The Evolution of Calcification in Reef-Building Corals

Corals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.     

Biogeography and Change among Regional Coral Communities across the Western Indian Ocean

Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions.     

Plankton Biogeography of the Indian Ocean

Knowledge of plankton biogeography for the Indian and adjacent seas is necessary for an understanding of the regional characteristics and changes in the plankton composition. Some of the plankters will serve as good biogeographical indicator species. Some phytoplankters and tintinnids among zooplankton are promising for use as such labels for the presence of different waters in the Porto Novo (Coromandel coast, Bay of Bengal) region. A biogeographical classification of the local phytoplankton and peculiarities in the distribution of some rare tintinnids occurring there are discussed.     

Adaptive Evolution of Multicolored Fluorescent Proteins in Reef-Building Corals

Here we investigate the evolutionary scenarios that led to the appearance of fluorescent color diversity in reef-building corals. We show that the mutations that have been responsible for the generation of new cyan and red phenotypes from the ancestral green were fixed with the help of positive natural selection. This fact strongly suggests that the color diversity is a product of adaptive evolution. An unexpected finding was a set of residues arranged as an intermolecular binding interface, which was also identified as a target of positive selection but is nevertheless not related to color diversification. We hypothesize that multicolored fluorescent proteins evolved as part of a mechanism regulating the relationships between the coral and its algal endosymbionts (zooxanthellae). We envision that the effect of the proteins’ fluorescence on algal physiology may be achieved not only through photosynthesis modulation, but also through regulatory photosensors analogous to phytochromes and cryptochromes of higher plants. Such a regulation would require relatively subtle, but spectrally precise, modifications of the light field. Evolution of such a mechanism would explain both the adaptive diversification of colors and the coevolutionary chase at the putative algae-protein binding interface in coral fluorescent proteins. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Rasmus Neilsen]     

Reef-Building Corals and Reefs of Vietnam: 2. The Gulf of Tonkin

This paper deals with the history and results of the studies of reefs and coral communities of the Gulf of Tonkin based on published and unpublished materials, including the author's. The state of the art in the study of reef-building scleractinian corals and reefs of this region is reported. The peculiar nature of the reefs studied is caused by the monsoon climate in the region and river runoff waters cooled to 16–18°C, silted to 100 g/m2 per day, and freshened to 28‰ in the wintertime, i.e., conditions far from optimum for reef formation. The silting and eutrophication of the gulf waters resulted in a change in the composition and structure of the coral reef communities via the reduction or elimination of certain coral species. Instead of acroporids, typical for the majority of other reefs, reef communities of the Gulf of Tonkin are dominated by poritids and faviids, which form the framework of the reefs. These peculiarities make the reefs of the Gulf of Tonkin really unique.     

Reef-Building Corals and Reefs of Vietnam: 1. The Gulf of Thailand

This paper deals with the history and investigations of the reefs and coral communities of the Gulf of Thailand based on published and unpublished materials, including the author's. The state of the art in the study of reef-building scleractinian corals and reefs of this region is presented. Characterized by remarkable distinctive features, the coral fauna and reefs of the Gulf of Thailand exhibit high similarity in coral species composition to other regions of Vietnam and form a single complex of species of the equatorial Indo-Pacific.     

Application of 1H-NMR Metabolomic Profiling for Reef-Building Corals

In light of global reef decline new methods to accurately, cheaply, and quickly evaluate coral metabolic states are needed to assess reef health. Metabolomic profiling can describe the response of individuals to disturbance (i.e., shifts in environmental conditions) across biological models and is a powerful approach for characterizing and comparing coral metabolism. For the first time, we assess the utility of a proton-nuclear magnetic resonance spectroscopy (¹H-NMR)-based metabolomics approach in characterizing coral metabolite profiles by 1) investigating technical, intra-, and inter-sample variation, 2) evaluating the ability to recover targeted metabolite spikes, and 3) assessing the potential for this method to differentiate among coral species. Our results indicate ¹H-NMR profiling of Porites compressa corals is highly reproducible and exhibits low levels of variability within and among colonies. The spiking experiments validate the sensitivity of our methods and showcase the capacity of orthogonal partial least squares discriminate analysis (OPLS-DA) to distinguish between profiles spiked with varying metabolite concentrations (0 mM, 0.1 mM, and 10 mM). Finally, ¹H-NMR metabolomics coupled with OPLS-DA, revealed species-specific patterns in metabolite profiles among four reef-building corals (Pocillopora damicornis, Porites lobata, Montipora aequituberculata, and Seriatopora hystrix). Collectively, these data indicate that ¹H-NMR metabolomic techniques can profile reef-building coral metabolomes and have the potential to provide an integrated picture of the coral phenotype in response to environmental change.     

