Variation in Symbiodinium ITS2 sequence assemblages among coral colonies

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.     

Scale-dependant control of motile epifaunal community structure along a coral reef fishing gradient

Large-scale fishing is mostly conducted using towed gears that reduce the biomass and diversity of benthic invertebrates. However, it is impossible to differentiate between the physical disturbance effect of towed gears from the effect of fish predator removal upon benthic invertebrate communities. Here we explore the impact of fish removal alone on the community structure of small motile coral reef invertebrates (epifauna) along a subsistence fishing intensity gradient in the Lau group, Fiji. We deployed settlement plates at three areas in each of six fishing grounds and examined the density and class richness of the motile epifaunal communities and the associated algal communities in relation to the structure of fish and benthic communities. Motile epifaunal density was unrelated to fishing intensity. However, at smaller inter-area scale (0.5-10 km) motile epifaunal density was negatively related to plate algal biomass, whereas at the larger inter-fishing-ground scale (4-180 km) motile epifaunal density was positively related to the rugosity (substrate complexity) of the surrounding benthos. The class richness and diversity (Margalef's d) of motile epifaunal communities were negatively related to fishing intensity, but unrelated to grazing intensity, rugosity or algal biomass at either scale. Benthic community structure varied significantly with fishing intensity; hard-coral cover was lower and turf-algal cover was higher at high fishing pressure. The variation in benthic community structure was associated with variation in fish community structure, which in turn varied with fishing intensity. Motile epifaunal community structure upon plates was linked to the structure of the surrounding benthic community, but was not directly linked to the plate algal community. We suggest the decline in richness of the motile epifauna community along the fishing gradient is attributable to either to exploiter-mediated coexistence or the reduction in ‘habitat quality’ of the surrounding benthos. At the large spatial scale substrate complexity is the key determinant of motile epifaunal density, suggesting predation by fishes plays an important structuring role at this scale. Assuming that rugosity is inversely related to predation risk then this study represents the first evidence for spatial-dependence on the top-down (predation) vs. bottom-up (algal biomass) control of community structure. We argue fisheries exploitation, in the absence of a physical disturbance can negatively influence motile epifaunal community structure at large spatial scales.     

Patterns of Symbiodinium (Dinophyceae) diversity and assemblages among diverse hosts and the coral reef environment of Lizard Island,Australia

Large‐scale environmental disturbances may impact both partners in coral host–Symbiodinium systems. Elucidation of the assembly patterns in such complex and interdependent communities may enable better prediction of environmental impacts across coral reef ecosystems. In this study, we investigated how the community composition and diversity of dinoflagellate symbionts in the genus Symbiodinium were distributed among 12 host species from six taxonomic orders (Actinaria, Alcyonacea, Miliolida, Porifera, Rhizostoma, Scleractinia) and in the reef water and sediments at Lizard Island, Great Barrier Reef before the 3rd Global Coral Bleaching Event. 454 pyrosequencing of the ITS2 region of Symbiodinium yielded 83 operational taxonomic units (OTUs) at a 97% similarity cut‐off. Approximately half of the Symbiodinium OTUs from reef water or sediments were also present in symbio. OTUs belonged to six clades (A‐D, F‐G), but community structure was uneven. The two most abundant OTUs (100% matches to types C1 and A3) comprised 91% of reads and OTU C1 was shared by all species. However, sequence‐based analysis of these dominant OTUs revealed host species specificity, suggesting that genetic similarity cut‐offs of Symbiodinium ITS2 data sets need careful evaluation. Of the less abundant OTUs, roughly half occurred at only one site or in one species and the background Symbiodinium communities were distinct between individual samples. We conclude that sampling multiple host taxa with differing life history traits will be critical to fully understand the symbiont diversity of a given system and to predict coral ecosystem responses to environmental change and disturbance considering the differential stress response of the taxa within.     

Recruitment and the structure of assemblages of fish on coral reefs

Much recent research has focused on the question of the high species richness and population densities of fish inhabiting coral reefs. Both density-dependent (post-recruitment) and density-independent (pre-recruitment) processes have been implicated in the regulation of these assemblages. These processes may operate at a variety of spatial and temporal scales. Here we review recent progress and point to some of the key questions for future research.     

