Influence of sponge morphology on the composition of the polychaete associated fauna from Rocas Atoll,northeast Brazil

The relationships between the morphology of sponges and variables describing their harbored polychaete fauna were analyzed along Rocas, the only known South Atlantic Atoll, together with the location on host and feeding habits. The identification and quantification of all the associated organisms highlighted the dominance of polychaetes. The adults of the symbiotic species Haplosyllis spongicola were the most dominant sponge endobionts. However, both juveniles and epitokes (reproductive individuals) of H. spongicola were also found, suggesting that this species completes its life cycle inside the host. Polychaete density was significantly greater in lobate sponges than in massive and encrusting forms. Conversely, the highly specific symbiotic mode of life of H. spongicola species seems to play a major role in structuring the composition of the polychaete fauna in relation to sponge morphotypes along Rocas Atoll.     

Nitrification in intertidal sponge <Emphasis Type="Italic">Cinachyrella cavernosa</Emphasis>

The nitrification process in different sections of the sponges remains unresolved, despite several studies on the nitrogen cycling pathways in the tissues of temperate and Arctic sponges. In this study, the abundance, diversity and activity of the associated nitrifying organisms in intracellular, intercellular, extracellular and cortex of a tropical intertidal sponge, Cinachyrella cavernosa, were investigated using most probable number, next-generation sequencing and incubation method, respectively. The nitrification rate and the abundance of nitrifying bacteria showed significant difference among different sections. The nitrification rate in C. cavernosa was 2–12× higher than the reported values in other sponge species from temperate and Arctic regions. Nitrification rate in sponge cortex was 2× higher than in intercellular and extracellular sections. Ammonium and nitrite oxidisers ranged from 10³ to 10⁴ CFU g^?1 in the sponge with a high number of ammonium and nitrite oxidisers in the cortex. Nitrifiers belonging to Nitrosomonas, Nitrospira, Nitrospina, Nitrobacter and Nitrosopumilus were present in different sections of the sponge, with nitrifying archaea dominating the intracellular section and nitrifying bacteria dominating other sections. This study reports for the first time the nitrification inside the sponge cells. The study also suggests that the intertidal sponge, C. cavernosa, harbours metabolically active nitrifiers in different sections of the sponge body with different rates of nitrification. Thus, nitrifiers play an important role in ammonia detoxification within the sponge and also contribute to the nitrogen budget of the coastal ecosystem.     

The potential of azooxanthellate poriferan hosts to assess the fundamental and realized <Emphasis Type="Italic">Symbiodinium</Emphasis> niche: evaluating a novel method to initiate <Emphasis Type="Italic">Symbiodinium</Emphasis> associations

On coral reefs, Symbiodinium spp. are found in most cnidarian species, but reside in only a small number of sponge species. Of the sponges that do harbor Symbiodinium, most are found in the family Clionaidae, which represents a minor fraction of the poriferan diversity on a reef. Our goal was to determine whether Symbiodinium can be taken up by sponge hosts that do not typically harbor these algal symbionts, and then to follow the fate of any Symbiodinium that enter the intracellular space. We used the filter-feeding capacity of sponges to initiate intracellular interactions between sponge-specialist clade G Symbiodinium and six sponge species that do not associate with Symbiodinium. Using a pulse-chase experimental design, we determined that all of the species we examined captured Symbiodinium, and undamaged intracellular algae were found up to 1 h after inoculation. In a longer-term experiment, Symbiodinium populations in Amphimedon erina persisted in sponge cells for at least 5 d post-inoculation. While no evidence of digestion was detected, the population decreased exponentially after inoculation. We contrast these data with the characteristics of symbiont acquisition and establishment in Cliona varians, which normally harbors Symbiodinium. Explants from experimentally derived aposymbiotic sponges were placed in the field where they acquired Symbiodinium from ambient sources (i.e., we did not inoculate them as in the pulse-chase experiments). We began to detect Symbiodinium cells in C. varians after 12 d, and the algal population increased exponentially until densities approached those typically found in this host (after ~128 d). We discuss the implications of this work in light of growing interest in the evolution of specificity between hosts and symbionts, and the fundamental and realized niche of Symbiodinium.     