Reef-Building Corals of Vietnam as a Part of the Indo-Pacific Reef Ecosystem

The paper analyzes both published and unpublished results of the investigations of Vietnamese reef-building corals and reefs performed in the last decades of the twentieth century. The state of the art in the study of reef-building scleractinian corals and reefs is presented. The scleractinian fauna of Vietnam is shown to match in species diversity (366 species of 70 genera) the tropical coral fauna of the Indonesian-Malacca fertile center, from which Indo-Pacific reef-building corals originated. The whole Vietnam coast from the Gulf of Tonkin to the Gulf of Siam is a biogeographically single whole and is a part of the Indo-Polynesian Province of the Indo-Pacific Area.     

Biogeography of Southern Ocean prokaryotes: a comparison of the Indian and Pacific sectors

We investigated the Southern Ocean (SO) prokaryote community structure via zero-radius operational taxonomic unit (zOTU) libraries generated from 16S rRNA gene sequencing of 223 full water column profiles. Samples reveal the prokaryote diversity trend between discrete water masses across multiple depths and latitudes in Indian (71–99°E, summer) and Pacific (170–174°W, autumn-winter) sectors of the SO. At higher taxonomic levels (phylum-family) we observed water masses to harbour distinct communities across both sectors, but observed sectorial variations at lower taxonomic levels (genus-zOTU) and relative abundance shifts for key taxa such as Flavobacteria, SAR324/Marinimicrobia, Nitrosopumilus and Nitrosopelagicus at both epi- and bathy-abyssopelagic water masses. Common surface bacteria were abundant in several deep-water masses and vice-versa suggesting connectivity between surface and deep-water microbial assemblages. Bacteria from same-sector Antarctic Bottom Water samples showed patchy, high beta-diversity which did not correlate well with measured environmental parameters or geographical distance. Unconventional depth distribution patterns were observed for key archaeal groups: Crenarchaeota was found across all depths in the water column and persistent high relative abundances of common epipelagic archaeon Nitrosopelagicus was observed in deep-water masses. Our findings reveal substantial regional variability of SO prokaryote assemblages that we argue should be considered in wide-scale SO ecosystem microbial modelling.     

印度洋可培养解有机磷细菌的多样性及解磷特性

【目的】筛选获得印度洋海水解有机磷细菌,研究其解有机磷作用机理,初步了解该地区可培养有机磷细菌的系统发育多样性。【方法】采用卵磷脂培养基从分离自印度洋的细菌中筛选解有机磷细菌,根据16S rRNA基因序列确定获得的有机磷细菌的分类地位;同时挑选解磷效果显著的3株细菌利用液体发酵进行产酶和解磷特性分析。【结果】自916株细菌中得到99株具有解有机磷活性的细菌,分属于16个属。在以卵磷脂为其有机磷来源时,菌株India-BSP-1 (Cobetia sp.)、India-BSP-21 (Pelagibaca sp.)、India-BSP-23 (Pelagibacterium sp.)的培养液中磷酸盐(DIP)浓度曲线为N型,并且碱性磷酸酶的检测活性滞后于DIP的生成。【结论】印度洋海水中解有机磷细菌种类多样性丰富,疑似有新种;解有机磷细菌的解磷特性受DIP和碱性磷酸酶相互作用的影响。     

Biogeography and diversification of hermit spiders on Indian Ocean islands (Nephilidae: Nephilengys)

The origin of the terrestrial biota of Madagascar and, especially, the smaller island chains of the western Indian Ocean is relatively poorly understood. Madagascar represents a mixture of Gondwanan vicariant lineages and more recent colonizers arriving via Cenozoic dispersal, mostly from Africa. Dispersal must explain the biota of the smaller islands such as the Comoros and the chain of Mascarene islands, but relatively few studies have pinpointed the source of colonizers, which may include mainland Africa, Asia, Australasia, and Madagascar. The pantropical hermit spiders (genus Nephilengys) seem to have colonized the Indian Ocean island arc stretching from Comoros through Madagascar and onto Mascarenes, and thus offer one opportunity to reveal biogeographical patterns in the Indian Ocean. We test alternative hypotheses on the colonization route of Nephilengys spiders in the Indian Ocean and simultaneously test the current taxonomical hypothesis using genetic and morphological data. We used mitochondrial (COI) and nuclear (ITS2) markers to examine Nephilengys phylogenetic structure with samples from Africa, southeast Asia, and the Indian Ocean islands of Madagascar, Mayotte, Réunion and Mauritius. We used Bayesian and parsimony methods to reconstruct phylogenies and haplotype networks, and calculated genetic distances and fixation indices. Our results suggest an African origin of Madagascar Nephilengys via Cenozoic dispersal, and subsequent colonization of the Mascarene islands from Madagascar. We find strong evidence of gene flow across Madagascar and through the neighboring islands north of it, while phylogenetic trees, haplotype networks, and fixation indices all reveal genetically isolated and divergent lineages on Mauritius and Réunion, consistent with female color morphs. These results, and the discovery of the first males from Réunion and Mauritius, in turn falsify the existing taxonomic hypothesis of a single widespread species, Nephilengys borbonica, throughout the archipelago. Instead, we diagnose three Nephilengys species: Nephilengys livida (Vinson, 1863) from Madagascar and Comoros, N. borbonica (Vinson, 1863) from Réunion, and Nephilengys dodo new species from Mauritius. Nephilengys followed a colonization route to Madagascar from Africa, and on through to the Mascarenes, where it speciated on isolated islands. The related golden orb-weaving spiders, genus Nephila, have followed the same colonization route, but Nephila shows shallower divergencies, implying recent colonization, or a moderate level of gene flow across the archipelago preventing speciation. Unlike their synanthropic congeners, N. borbonica and N. dodo are confined to pristine island forests and their discovery calls for evaluation of their conservation status.     

