatophores in the oral epidermis. Autofluorescent pigments of the host may enhance photosynthesis of the symbionts as in Leptoseris fragilis. Short wavelength irradiance, less suitable for photosynthesis, is transformed by host pigments into longer wavelengths which are photosynthetically more effective. Thus, host species possessing autofluorescent chromatophores might have selective advantage over non-fluorescent species, and have the potential to survive in light-limited habitats. Furthermore, the daily period of photosynthesis is extended, thus increasing the energy supply and enhancing the deposition of skeletal carbonate. The absence or presence of chromatophores may have value in taxonomy and could putatively be of plalaeontological and palaeoecological interest.     

Microanalysis of C and O isotopes of azooxanthellate and zooxanthellate corals by ion microprobe

We have determined the ¹⁸O and ¹³C values of azooxanthellate (Lophelia pertusa) and zooxanthellate (Porites lutea) corals at a micrometer scale using an ion microprobe (SIMS—secondary ion mass spectrometry). In P. lutea, centers of calcification are small (10 to 15 m) and difficult to locate during measurements. In L. pertusa, they are large (50 m) and arranged in lines of centers of calcification. Our results show that centers of calcification in L. pertusa have a restricted range of variation in ¹⁸O [-2.8±0.3 (PDB)], and a larger range in ¹³C [14.3 to 10.9 (PDB)]. Surrounding skeletal fibers exhibit large isotopic variation both for C and O (up to 12), and ¹³C and ¹⁸O are positively correlated. The C and O isotopic compositions of the center of calcification deviate from this linear trend at the lightest ¹⁸O values of the surrounding fibers. Ion microprobe results on P. lutea demonstrate also a large range of variation for the ¹⁸O values (up to 10). No correlation is found with C isotopes that exhibit, in comparison with L. pertusa, a small range of variation (2). This variation of ¹⁸O at a micrometer scale is probably the result of two processes: (1) an isotopic equilibrium calcification with 1 pH unit variation in the calcification fluid as indicated by direct measurements of coelenteron pH in the coral Galaxea fascicularis (Al-Horani et al. 2003) and (2) a kinetic fractionation. The ¹³C apparent disequilibrium in P. lutea may be the result of mixing between metabolic CO₂ (respiration) and dissolved inorganic carbon (DIC) coming directly from seawater.     

Two new species ofCerioxynus (Copepoda: Poecilostomatoida) parasitic in corals (Scleractinia: Faviidae) in the South Pacific

Summary The copepodsCerioxynus oulophylliae n. sp., parasitizing the hard coralOulophyllia crispa (Lamarck) on the Great Barrier Reef, Australia, and at Banda in the Moluccas, andCerioxynus montastreae n. sp., living inMontastrea curta (Dana) on the Great Barrier Reef, are described and illustrated. Both new species are distinguished from their four congeners by having wing-like epimera on the segments bearing leg 2 and leg 3. ac]19850419     

The endosymbiotic dinoflagellates (Symbiodinium sp.) of corals are parasites and mutualists

The evolutionary success and continued survival of reef-building corals under increasing environmental change will, in part, be determined by the composition of their endosymbiotic dinoflagellate communities (Symbiodinium sp.). Recent research suggests that differences in the phylotype composition of Symbiodinium in the same host can lead to different outcomes for the host when exposed to similar environmental conditions. One explanation for these observations is that symbioses between corals and Symbiodinium represent a continuum of interaction states that encompass mutualisms and parasitisms consistent with current evolutionary theory developed for other symbiotic systems. Here, we discuss the evidence supporting the existence of a parasitic to mutualistic continuum in Symbiodinium interactions and propose that a consideration of the evolutionary ecology of these associations will advance our understanding of how environmental change will influence the ecological outcomes in these important symbioses. We advocate that a robust taxonomic structure for Symbiodinium sp. and empirical studies on sexual reproduction in Symbiodinium, the stability of interaction states among Symbiodinium symbioses spatially and temporally and how interaction states change as the environment changes will generate data for models that accurately forecast how climate change will influence the persistence of corals and the reefs they structure.     