Phylogenetic relationships and intraspecific diversity of a North Patagonian Fescue: evidence of differentiation and interspecific introgression at peripheral populations

Peripheral sites usually offer suboptimal conditions for species with wide distributions, where expression of phenotypic variability and potential interspecific hybridization might be enhanced. The Patagonian steppe, the largest and southernmost dryland ecosystem in South America, is characterized by natural rangelands dominated by grasses. Festuca pallescens is a keystone species with a wide distribution in Patagonia over diverse environments reaching the extreme arid zones in the Somuncura plateau, a biogeographical island. Our aim is to study the phylogenetic relationships among Festuca pallescens populations as well as between this species and the sympatric F. argentina in North Patagonia. We analysed fourteen populations along a west-east transect of about 500 km in North Patagonia with three types of molecular markers: ITS, chloroplast trnL-F and eight nuclear microsatellites. Bayesian inferences, maximum parsimony and maximum likelihood analyses with trnL-F and ITS showed that F. pallescens is related to the Patagonian clade within the Festuca phylogeny. However, the easternmost populations of F. pallescens at Somuncura plateau were highly differentiated from the other populations and clustered with F. argentina (a sympatric species of the Asian-American clade). Principal coordinates analyses and Bayesian clustering performed with nuclear microsatellites as well as morphoanatomical traits, showed an intermediate position of one of these easternmost populations with respect to the two species, suggesting admixture. The high genetic variability observed in these peripheral populations highlight their relevance for conservation and might be indicating the existence of evolutionary processes triggering events of speciation in the Patagonian fescues.     

Identifying miRNA sponge modules using biclustering and regulatory scores

Background

MicroRNA (miRNA) sponges with multiple tandem miRNA binding sequences can sequester miRNAs from their endogenous target mRNAs. Therefore, miRNA sponge acting as a decoy is extremely important for long-term loss-of-function studies both in vivo and in silico. Recently, a growing number of in silico methods have been used as an effective technique to generate hypotheses for in vivo methods for studying the biological functions and regulatory mechanisms of miRNA sponges. However, most existing in silico methods only focus on studying miRNA sponge interactions or networks in cancer, the module-level properties of miRNA sponges in cancer is still largely unknown.

Results

We propose a novel in silico method, called miRSM (miRNA Sponge Module) to infer miRNA sponge modules in breast cancer. We apply miRSM to the breast invasive carcinoma (BRCA) dataset provided by The Cancer Genome Altas (TCGA), and make functional validation of the computational results. We discover that most miRNA sponge interactions are module-conserved across two modules, and a minority of miRNA sponge interactions are module-specific, existing only in a single module. Through functional annotation and differential expression analysis, we also find that the modules discovered using miRSM are functional miRNA sponge modules associated with BRCA. Moreover, the module-specific miRNA sponge interactions among miRNA sponge modules may be involved in the progression and development of BRCA. Our experimental results show that miRSM is comparable to the benchmark methods in recovering experimentally confirmed miRNA sponge interactions, and miRSM outperforms the benchmark methods in identifying interactions that are related to breast cancer.

Conclusions

Altogether, the functional validation results demonstrate that miRSM is a promising method to identify miRNA sponge modules and interactions, and may provide new insights for understanding the roles of miRNA sponges in cancer progression and development.

     

Does allelopathy affect co-culturing <Emphasis Type="Italic">Haslea ostrearia</Emphasis> with other microalgae relevant to aquaculture?