Latitudinal variation in monthly-scale reproductive synchrony among Acropora coral assemblages in the Indo-Pacific

Early research into coral reproductive biology suggested that spawning synchrony was driven by variations in the amplitude of environmental variables that are correlated with latitude, with synchrony predicted to break down at lower latitudes. More recent research has revealed that synchronous spawning, both within and among species, is a feature of all speciose coral assemblages, including equatorial reefs. Nonetheless, considerable variation in reproductive synchrony exists among locations and the hypothesis that the extent of spawning synchrony is correlated with latitude has not been formally tested on a large scale. Here, we use data from 90 sites throughout the Indo-Pacific and a quantitative index of reproductive synchrony applied at a monthly scale to demonstrate that, despite considerable spatial and temporal variation, there is no correlation between latitude and reproductive synchrony. Considering the critical role that successful reproduction plays in the persistence and recovery of coral reefs, research is urgently needed to understand the drivers underpinning variation in reproductive synchrony.

     

Distance decay of similarity among parasite communities of three marine invertebrate hosts

The similarity in species composition between two communities generally decays as a function of increasing distance between them. Parasite communities in vertebrate definitive hosts follow this pattern but the respective relationship in intermediate invertebrate hosts of parasites with complex life cycles is unknown. In intermediate hosts, parasite communities are affected not only by the varying vagility of their definitive hosts (dispersing infective propagules) but also by the necessary coincidence of all their hosts in environmentally suitable localities. As intermediate hosts often hardly move they do not contribute to parasite dispersal. Hence, their parasite assemblages may decrease faster in similarity with increasing distance than those in highly mobile vertebrate definitive hosts. We use published field survey data to investigate distance decay of similarity in trematode communities from three prominent coastal molluscs of the Eastern North-Atlantic: the gastropods Littorina littorea and Hydrobia ulvae, and the bivalve Cerastoderma edule. We found that the similarity of trematode communities in all three hosts decayed with distance, independently of local sampling effort, and whether or not the parasites used the mollusc as first or second intermediate host in their life cycle. In H. ulvae, the halving distance (i.e. the distance that halves the similarity from its initial similarity at 1 km distance) for the trematode species using birds as definitive hosts was approximately two to three times larger than for species using fish. The initial similarities (estimated at 1 km distance) among trematode communities were relatively higher, whereas mean halving distances were lower, compared to published values for parasite communities in vertebrate hosts. We conclude that the vagility of definitive hosts accounts for a high similarity at the local scale, while the strong decay of similarity across regions is a consequence of the low probability that all necessary hosts and suitable environmental conditions coincide on a large scale.     

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.     

Variation in clone structure of fragmenting coral reef sponges

Populations of three branching Caribbean demosponge species are composed of clones produced by asexual fragmentation. Dispersal of the fragments before they become established as independent individuals scatters clone members widely and intermixes members of different clones, complicating study of the clone structure of these populations and contrasting with many other sessile clonal organisms. Clone structures of these populations were inferred using a combination of tissue-compatibility relationships and an analysis of variations in morphology and colour. Although tissue compatibility cannot be used for precise identification of sponge clones, in general, patterns of variation in morphological characters influencing fragmentation and patterns of fragment dispersal and recruitment suggest that, in these populations, tissue-compatibility relationships closely reflect clone structure. Conditions that must be met in order to use tissue compatibility for study of sponge clones are discussed, and previous results, from which conflicting conclusions have been drawn, reconciled in this context. Variations among clones in numbers of physiologically independent members and in size and shape of areal extent are discussed in the context of processes that may affect evolution of clonal characters in these populations and in other species that propagate by dispersing asexual fragments.     

Ecological structure of assemblages of coral reef fishes on isolated patch reefs

A 9-year study of the structure of assemblages of fish on 20 coral patch reefs, based on 20 non-manipulative censuses, revealed a total of 141 species from 34 families, although 40 species accounted for over 95% of sightings of fish. The average patch reef was 8.5 m² in surface area, and supported 125 fish of 20 species at a census. All reefs showed at least a two-fold variation among censuses in total numbers of fish present, and 12 showed ten-fold variations. There was also substantial variation in the composition and relative abundances of species present on each patch reef, such that censuses of a single patch reef were on average about 50% different from each other in percent similarity of species composition (Czekanowski's index). Species differed substantially in the degree to which their numbers varied from census to census, and in the degree to which their dispersion among patch reefs was modified from census to census. We characterize the 40 most common species with respect to these attributes. The variations in assemblage structure cannot be attributed to responses of fish to a changing physical structure of patch reefs, nor to the comings and goings of numerous rare species. Our results support and extend earlier reports on this study, which have stressed the lack of persistant structure for assemblages on these patch reefs. While reef fishes clearly have microhabitat preferences which are expressed at settlement, the variations in microhabitat offered by the patch reefs are insufficient to segregate many species of fish by patch reef. Instead, at the scale of single patch reefs, and, to a degree, at the larger scale of the 20 patch reefs, most of the 141 species of fish are distributed without regard to differences in habitat structure among reefs, and patterns of distribution change over time. Implications for general understanding of assemblage dynamics for fish over more extensive patches of reef habitat are considered.     