Influenza A Virus on Oceanic Islands: Host and Viral Diversity in Seabirds in the Western Indian Ocean

Ducks and seabirds are natural hosts for influenza A viruses (IAV). On oceanic islands, the ecology of IAV could be affected by the relative diversity, abundance and density of seabirds and ducks. Seabirds are the most abundant and widespread avifauna in the Western Indian Ocean and, in this region, oceanic islands represent major breeding sites for a large diversity of potential IAV host species. Based on serological assays, we assessed the host range of IAV and the virus subtype diversity in terns of the islands of the Western Indian Ocean. We further investigated the spatial variation in virus transmission patterns between islands and identified the origin of circulating viruses using a molecular approach. Our findings indicate that terns represent a major host for IAV on oceanic islands, not only for seabird-related virus subtypes such as H16, but also for those commonly isolated in wild and domestic ducks (H3, H6, H9, H12 subtypes). We also identified strong species-associated variation in virus exposure that may be associated to differences in the ecology and behaviour of terns. We discuss the role of tern migrations in the spread of viruses to and between oceanic islands, in particular for the H2 and H9 IAV subtypes.     

Reef-Building Corals—Symbiotic Autotrophic Organisms: 2. Pathways and Mechanisms of Adaptation to Light

Ways, mechanisms, and responses of ontogenetic adaptation of reef-building corals to light are discussed on the basis of original and literature data. The possible ways of photoacclimation of corals within the range of tolerance to light are shown: (1) adaptation to bright light (>70% incident photosynthetic active radiation, PAR_s), (2) adaptation to moderate shade (50–10% PAR_s), and (3) adaptation to extremely low light (<5% PAR_s). In each of the ways, general and specific mechanisms and reactions are involved in photoacclimation of corals. Adaptive changes take place in plant (zooxanthellae) and animal (polyps) components of the symbiotic organism. They involve morphology, physiology, and biochemistry of colonial polyps and their zooxanthellae. During changes of the light regime, some adaptive reactions last several months and others occur within a few days. Some physiological and biochemical alterations occur as early as the next day after the light regime changes. The wide range of light tolerance of corals and a great number of mechanisms and reactions of photoacclimation allowing corals to adapt to bright and low light with minimum losses in their metabolic activity give grounds to classify them as a single ecological group of light- and shade-tolerant organisms.     

印度洋表层海水石油降解菌的多样性分析

【目的】为了研究印度洋石油降解菌多样性,并获得新的石油降解菌。【方法】本研究通过印度洋表层海水样品采集、以柴油与原油1:1混合物作为碳源,从中富集、分离筛选石油降解菌,并通过PCR-DGGE对13个站点富集菌群的菌群结构进行分析。【结果】通过形态观察、生理生化反应和16SrRNA分析,共得到共29个属的51株不同的细菌,它们主要是属于α亚群和γ亚群。其中,Alcanivorax属(占18%),Novosphingobium属(占10%)和Marinobacter(占6%)Thalassospira(占6%)为主要的优势菌。通过生态多样性分析表明,Shannon-Winner指数(H)为4.57968,说明其具有较高的多样性;均匀度指数(E)为0.8664771,表示其分布比较均匀。单菌实验表明,49株具有石油降解能力其中,Sinomonas,Knoellia,Mesoflavibacter等属的细菌为首次发现有降解能力。DGGE分析表明Alcanivorax属的细菌是印度洋表层海水中的重要石油降解菌。【结论】本研究首次揭示了印度洋表层海水中石油降解菌的多样性,并获取了若干在海洋石油污染生物修复中具有应用前景的降解菌。     

The Biogeography of Tropical Phytoplankton Species in the Pacific Ocean

The ranges of 10 tropical Pacific phytoplankton species are shown in the maps. Five types of these ranges are discussed. Except for broadly tropical species some species with much narrower ranges are characterized. The bases of ranges and the expatriation areas are given. The bases of ranges of all the species studied fall into similar temperature and salinity limits. Most of the species inhabit a wide range of nutrients concentration, but Climacodium frauenfeldianum and Hemiaulus hauckii are only found at low phosphate and silicate concentrations. These peculiarities determine the geography of ranges of these two species. Among the species investigated only Ceratium gravidum belongs to the shade flora.     