Haslea ostrearia is a marine diatom known to produce marennine, a water-soluble blue-green pigment responsible for the greening of oysters in ponds along the French Atlantic coast. This phenomenon occurs seasonally when H. ostrearia blooms in oyster ponds, and it increases the economic value of cultured oysters. From an ecological perspective, H. ostrearia blooms are accompanied by a decrease in the abundance of other microalgae, suggesting that this diatom produces allelochemicals. Recent studies showed that purified marennine has other biological activities, for instance antioxidant, antibacterial, and antiviral activities, which could be used in aquaculture to promote this pigment as a natural antipathogen agent. One important issue regarding the possible use of H. ostrearia in aquaculture as a mixed algal diet, however, is the importance of marennine allelopathy. In this study, we investigated the allelopathic effect of H. ostrearia on the growth of five microalgal species relevant to aquaculture: Chaetoceros calcitrans, Skeletonema costatum, Phaeodactylum tricornutum, Tetraselmis suecica, and Tisochrysis lutea. Allelopathic tests were realized by co-culturing these microalgae with H. ostrearia in batch and in semi-continuous mode, based on initial biovolume ratios. Our findings showed that inhibition of the growth of microalgae due to the presence of H. ostrearia and marennine was species dependent. Skeletonema costatum, C. calcitrans, and T. lutea were significantly more sensitive, whereas T. suecica and P. tricornutum appeared to be more resistant. Growth irradiance significantly influenced the allelopathic effect against the sensitive species S. costatum, and the H. ostrearia production of marennine increases with irradiance. Data presented in this study partly support the hypothesis that marennine released into the culture medium possibly acts as an allelochemical compound, thus explaining the dominance of H. ostrearia and the loss of sensitive algae in oyster ponds, but also that some species are insensitive, which allows co-culturing and use in a mixed algal diet in aquaculture.     

Experimental study of the ability of the sponge <Emphasis Type="Italic">Halichondria panicea</Emphasis> (Porifera: Demospongiae) to compete for a substrate in shallow-water fouling communities of the White Sea

The ability of the sponge Halichondria panicea to assimilate into the fouling communities of the blue mussel Mytilus edulis and the solitary ascidian Styela rustica has been studied in a field experiment, in which sponge fragments have been introduced artificially into epibenthic communities. The growth of H. panicea was suppressed greatly in the presence of young mussels; its survival rate averaged 40%. In the communities where S. rustica dominated, the survival rate of H. panicea reached 100%, but the growth rate was lower than in the control group (without competitor species). Despite the high natural growth rate and toxicity, the settlement success of H. panicea was low on the substrate occupied by another fouling species.     

Interactions of Algae within the Community of <Emphasis Type="Italic">Gracilaria gracilis</Emphasis> (Rhodophyta)

Interactions among the unattached red alga Gracilaria gracilis, the dominant species of an algal community, and associated algal species Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. were studied during and after an algal bloom. It was shown that during their bloom the associated algae Enteromorpha and Polysiphonia sp. significantly decreased the photosynthetic rate of G. gracilis but did not affect its growth rate. It is suggested that the inhibition of Gracilaria gracilis photosynthesis is connected to the impact of extracellular metabolites excreted by Chaetomorpha linum, Enteromorpha prolifera f. prolifera, and Polysiphonia sp. In laboratory experiments, the photosynthetic rate of the associated species was enhanced in the presence of Gracilaria. However, no significant alterations were observed in the content of chlorophyll a, growth, and the dark respiration rates of associated algae when they were kept together with Gracilaria. It was suggested that allelopathic interactions observed among algal species during the formation of the monospecific Gracilaria community, as well as during algal blooms, are not determinative.     

Upper Triassic (Norian) hypercalcified sponges from the Musandam Peninsula (United Arab Emirates and Oman)

Supercalcified sponges, including sphinctozoans, inozoans, chaetetids, spongiomorphids, occurring in Upper Triassic (Norian-Rhaetian) shallow-marine limestones of Musandam Mountains in United Arab Emirates (UAE), are described. The following taxa were determined: sphinctozoans: Hajarispongia osmani Senowbari-Daryan and Yancey, Nevadathalamia arabica n. sp., Nevadathalamia conica n. sp., Fanthalamia milahaensis n. sp., Iranothalamia incrustans (Boiko), Cinnabaria regularis n. sp.; inozoans: Cavsonella triassica n. sp., Molengraaffia regularis Vinassa de Regny, Peronidella? sp., Circopora cf. caucasica Moiseev, Circopora? sp.; spongiomorphids: Spongiomorpha sp.; chaetetids: Lovcenipora chaetetiformis Vinassa de Regny, Lovcenipora musandamensis n. sp., Lovcenipora sp., chaetetid sponge gen. et sp. indet. The most abundant sponge in the studied material is Nevadathalamia arabica n. sp. The described sponge association of the Arabian shelf (Musandam Mountains) shows close affinity to the sponge association known from age-equivalent terranes in the Panthalassa Ocean (Sonora Mountains in Mexico; Pilot Mountains in Nevada, USA), but is remarkably different from sponge associations in carbonates bordering the Tethys. This difference goes along with the biogeography of wallowaconchid bivalves and is most likely attributed to climatic, palaeogeographic or oceanographic factors.     

