Carbon and nitrogen cycling by Red Sea coral reef sponges

Sponges are dominant components of coral reefs where they fulfil a number of structural and functional roles that make them key ecosystems engineers. In particular, their high filtering capacity and association with diverse microbial communities enables sponges to moderate flows of organic matter and inorganic nutrients, thereby influencing the biogeochemical cycling of carbon (C) and nitrogen (N) on coral reefs. This cycling of C and N is central to understanding how coral reefs, some of the most productive and diverse ecosystems on Earth, can thrive in such nutrient poor environments. Studying the fluxes of organic matter and nutrients mediated by sponges is therefore essential to understanding coral reef ecosystem functioning. However, many of these fluxes are poorly understood. By investigating the mechanisms and rates at which sponges retain, transform, and transfer organic matter and inorganic nutrients within coral reef ecosystems, this thesis provides new insights into roles that sponges play in the biogeochemical cycling of C and N on coral reefs

Distance from a fishing community explains fish abundance in a no-take zone with weak compliance

There are numerous examples of no-take marine reserves effectively conserving fish stocks within their boundaries. However, no-take reserves can be rendered ineffective and turned into ‘paper parks’ through poor compliance and weak enforcement of reserve regulations. Long-term monitoring is thus essential to assess the effectiveness of marine reserves in meeting conservation and management objectives. This study documents the present state of the 15-year old no-take zone (NTZ) of South El Ghargana within the Nabq Managed Resource Protected Area, South Sinai, Egyptian Red Sea. Previous studies credited willing compliance by the local fishing community for the increased abundances of targeted fish within the designated NTZ boundaries compared to adjacent fished or take-zones. We compared benthic habitat and fish abundance within the NTZ and the adjacent take sites open to fishing, but found no significant effect of the reserve. Instead, the strongest evidence was for a simple negative relationship between fishing pressure and distance from the closest fishing village. The abundance of targeted piscivorous fish increased significantly with increasing distance from the village, while herbivorous fish showed the opposite trend. This gradient was supported by a corresponding negative correlation between the amount of discarded fishing gear observed on the reef and increasing distance from the village. Discarded fishing gear within the NTZ suggested decreased compliance with the no-take regulations. Our findings indicate that due to non-compliance the no-take reserve is no longer functioning effectively, despite its apparent initial successes and instead a gradient of fishing pressure exists with distance from the nearest fishing community

The sponge holobiont in a changing ocean: from microbes to ecosystems

The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. Animals, plants, and algae are now considered holobionts, complex ecosystems consisting of the host, the microbiota, and the interactions among them. Accordingly, ecological concepts can be applied to understand the host-derived and microbial processes that govern the dynamics of the interactive networks within the holobiont. In marine systems, holobionts are further integrated into larger and more complex communities and ecosystems, a concept referred to as “nested ecosystems.” In this review, we discuss the concept of holobionts as dynamic ecosystems that interact at multiple scales and respond to environmental change. We focus on the symbiosis of sponges with their microbial communities—a symbiosis that has resulted in one of the most diverse and complex holobionts in the marine environment. In recent years, the field of sponge microbiology has remarkably advanced in terms of curated databases, standardized protocols, and information on the functions of the microbiota. Like a Russian doll, these microbial processes are translated into sponge holobiont functions that impact the surrounding ecosystem. For example, the sponge-associated microbial metabolisms, fueled by the high filtering capacity of the sponge host, substantially affect the biogeochemical cycling of key nutrients like carbon, nitrogen, and phosphorous. Since sponge holobionts are increasingly threatened by anthropogenic stressors that jeopardize the stability of the holobiont ecosystem, we discuss the link between environmental perturbations, dysbiosis, and sponge diseases. Experimental studies suggest that the microbial community composition is tightly linked to holobiont health, but whether dysbiosis is a cause or a consequence of holobiont collapse remains unresolved. Moreover, the potential role of the microbiome in mediating the capacity for holobionts to acclimate and adapt to environmental change is unknown. Future studies should aim to identify the mechanisms underlying holobiont dynamics at multiple scales, from the microbiome to the ecosystem, and develop management strategies to preserve the key functions provided by the sponge holobiont in our present and future oceans

Reef sponges facilitate the transfer of coral-derived organic matter to their associated fauna via the sponge loop