Habitat structure and invertebrate assemblages on stream stones: A multivariate view from the riffle

Abstract Highly structured habitats, those with complex or heterogeneous physical structure, commonly contain more species than simply structured ones. However, tests of this relationship have been hampered by habitat-specific definitions and measurements of habitat structure and, in stream studies, by insufficient information on spatial variation in faunal abundances. We sampled the fauna of 90 stones collected from an order 4 section of the Taggerty and Steavenson Rivers, southeastern Australia. The spatially nested sampling design encompassed three spatial scales (sites within the same stream order, riffles at the same site and groups of stones within the same riffle) but no temporal replication, as we were only able to sample once. Habitat structure of stones was quantified by measuring the amount and type of epilithon on stones, together with stone shapes, sizes, textures and surface complexities. For the latter two attributes, we used a new method, involving image analysis, which can be used to quantify habitat structure in comparable ways in other systems. Species richness (S) was related to some measures of habitat structure, being higher on stones with a rough texture and weakly related to the amount of epilithon present. Total numbers of individuals (N) were also higher on rough stones, and faunal composition (as quantified by hybrid multidimensional scaling) was related to abundance of epilithon. However, flow environments, as quantified by water velocities and depths, were also related to faunal composition. Riffles varied in both faunal densities and near-bed flow environment, but not in any consistent way. Such variability means that individual riffles cannot be reasonably used to ‘represent’ stream sections or orders, an assumption commonly made in stream studies. Neglect of such issues has also resulted in poor conceptual integration between large- and small-scale studies in stream ecology.     

Disturbance and recovery of coral assemblages

Coral Reefs -  Trends in the health of coral reefs worldwide were examined by surveying the literature for quantitative studies of coral abundance that were at least four years long and...     

Patterns of spatial resource use in lotic invertebrate assemblages

Spatial resource overlap by benthic invertebrates was investigated between stones in 11 freshwater habitats (10 streams and a wind-swept lake shore) of similar physicochemical nature but different thermal and hydrologic stability in the Cass-Craigieburn region, New Zealand. Both overlap and breadth of stone use by the invertebrate taxa decreased as stability declined, in part because of the lower number of species available with which to share resources at unstable sites. Although there was no evidence for resource partitioning of stones, communities at stable sites and on more stable substrates differed from those that would have been expected to accumulate by chance colonisation alone. Stone assemblages at unstable sites are dominated by the same general suite of species well suited to surviving disturbances, while conditions at stable sites allow more specialised taxa to colonise individual stones differentially.     

Acanthaster planci outbreak: decline in coral health, coral size structure modification and consequences for obligate decapod assemblages

Although benthic motile invertebrate communities encompass the vast majority of coral reef diversity, their response to habitat modification has been poorly studied. A variety of benthic species, particularly decapods, provide benefits to their coral host enabling them to cope with environmental stressors, and as a result benefit the overall diversity of coral-associated species. However, little is known about how invertebrate assemblages associated with corals will be affected by global perturbations, (either directly or indirectly via their coral host) or their consequences for ecosystem resilience. Analysis of a ten year dataset reveals that the greatest perturbation at Moorea over this time was an outbreak of the corallivorous sea star Acanthaster planci from 2006 to 2009 impacting habitat health, availability and size structure of Pocillopora spp. populations and highlights a positive relationship between coral head size and survival. We then present the results of a mensurative study in 2009 conducted at the end of the perturbation (A. planci outbreak) describing how coral-decapod communities change with percent coral mortality for a selected coral species, Pocillopora eydouxi. The loss of coral tissue as a consequence of A. planci consumption led to an increase in rarefied total species diversity, but caused drastic modifications in community composition driven by a shift from coral obligate to non-obligate decapod species. Our study highlights that larger corals left with live tissue in 2009, formed a restricted habitat where coral obligate decapods, including mutualists, could subsist. We conclude that the size structure of Pocillopora populations at the time of an A. planci outbreak may greatly condition the magnitude of coral mortality as well as the persistence of local populations of obligate decapods.     