Unique configuration of genes of silicon transporter in the freshwater pennate diatom <Emphasis Type="Italic">Synedra acus</Emphasis> subsp. <Emphasis Type="Italic">radians</Emphasis>

The existence of the cluster of duplicated sit silicon transporter genes in the chromosome of the diatom Synedra acus subsp. radians was shown for the first time. Earlier, the localization of sit genes in the same chromosome and cluster formation caused by gene duplication was shown only for the marine raphid pennate diatom P. tricornutum. Only non-clustered sit genes were found in the genomes of other diatoms. It is reasonable to assume that sit tandem (sit-td) and sit triplet (sit-tri) genes of S. acus subsp. radians occurred as a result of gene duplication followed by divergence of gene copies.     

Population surveys of fork-marked dwarf lemurs and needle-clawed galagos

Fork-marked dwarf lemurs (Phaner spp.) of Madagascar and the needle-clawed galagos (Euoticus spp.) of Central-West Africa are two genera within the primate suborder Strepsirrhini. Despite their distant relationship, these genera share remarkably convergent anatomical, behavioural and ecological characteristics. However, like most nocturnal primates in sub-Saharan Africa they are poorly studied and little is known about the population estimates of both genera. I conducted surveys of wild populations of Phaner pallescens, P. parienti and P. furcifer in Madagascar as well as Euoticus elegantulus and E. pallidus in Cameroon. Six transects were established in Madagascar covering a total distance of 20 km, within which I encountered 52 fork-marked dwarf lemurs. In Cameroon three transects were established covering a total distance of 8.5 km, and 56 encounters of needle-clawed galagos were made. Population encounter rates of P. pallescens, P. parienti, P. furcifer, E. elegantulus and E. pallidus were 3.3, 2.4, 2.3, 9.9 and 8.3 individuals per kilometre, respectively. Compared to previous estimates of population encounter rates in other study sites, these values are lower. Low population encounter rates of fork-marked dwarf lemurs and needle-clawed galagos may be due to environmental and anthropogenic pressures at the study sites. Further ecological, behavioural and conservation studies are required for these genera.     

Molecular phylogeny of a green microalga isolated from White Sea sponge <Emphasis Type="Italic">Halichondria panicea</Emphasis> (Pallas, 1766)

Molecular identification of eukaryotic microalga 1Hp86E-2 isolated from White Sea sponge Halichondria panicea (Pallas, 1766) was conducted, and phylogenetic analysis was carried out using the nucleotide sequence of 18S rRNA gene (GenBank, no. JX437624). Isolated microalga was classified to the genus Desmodesmus. Microalga 1Hp86E-2 proved to be closely related to the algae Desmodesmus sp. 3Dp86E-1, Desmodesmus sp. 2C166E, and Desmodesmus sp. 1Pm66B isolated from White Sea invertebrates. Phylogenetic analysis showed that these closely related organisms belong to a monophyletic group.     

Diatoms (Bacillariophyceae) associated with free-drifting Antarctic icebergs: taxonomy and distribution