The high biodiversity of coral reefs results in complex trophic webs where energy and nutrients are transferred between species through a multitude of pathways. Here, we hypothesize that reef sponges convert the dissolved organic matter released by benthic primary producers (e.g. corals) into particulate detritus that is transferred to sponge-associated detritivores via the sponge loop pathway. To test this hypothesis, we conducted stable isotope (13C and15N) tracer experiments to investigate the uptake and transfer of coral-derived organic matter from the sponges Mycale fistulifera and Negombata magnifica to 2 types of detritivores commonly associated with sponges: ophiuroids (Ophiothrix savignyi and Ophiocoma scolopendrina) and polychaetes (Polydorella smurovi). Findings revealed that the organic matter naturally released by the corals was indeed readily assimilated by both sponges and rapidly released again as sponge detritus. This detritus was subsequently consumed by the detritivores, demonstrating transfer of coral-derived organic matter from sponges to their associated fauna and confirming all steps of the sponge loop. Thus, sponges provide a trophic link between corals and higher trophic levels, thereby acting as key players within reef food webs

The untapped potential of seascape genomics in the North Pacific

Seascape genomics provides a powerful framework to evaluate the presence and strength of environmental pressures on marine organisms, as well as to forecast long term species stability under various perturbations. In the highly productive North Pacific, forage fishes, key trophic links across ecosystems, are also contending with a rapidly warming climate and a litany of associated oceanographic changes (e.g., changes in salinity, dissolved oxygen, pH, primary production, etc.). These changes can place substantial selective pressures on populations over space and time. While several population genomics studies have targeted forage fishes in the North Pacific, none have formally analyzed the interactions between genotype and environment. However, when population genomics studies provide collection location information and other critical data, it is possible to supplement a published genomic dataset with environmental data from existing public databases and perform “post hoc seascape genomics” analyses. In reviewing the literature, we find pertinent metadata (dates and locations of sample collection) are rarely provided. We identify specific factors that may impede the application of seascape genomics methods in the North Pacific. Finally, we present an approach for supplementing data in a reproducible way to allow for post hoc seascape genomics analysis, in instances when metadata are reported. Overall, our goal is to demonstrate – via literature review – the utility and importance of seascape genomics to understanding the long term health of forage fish species in the North Pacific

Black hole masses and enrichment of z ~ 6 SDSS quasars

We present sensitive near-infrared spectroscopic observations for a sample of five z ~ 6 quasars. These are amongst the most distant, currently known quasars in the universe. The spectra have been obtained using ISAAC at the VLT and include the CIV, MgII and FeII lines. We measure the FeII/MgII line ratio, as an observational proxy for the Fe/alpha element ratio. We derive a ratio of 2.7+/-0.8 for our sample, which is similar to that found for lower redshift quasars, i.e., we provide additional evidence for the lack of evolution in the FeII/MgII line ratio of quasars up to the highest redshifts. This result demonstrates that the sample quasars must have undergone a major episode of iron enrichment in less than one Gyr and star formation must have commenced at z > 8. The linewidths of the MgII and CIV lines give two estimates for the black hole masses. A third estimate is given by assuming that the quasars emit at their Eddington luminosity. The derived masses using these three methods agree well, implying that the quasars are not likely to be strongly lensed. We derive central black hole masses of 0.3-5.2 10^9 solar masses. We use the difference between the redshift of MgII (a proxy for the systemic redshift of the quasar) and the onset of the Gunn Peterson trough to derive the extent of the ionized Stromgren spheres around our target quasars. The derived physical radii are about five Mpc. Using a simple ionization model, the emission of the central quasars would need of order 10^6-10^8 year to create these cavities in a surrounding intergalactic medium with a neutral fraction between 0.1 and 1.0. As the e-folding time scale for the central accreting black hole is on the order of a few times 10^7 year, it can grow by one e-folding or less within this time span.Comment: Accepted by ApJ, 15 pages, 8 figure

Heterotrophy in the earliest gut: a single-cell view of heterotrophic carbon and nitrogen assimilation in sponge-microbe symbioses