Ecological condition of coral reef assemblages in the Cuban Archipelago

The condition of coral reefs in the Cuban Archipelago is poorly known. We aimed to analyse coral assemblages across 199 reef sites belonging to 12 localities. Crest and fore reefs were assessed using six metrics: species richness, density, coral cover, mortality, coral size and reef complexity. The condition of reefs varied across the archipelago from healthy to depleted reefs. The localities with best scores were Cienfuegos, Bahía de Cochinos and Cazones. These reefs have values of living coral cover (>20%) and complexity (>50?cm) similar to the best preserved Caribbean reefs. However, the majority of crest biotopes suffered important deterioration with old mortality of Acropora palmata populations and moderate coral cover (15%); although crest reefs still maintained their structural complexity. Despite moderate levels of coral cover in fore reefs (18%), their condition was alarming because 25% of the sites had cover below the recovery threshold of 10%, accumulated mortality and structural flattening. Compared with the 1980s, the species richness was roughly the same (42) for crest and fore reefs, although dominance has changed to widespread tolerant species. Coral reef assemblages varied at local and regional scales in similar magnitude, suggesting the combined effects of natural and anthropogenic drivers.     

Variation of aquatic insect assemblages among seasons and microhabitats in Hungarian second-order streams

The assemblages of aquatic insects are important members of water ecosystems. Based on former studies among the most important factors structuring the assemblages are numerous abiotic ones, such as the sort and the particle size of the substratum. Most of the sampling protocols, e.g. AQEM, determine microhabitats based on those. Nevertheless, we have no information yet about whether or not these different, precisely determined microhabitats have different assemblages. In this study we compared the aquatic insect assemblages of different microhabitat types in three seasons using ADONIS and linear discriminant analyses. We proved that seasonal changes of abiotic factors had a major role in structuring the assemblages. In spring and summer the assemblages differed significantly, however, in autumn no significant differences were found. We supposed that the variation among the assemblages was due to the abundance patterns of frequent species instead of the presence of rare or sparse species. The indicator species analyses also corroborated this suppososition while symmetrical indicator species were not found.     

Transmission of freshwater myxozoans during the asexual propagation of invertebrate hosts

The phylum Myxozoa contains over 1350 species almost all of which are considered to be obligate parasites of aquatic animals. The phylum is composed of two classes, the Myxosporea and the Malacosporea, species of which are important pathogens responsible for severe economic losses in cultured fisheries. The life cycles of freshwater Myxozoa are believed to involve horizontal, indirect transmission, involving an invertebrate (oligochaetes or bryozoans) and a vertebrate host (fish or amphibians). Here, we describe myxozoan propagation through the fragmentation of invertebrate hosts to form new infected individuals. The two hosts examined are an oligochaete Lumbriculus variegatus infected with an unidentified myxosporean (Triactinomyxon sp.) and the bryozoan Fredericella sultana infected with the malacosporean Tetracapsuloides bryosalmonae which causes proliferative kidney disease, a major constraint of the European rainbow trout industry. Such intra-clonal propagation is a novel form of vertical transmission that is likely to be widespread within the Myxozoa and could form an important method by which some of these parasites maintain and proliferate within the aquatic environment.     

Biodiversity and trophic structure of invertebrate assemblages associated with understorey red algae in a Laminaria digitata bed

Although the composition of invertebrate assemblages associated with kelps has motivated several studies in the recent past, little is known about assemblages associated with smaller, understorey macroalgae in these ecosystems. Here, the composition of invertebrate assemblages living within understorey macroalgae of a kelp (Laminaria digitata) forest has been studied over two sampling dates, and the structure of the food web investigated using stable isotopes. A total of 145 species of mobile fauna, mainly amphipods and gastropods, were identified. Although differences were date-dependent, we showed that the three species considered (Palmaria palmata, Mastocarpus stellatus, Ellisolandia elongata) sheltered different associated assemblages, including high host-specificity, which suggests that the animal diversity associated with rocky shores is enhanced by a high algal diversity. Overall, a dominance of gastropods was observed for the two-dimensional, leaf-like P. palmata, while the three-dimensionally structured species (M. stellatus, E. elongata) were characterized by a dominance of amphipods. Stable isotopes highlighted different trophic structures; E. elongata-associated assemblages were most likely relying on a dominant food source, sediment organic matter, while other assemblages were based on a wider diversity of food sources (algae, sediment, suspended organic matter). Our results illustrate the need to consider the microhabitats formed by understorey macroalgae in order to thoroughly assess the diversity and understand the functioning of coastal rocky ecosystems.