Free-drifting Antarctic icebergs can alter the phytoplankton in surrounding waters. In addition, diatom mats live attached to the submerged walls of the icebergs. In this study we describe a diverse diatom community associated with these mats and an atypical planktonic community in waters affected by icebergs. Samples were collected in the winter of 2008 and fall of 2009 from Antarctic icebergs and their adjacent waters, utilizing a remote operated vehicle and plankton nets, respectively, and subsequently analyzed using light and electron microscopy. Thalassioneis signyensis, dominant species growing on the icebergs’ flanks, provided substrate for other diatoms, mainly Synedropsis lata var. angustata, Synedropsis recta, Fragilaria cf. islandica var. adeliae, Attheya gaussii, Navicula cf. perminuta, Amphora sp. and Nitzschia spp. New morphological characteristics are given for S. lata var. angustata, S. recta and A. gaussii. We report also Biddulphia alternans and Coscinodiscus concinnus for the first time in Antarctic waters. Similar to sea ice algae, the term sympagic is used to describe the habitat of these diatom communities. A particular planktonic community is also found close to icebergs, including diatoms known to have a benthic, epiphytic, sympagic or freshwater habitat: Amphora sp., B. alternans, Cocconeis spp., Delphineis minutissima, Licmophora gracilis, Luticola cf. australomutica, Opephora sp., Pinnularia spp., Plagiogramma sp., Psammodictyon panduriforme var. minor, Pseudogomphonema kamtschaticum, Rhaphoneis amphiceros, S. recta and T. signyensis. Our results support the hypothesis that species associated with icebergs exchange freely with plankton, ice shelves and sea ice, suggesting that icebergs can act as physical agents to transport and distribute organisms in between these habitats.     

Variability in chemical defense across a shallow to mesophotic depth gradient in the Caribbean sponge <Emphasis Type="Italic">Plakortis angulospiculatus</Emphasis>

The transition between shallow and mesophotic coral reef communities in the tropics is characterized by a significant gradient in abiotic and biotic conditions that could result in potential trade-offs in energy allocation. The mesophotic reefs in the Bahamas and the Cayman Islands have a rich sponge fauna with significantly greater percent cover of sponges than in their respective shallow reef communities, but relatively low numbers of spongivores. Plakortis angulospiculatus, a common sponge species that spans the depth gradient from shallow to mesophotic reefs in the Caribbean, regenerates faster following predation and invests more energy in protein synthesis at mesophotic depths compared to shallow reef conspecifics. However, since P. angulospiculatus from mesophotic reefs typically contain lower concentrations of chemical feeding deterrents, they are not able to defend new tissue from predation as efficiently as conspecifics from shallow reefs. Nonetheless, following exposure to predators on shallow reefs, transplanted P. angulospiculatus from mesophotic depths developed chemical deterrence to predatory fishes. A survey of bioactive extracts indicated that a specific defensive metabolite, plakortide F, varied in concentration with depth, producing altered deterrence between shallow and mesophotic reef P. angulospiculatus. Different selective pressures in shallow and mesophotic habitats have resulted in phenotypic plasticity within this sponge species that is manifested in variable chemical defense and tissue regeneration at wound sites.     

Hypercalcified segmented sponges (“sphinctozoans”) from the Upper Triassic (Norian) reef boulders of Taurus Mountains (southern Turkey)

Upper Triassic Norian reef boulders, exposed in a locality near the fountain “Tavuk Cesme” (“Chicken Fountain”) in Taurus Mountains, southern Turkey yielded a large number of hypercalcified sponges, including “sphinctozoans”, “inozoans”, “spongiomorphids”, and “chaetetids”. The sphinctozoans from this locality are described in this paper. Geologically, this locality belongs to the Anamas-Akseki autochthonous. The reef boulders of this locality are exposed near the “Tavuk Cesme” fountain, located at the road, leading from the town of Aksu to Yenisarbademli. The following taxa are described: Amblysiphonella taurica nov. sp., Anthalythalamia riedeli Senowbari-Daryan, Calabrisiphonella sphaerica nov. sp., Calabrisiphonella cuifi nov. sp., Cinnabaria minima Senowbari-Daryan, Colospongia recta nov. sp., Colospongia sp. 1, Colospongia sp. 2, Colospongia sp. 3, Cryptocoelia compacta nov. sp., Cryptocoelia? sp., Deningeria crassireticulata Senowbari-Daryan, Zühlke, Bechstädt and Flügel, Discosiphonella minima Senowbari-Daryan and Link, Gigantothalamia ovoidalis Senowbari-Daryan, Hajarispongia dipoyrazensis nov. sp., Hajarispongia cortexifera nov. sp., Kashanella irregularis Senowbari-Daryan, Kashanella cylindrica nov. sp., Parauvanella ferdowsensis Senowbari-Daryan, Parastylothalamia cylindrica nov. gen., nov. sp., Asiphothalamia polyosculata nov. gen, nov. sp., Sollasia norica nov. sp., and Thaumastocoelia sphaeroida Senowbari-Daryan. The most abundant sponge is Amblysiphonella taurica nov. sp. followed by Hajarispongia dipoyrazensis nov. sp., Colospongia and Discosiphonella minima Senowbari-Daryan and Link are also relatively abundant. The stylothalamid sponge Parastylothalamia nov. gen. is an abundant sponge genus in other Norian reefs of the Taurus Mountains, but is rare at the “Tavuk Cesme” locality.     