Sponges are the oldest known extant animal-microbe symbiosis. These ubiquitous benthic animals play an important role in marine ecosystems in the cycling of dissolved organic matter (DOM), the largest source of organic matter on Earth. The conventional view on DOM cycling through microbial processing has been challenged by the interaction between this efficient filter-feeding host and its diverse and abundant microbiome. Here we quantify, for the first time, the role of host cells and microbial symbionts in sponge heterotrophy. We combined stable isotope probing and nanoscale secondary ion mass spectrometry to compare the processing of different sources of DOM (glucose, amino acids, algal-produced) and particulate organic matter (POM) by a high-microbial abundance (HMA) and low-microbial abundance (LMA) sponge with single-cell resolution. Contrary to common notion, we found that both microbial symbionts and host choanocyte (i.e. filter) cells and were active in DOM uptake. Although all DOM sources were assimilated by both sponges, higher microbial biomass in the HMA sponge corresponded to an increased capacity to process a greater variety of dissolved compounds. Nevertheless, in situ feeding data demonstrated that DOM was the primary carbon source for both the LMA and HMA sponge, accounting for ~90% of their heterotrophic diets. Microbes accounted for the majority (65–87%) of DOM assimilated by the HMA sponge (and ~60% of its total heterotrophic diet) but <5% in the LMA sponge. We propose that the evolutionary success of sponges is due to their different strategies to exploit the vast reservoir of DOM in the ocean

Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size.

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.Thiswork was supported by the Natural Environment ResearchCouncil (grant no. NE/G017 24/1), the Czech Science Fou nda-tion (grant no. P501/12/G090), the AVCR (grant no.RVO:60077344) and a Beatriu de Pinos postdoctoral fellowshipto J.P. (grant no. 2011-A-00292; Catalan Government-E.U. 7thF.P.)

Effects of Water Column Mixing and Stratification on Planktonic Primary Production and Dinitrogen Fixation on a Northern Red Sea Coral Reef

The northern Red Sea experiences strong annual differences in environmental conditions due to its relative high-latitude location for coral reefs. This allows the study of regulatory effects by key environmental parameters (i.e., temperature, inorganic nutrient, and organic matter concentrations) on reef primary production and dinitrogen (N2) fixation, but related knowledge is scarce. Therefore, this study measured environmental parameters, primary production and N2 fixation of phytoplankton groups in the water overlying a coral reef in the Gulf of Aqaba. To this end, we used a comparative approach between mixed and stratified water column scenarios in a full year of seasonal observations. Findings revealed that inorganic nutrient concentrations were significantly higher in the mixed compared to the stratified period. While gross photosynthesis and N2 fixation rates remained similar, net photosynthesis decreased from mixed to stratified period. Net heterotrophic activity of the planktonic community increased significantly during the stratified compared to the mixed period. While inorganic nitrogen (N) availability was correlated with net photosynthesis over the year, N2 fixation only correlated with N availability during the mixed period. This emphasizes the complexity of planktonic trophodynamics in northern Red Sea coral reefs. Comparing mixed and stratified planktonic N2 fixation rates with those of benthic organisms and substrates revealed a close seasonal activity similarity between free-living pelagic and benthic diazotrophs. During the mixed period, N2 fixation potentially contributed up to 3% of planktonic primary production N demand. This contribution increased by ca. one order of magnitude to 21% during the stratified period. Planktonic N2 fixation is likely a significant N source for phytoplankton to maintain high photosynthesis under oligotrophic conditions in coral reefs, especially during stratified conditions

Evolution of the Ionizing Background and the Epoch of Reionization from the Spectra of z~6 Quasars

We study the process of cosmic reionization and estimate the ionizing background in the IGM using the Lyman series absorption in the spectra of the four quasars at 5.7<z<6.3 discovered by the SDSS. We derive the evolution of the ionizing background at high redshifts, using both semi-analytic techniques and cosmological simulations to model the density fluctuations in the IGM. The existence of the complete Ly alpha Gunn-Peterson trough in the spectrum of the z=6.28 quasar SDSS 1030+0524 indicates a photoionization rate Gamma_{-12} at z~6 lower than 0.08, at least a factor of 6 smaller than the value at z~3. The Ly beta and Ly gamma Gunn-Peterson troughs give an even stronger limit Gamma_{-12}<0.02 due to their smaller oscillator strengths, indicating that the ionizing background in the IGM at z~6 is more than 20 times lower than that at z~3. Meanwhile, the volume-averaged neutral hydrogen fraction increases from 10^{-5} at z~3 to >10^{-3} at z~6. At this redshift, the mass-averaged neutral hydrogen fraction is larger than 1%; the mildly overdense regions (delta > 3) are still mostly neutral and the comoving mean free path of ionizing photons is shorter than 8 Mpc. Comparison with simulations of cosmological reionization shows that the observed properties of the IGM at z~6 are typical of those in the era at the end of the overlap stage of reionization when the individual HII regions merge. Thus, z~6 marks the end of the reionization epoch. The redshift of reionization constrains the small scale power of the mass density fluctuations and the star forming efficiency of the first generation of objects.Comment: AJ accepted, 27 pages; minor change