Habitat-forming seaweeds in Japan (fucoids and temperate kelps)

This paper describes the flora of habitat-forming seaweeds (fucoids and temperate kelps) at 7673 sites of the Japanese coast encompassing its warm to cold temperate zone, recorded from 1887 to 2014. The data set includes 86 species (21,168 presence and 20,845 absence records), compiled from 355 literature sources, most of which were written in Japanese and published as grey literature in local journals or individual reports. Scientific names were consolidated under currently-accepted nomenclature based on Algaebase (http://www.algaebase.org). The data set compiled the seaweed flora at each study site each year, the geographical location and the scientific names. Additionally, three supporting data sets were created respectively including name of each site, synonyms of the seaweeds, and the corresponding literature list. This rich collection of data can be used to study the biogeography and long-term changes of particular species and the diversity of habitat-forming seaweeds of the Japanese coast.     

Sedimentary nitrogen uptake and assimilation in the temperate zooxanthellate sea anemone Anthopleura aureoradiata

The sea anemone Anthopleura aureoradiata (Carlgren), which harbours symbiotic dinoflagellates (zooxanthellae), is abundant on mudflats and rocky shores around New Zealand. We measured the potential for particulate nitrogen uptake from sediment by A. aureoradiata and the subsequent consequences of this uptake on the nitrogen status of its zooxanthellae. Sediment was rinsed, labelled with (¹⁵NH₄)₂SO₄, and provided to anemones at low (0.23 g ml^− 1) and high (1.33 g ml^− 1) sediment loads for 6 h. Both anemone tissues and zooxanthellae became enriched with ¹⁵N. Enrichment of anemone tissues was similar at both high and low sediment loads, but the zooxanthellae became more enriched at the lower load. This was presumably because the uptake of ammonium, arising from host catabolism, by zooxanthellae is light driven and because the anemones at the lower load were able to extend their tentacles into the light while those at the higher load were not. The influence of sediment uptake on the nitrogen status of the zooxanthellae was determined by measuring the extent to which 20 μM NH₄⁺ enhanced the rate of zooxanthellar dark carbon fixation above that seen in filtered seawater (FSW) alone; the ammonium enhancement ratio (AER) was expressed as [dark NH₄⁺ rate/dark FSW rate], where ‘rate’ refers to C fixation and a ratio of 1.0 or less indicates nitrogen sufficiency. When anemones were starved with and without rinsed sediment in nitrogen-free artificial seawater for 8 weeks, zooxanthellar nitrogen deficiency became apparent at 2-4 weeks and reached similar levels in both treatments (AER = ~ 2). In contrast, anemones fed 5 times per week for 8 weeks with Artemia nauplii were nitrogen sufficient (AER = 1.03). In the field, zooxanthellae from mudflat anemones were largely nitrogen sufficient (AER = 1.26), while nitrogen deficient zooxanthellae were present in anemones from a rocky intertidal site (AER = 2.93). These results suggest that, while there was evidence for particulate nitrogen uptake, dissolved inorganic nitrogen (especially ammonium) in interstitial pore water may be a more important source of nitrogen for the zooxanthellae in mudflat anemones, and may explain the marked difference in nitrogen status between the mudflat and rocky shore populations.     

Low genetic diversity of symbiotic dinoflagellates (Symbiodinium) in scleractinian corals from tropical reefs in southern Hainan Island, China

Endosymbiotic dinoflagellates in the genus Symbiodinium are among the most abundant and important group of photosynthetic protists found in coral reef ecosystems.In order to further characterize this diversity and compare with other regions of the Pacific,samples from 44 species of scleractinian corals representing 20 genera and 9 families,were collected from tropical reefs in southern Hainan Island,China.Denaturing gradient gel electrophoresis fingerprinting of the ribosomal internal transcribed spacer 2 identified 11 genetically distinct Symbiodinium types that have been reported previously.The majority of reef-building coral species (88.6％) harbored only one subcladal type of symbiont,dominated by host-generalist C1 and C3,and was influenced little by the host’s apparent mode of symbiont acquisition.Some species harbored more than one clade of Symbiodinium (clades C,D) concurrently.Although geographically isolated from the rest of the Pacific,the symbiont diversity in southern Hainan Island was relatively low and similar to both the Great Barrier Reef and Hawaii symbiont assemblages (dominated by clade C Symbiodinium).These results indicate that a specialist symbiont is not a prerequisite for existence in remote and isolated areas,but additional work in other geographic regions is necessary to test this idea.     