Transformation of Baikal sponges (family Lubomirskiidae) after penetration into the Angara River

Genetic and morphological analysis of endemic sponges of the Lubomirskiidae family from Lake Baikal and the upper reaches of the Angara River was performed. Various sponge species acquired a number of similar morphological traits after the transition from the lake into the river. These traits enabled an increase of sponge skeleton strength under the conditions of elevated hydrodynamic activity. The changes significantly impeded morphology-based species identification of Angara sponges. Phylogenetic analysis of ITS regions and noncoding mitochondrial DNA fragments confirmed that the Angara sponges belonged to the Baikalian Lubomirskiidae family and demonstrated the polyphyletic origin of the sponges. The use of combined molecular and morphological data allowed for the clustering of some sponge samples into groups that corresponded to individual species. The absence of genetic isolation between the Baikalospongia intermedia and Lubomirskia baicalensis species was demonstrated, whereas the B. intermedia profundalis subspecies was well separated from B. intermedia. This finding pointed to the necessity of further studies for the clarification of the taxonomic status of this subspecies.     

Metatrancriptomic analysis from the Hepatopancreas of adult white leg shrimp (<Emphasis Type="Italic">Litopenaeus vannamei)</Emphasis>

The amoeba, Mayorella viridis contains several hundred symbiotic green algae in its cytoplasm. Transmission electron microscopy revealed strong resemblance between symbiotic algae from M. viridis the symbiotic Chlorella sp. in the perialgal vacuoles of Paramecium bursaria and other ciliates. Although it is thought that the M. viridis and symbiotic algae could be model organisms for studying endosymbiosis between protists and green algae, few cell biological observations of the endosymbiosis between M. viridis and their symbiotic algae have been published. In this study, we characterized the specificity of endosymbiotic relationships between green algae and their hosts. Initially, we established stable cultures of M. viridis in KCM medium by feeding with Chlorogonium capillatum. Microscopic analyses showed that chloroplasts of symbiotic algae in M. viridis occupy approximately half of the algal cells, whereas those in P. bursaria occupy entire algal cells. The symbiotic algae in P. bursaria contain several small spherical vacuoles. The labeling of actin filaments using Acti-stain? 488 Fluorescent Phalloidin revealed no relationship between host actin filaments and symbiotic algal localization, although the host mitochondria were localized around symbiotic algae. Symbiotic algae from M. viridis could infect algae-free P. bursaria but could not support P. bursaria growth without feeding, whereas the original symbiotic algae of P. bursaria supported its growth without feeding. These data indicated the specificity of endosymbiotic algae relationships in M. viridis and P. bursaria.     

New and little-known crickets of the subfamily Phalangopsinae (Orthoptera,Gryllidae). 11. The genus <Emphasis Type="Italic">Parendacustes</Emphasis> (Part 2)

Discussions concerning the composition of the genus Parendacustes Chop., in particular, its subgenus Minizacla Gor., are continued. Eleven new taxa of this subgenus are described: P. trusmadi sp. n., P. mulu sp. n., P. brevispina sp. n., P. modispina sp. n., P. longispina sp. n., P. forficula sabah subsp. n., P. doloduo sp. n., P. buton sp. n., P. pallescens sp. n., P. kendari sp. n., and P. lindu sp. n. New data on P. makassari Gor. are also provided.