Phytoplankton Biogeography and Community Stability in the Ocean

Background

Despite enormous environmental variability linked to glacial/interglacial climates of the Pleistocene, we have recently shown that marine diatom communities evolved slowly through gradual changes over the past 1.5 million years. Identifying the causes of this ecological stability is key for understanding the mechanisms that control the tempo and mode of community evolution.

Methodology/Principal Findings

If community assembly were controlled by local environmental selection rather than dispersal, environmental perturbations would change community composition, yet, this could revert once environmental conditions returned to previous-like states. We analyzed phytoplankton community composition across >10⁴ km latitudinal transects in the Atlantic Ocean and show that local environmental selection of broadly dispersed species primarily controls community structure. Consistent with these results, three independent fossil records of marine diatoms over the past 250,000 years show cycles of community departure and recovery tightly synchronized with the temporal variations in Earth''s climate.

Conclusions/Significance

Changes in habitat conditions dramatically alter community structure, yet, we conclude that the high dispersal of marine planktonic microbes erases the legacy of past environmental conditions, thereby decreasing the tempo of community evolution.     

Microsatellite Markers and Genetic Diversity of Four Scleractinian Corals

Russian Journal of Marine Biology - Eighteen microsatellite sequences were isolated from Platygyra acuta through magnetic bead hybridization enrichment method, and the site primers were used to...     

Two peculiar new genera of Typhloplanoida from the Western Indian Ocean

Three new species and two new genera of Typhloplanoida from the Western Indian Ocean are described. Feanora brevicirrus gen. et.sp. n. is a member of the Trigonostomidae von Graff, 1905 sensu Den Hartog, 1964. It has a cirrus, paired ovovitellaria and an undifferentiated afferent duct. An excentric bursa opens in the fecundatorium and a large ovoid vesicle enters the afferent duct in its distal part. Gaziella pileola gen. et sp. n. and G. lacertosa sp.n. are two new members of the Promesostomidae Den Hartog, 1964. They have a long cirrus, ovovitellaria and a long muscular female duct with two excentrically placed sperm-receiving vesicles. Their most striking feature is the proboscis-like structure. Feanora and Gaziella are provisionally considered as genera incertae sedis within the resp. families.     

The Footprint of Continental-Scale Ocean Currents on the Biogeography of Seaweeds

Explaining spatial patterns of biological organisation remains a central challenge for biogeographic studies. In marine systems, large-scale ocean currents can modify broad-scale biological patterns by simultaneously connecting environmental (e.g. temperature, salinity and nutrients) and biological (e.g. amounts and types of dispersed propagules) properties of adjacent and distant regions. For example, steep environmental gradients and highly variable, disrupted flow should lead to heterogeneity in regional communities and high species turnover. In this study, we investigated the possible imprint of the Leeuwin (LC) and East Australia (EAC) Currents on seaweed communities across ~7,000 km of coastline in temperate Australia. These currents flow poleward along the west and east coasts of Australia, respectively, but have markedly different characteristics. We tested the hypothesis that, regional seaweed communities show serial change in the direction of current flow and that, because the LC is characterised by a weaker temperature gradient and more un-interrupted along-shore flow compared to the EAC, then coasts influenced by the LC have less variable seaweed communities and lower species turnover across regions than the EAC. This hypothesis was supported. We suggest that this pattern is likely caused by a combination of seaweed temperature tolerances and current-driven dispersal. In conclusion, our findings support the idea that the characteristics of continental-scale currents can influence regional community organisation, and that the coupling of ocean currents and marine biological structure is a general feature that transcends taxa and spatial scales.     

Are the Indonesian and Western Indian Ocean Coelacanths Conspecific: A Prediction

It is hypothesized that the ancestor of the extant western Indian Ocean and Indonesian populations of Latimeria was continuously distributed along the deeper coasts of massed Africa–Madagascar–Eurasia in early geologic time. The collision of India with Eurasia, roughly 50 MY ago, caused the formation of the Himalayan Mountains and subsequent developement of numerous rivers. The rivers, which flow down both coasts of India, and areas even further east, deposited, and continue to deposit, great amounts of silt along both coasts of India. The siltation destroyed possible coelacanth habitats, thus isolating coelacanth populations to the west of India from those to the east and allowing them to diverge.