Calcium localisation by X-ray microanalysis and fluorescence microscopy in larvae of zooxanthellate and azooxanthellate corals

X-ray microanalysis and fluorescence microscopy (Calcium Orangetrade mark) was used to determine the distribution of intracellular calcium (I(Ca)), in the form of total and ionic calcium respectively, in planulae and settled larvae of a zooxanthellate coral. The distribution of total calcium only was determined in larvae of an azooxanthellate coral. In azooxanthellate planulae and settled larvae, total I(Ca) concentration in the oral ectoderm was high and similar to that in seawater (SW). Calcium concentration did not vary (P > 0.05) between planulae and settled larvae. However, settled larvae accumulated large amounts of calcium in gastrodermal lipid-containing cells. In contrast, zooxanthellate planulae possessed significantly (P < 0.01) lower concentrations of total I(Ca) within ectodermal cells in comparison to settled larvae. In addition, in settled zooxanthellate larvae total calcium concentration in the mesogloea and coelenteron was significantly (P < 0.05) higher than in the oral ectodermal and gastrodermal cells, respectively. Total I(Ca) concentrations in the oral ectoderm of settled larvae were also significantly (P < 0.01) lower than that of the calicoblastic ectoderm. In zooxanthellate settled larvae, ionic I(Ca) levels in the aboral epithelium surrounding rapidly growing septa were high. These levels increased significantly (P < 0.05) within the tissue surrounding growing septa after incubation in high-calcium SW.     

Impact of secondary forest management on ant assemblage composition in the temperate region in Japan

In Japan, the impacts of human disturbance on ant assemblages have been intensively studied mainly in suburban areas. In contrast, the impact on ant assemblages of long-term human management and abandonment of forests is not well studied even though forestry is viewed as a process that seriously impacts ant assemblages. Besides, the studies focused on the relationship between secondary forest management for producing the firewood and charcoal which is considered to be characteristic of Japan and ant assemblage is not well studied. Do the long-term impacts on the secondary forest alter the ant composition? The effects of forest management on ant assemblages were studied through comparisons of managed, unmanaged and clear cut forest plots in secondary tree stands that had been used previously for producing firewood and charcoal. Ant species richness did not differ among forest categories, but ant species composition varied among forest categories. The absence or presence of openland and woodland ant specialist species is considered a good indicator for secondary forest management.     

Disturbance-induced bird diversity in early successional habitats in the humid temperate region of northern Japan

The positive role of moderate natural disturbance is less known for a mobile organism such as birds, compared to sessile organisms. In the face of recent declines of grassland birds, it is necessary to identify the mechanism to maintain avian diversity in early successional open habitats in different regions. In the humid temperate region, the predominant habitat type is woody vegetation. Therefore, bird communities were studied along vegetational succession using a chronosequence method. TWINSPAN identified three distinctive habitat types (barren, grass-fen and shrubland) and four habitat guilds of birds (pioneer, grassland, ubiquitous and shrub) in the study sites. Path analysis determined the direct and indirect effects of disturbance on the habitat guilds of birds. Short and intermediate intervals of the water disturbance are important to pioneer guilds and grass-fen habitat, respectively. The frequent occurrence of large animals had a negative impact on grassland guild. It suggests that grassland birds less tolerate cattle grazing or human activities in a region with intensive land use. The chronosequence study revealed the dynamic nature of the bird community. Birds occupy habitats following the successional sere of vegetation, responding to animal occurrence and human activities in various manners.     

Comparison of stream benthic invertebrate assemblages among forest types in the temperate region of Japan

We compared benthic invertebrate assemblages among headwater streams in several forest types in Japan. Forests were divided into three clusters based on vegetation composition: old-growth broad-leaved forest, planted coniferous forest, and mixed forest. The numbers of individuals and families and the diversity (Shannon-Wiener) of benthic invertebrate assemblages did not differ significantly among the three forest clusters. However, principal components analysis of family abundance showed differences in the benthic invertebrate assemblages among the three forest clusters. No environmental factors were correlated with these differences. Benthic invertebrate assemblages differed depending on forest composition. The abundances of Taeniopterygidae and Athericidae in old-growth broad-leaved forest were significantly greater than in planted coniferous forest. The abundances of Heptageniidae, Baetiidae, Stenopsychidae, Uenoidae, Chironomidae, and Potamidae in planted coniferous forest were significantly greater than in old-growth broad-leaved forest. If the remaining old-growth broad-leaved forest were to be converted to coniferous plantation, species that inhabit old-growth forest may become extinct.     

Niche specialization of reef-building corals in the mesophotic zone: metabolic trade-offs between divergent Symbiodinium types

The photobiology of two reef corals and the distribution of associated symbiont types were investigated over a depth gradient of 0-60 m at Scott Reef, Western Australia. Pachyseris speciosa hosted mainly the same Symbiodinium C type similar to C3 irrespective of sampling depth. By contrast, Seriatopora hystrix hosted predominantly Symbiodinium type D1a or D1a-like at shallow depths while those in deeper water were dominated by a Symbiodinium C type closely related to C1. The photosynthesis/respiration (P/R) ratio increased consistently with depth at the two sampling times (November 2008 and April 2009) for P. speciosa and in November 2008 only for S. hystrix, suggesting a reduction in metabolic energy expended for every unit of energy obtained from photosynthesis. However, in April 2009, shallow colonies of S. hystrix exhibited decreased P/R ratios down to depths of approximately 23 m, below which the ratio increased towards the maximum depth sampled. This pattern was mirrored by changes in tissue biomass determined as total protein content. The depth of change in the direction of the P/R ratio correlated with a shift from Symbiodinium D to C-dominated colonies. We conclude that while photobiological flexibility is vital for persistence in contrasting light regimes, a shift in Symbiodinium type may also confer a functional advantage albeit at a metabolic cost with increased depth.     

Molecular identification of symbiotic dinoflagellates (Symbiodinium spp.) from Palythoa spp. (Anthozoa: Hexacorallia) in Japan

In Japan, zooxanthellate Palythoa tuberculosa Klunzinger and Palythoa mutuki Verrill (Anthozoa: Hexacorallia: Zoantharia) are found over a 1,000 + km latitudinal range, often in environments where most other zooxanthellate anthozoans are not found (i.e. tidal lagoon pools, around shallow water hydrothermal vents, subtropical rocky shorelines). Sequences of internal transcribed spacer of ribosomal DNA (ITS-rDNA) of the symbiotic dinoflagellate genus Symbiodinium (zooxanthellae) Freudenthal (Order Suessiales) from P. tuberculosa and P. mutuki from several locations in Japan (34°11′N–24°16′N) were analysed. Unexpectedly, despite the ability of the genus Palythoa to be flexible in association with different Symbiodinium subclades, most (35 of 36) Palythoa investigated here specifically associate with subclade C1 and closely related types. Symbiodinium subclade C1 has been characterized as a “generalist” in terms of the ability to associate with a range of hosts, but present results suggest that subclade C1 may also be a “generalist” in terms of being able to live in a variety of environments over a latitudinal range. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

Modern hard corals (Class Hexacorallia; Order Scleractinia) are widely studied because of their fundamental role in reef building and their superb fossil record extending back to the Triassic. Nevertheless, interpretations of their evolutionary relationships have been in flux for over a decade. Recent analyses undermine the legitimacy of traditional suborders, families and genera, and suggest that a non-skeletal sister clade (Order Corallimorpharia) might be imbedded within the stony corals. However, these studies either sampled a relatively limited array of taxa or assembled trees from heterogeneous data sets. Here we provide a more comprehensive analysis of Scleractinia (127 species, 75 genera, 17 families) and various outgroups, based on two mitochondrial genes (cytochrome oxidase I, cytochrome b), with analyses of nuclear genes (ss-tubulin, ribosomal DNA) of a subset of taxa to test unexpected relationships. Eleven of 16 families were found to be polyphyletic. Strikingly, over one third of all families as conventionally defined contain representatives from the highly divergent "robust" and "complex" clades. However, the recent suggestion that corallimorpharians are true corals that have lost their skeletons was not upheld. Relationships were supported not only by mitochondrial and nuclear genes, but also often by morphological characters which had been ignored or never noted previously. The concordance of molecular characters and more carefully examined morphological characters suggests a future of greater taxonomic stability, as well as the potential to trace the evolutionary history of this ecologically important group using fossils.