Oyster reef restoration fails to recoup global historic ecosystem losses despite substantial biodiversity gain

Human activities have led to degradation of ecosystems globally. The lost ecosystem functions and services accumulate from the time of disturbance to the full recovery of the ecosystem and can be quantified as a “recovery debt,” providing a valuable tool to develop better restoration practices that accelerate recovery and limit losses. Here, we quantified the recovery of faunal biodiversity and abundance toward a predisturbed state following structural restoration of oyster habitats globally. We found that while restoration initiates a rapid increase in biodiversity and abundance of reef-associated species within 2 years, recovery rate then decreases substantially, leaving a global shortfall in recovery of 35% below a predisturbed state. While efficient restoration methods boost recovery and minimize recovery shortfalls, the time to full recovery is yet to be quantified. Therefore, potential future coastal development should weigh up not only the instantaneous damage to ecosystem functions but also the potential for generational loss of services

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

<p>Abstract</p> <p>Background</p> <p>Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted.</p> <p>Results</p> <p>We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach.</p> <p>Conclusion</p> <p>Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.</p

Bound Water at Protein-Protein Interfaces: Partners, Roles and Hydrophobic Bubbles as a Conserved Motif

Background There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region. Methodology A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules. Results The water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins\u27 interaction (−0.46 kcal mol−1), but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol−1). Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or “hydrophobic bubbles”. Such water molecules may have an important biological purpose in mediating protein-protein interactions

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.Thomas Wernberg, Mads S. Thomsen, Sean D. Connell, Bayden D. Russell, Jonathan M. Waters, Giuseppe C. Zuccarello, Gerald T. Kraft, Craig Sanderson, John A. West, Carlos F. D. Gurge

Context-dependency in the effects of nutrient loading and consumers on the availability of space in marine rocky environments

Background: Enhanced nutrient loading and depletion of consumer populations interact to alter the structure of aquatic plant communities. Nonetheless, variation between adjacent habitats in the relative strength of bottom-up (i.e. nutrients) versus top-down (i.e. grazing) forces as determinants of community structure across broad spatial scales remains unexplored. We experimentally assessed the importance of grazing pressure and nutrient availability on the development of macroalgal assemblages and the maintenance of unoccupied space in habitats differing in physical conditions (i.e. intertidal versus subtidal), across regions of contrasting productivity (oligotrophic coasts of South Australia versus the more productive coasts of Eastern Australia). Methodology/Principal findings: In Eastern Australia, grazers were effective in maintaining space free of macroalgae in both intertidal and subtidal habitats, irrespective of nutrient levels. Conversely, in South Australia, grazers could not prevent colonization of space by turf-forming macroalgae in subtidal habitats regardless of nutrients levels, yet in intertidal habitats removal of grazers reduced unoccupied space when nutrients were elevated. Conclusions/Significance: Assessing the effects of eutrophication in coastal waters requires balancing our understanding between local consumer pressure and background oceanographic conditions that affect productivity. This broader-based understanding may assist in reconciling disproportionately large local-scale variation, a characteristic of ecology, with regional scale processes that are often of greater relevance to policy making and tractability to management.Fabio Bulleri, Bayden D. Russell, Sean D. Connel

Reduction in crystallization time of Sb:Te films through addition of Bi

The electrical, optical and phase change properties of bismuth doped Sb8Te2 as-deposited and re-amorphised films have been characterised. Thin films of the material, with up to 15 atomic percent bismuth, have been synthesised by sputter deposition. As deposited amorphous films were stable at room temperature with a bismuth concentration upto 13 atomic percent. We show that effect of bismuth on the phase change properties of the films is to reduce the crystallization time by an order of magnitude. Both static and dynamic measurements of the as-deposited and reamorphised films have showed similar decreases of crystallisation time with bismuth increases. The crystallisation activation energy reduction appears unaffected by the bismuth atoms up to a concentration of 13 atomic percent. The structure of the films after annealing at 180ºC has been measured by X-ray diffraction; the material shows the same A7-type structure as that previously reported for the well known phase change film Ag3.4In3.7Sb76.4Te16.5. A reduction in the material viscosity with increasing bismuth is suggested as a means by which the reduction in crystallisation time is achieved while a negligible change in activation energy and structure is possible. The effect of bismuth dopants on the Sb8Te2 materialʼs physical properties and the consequent performance of optical media and electrical devices will be discussed

The direct effects of increasing CO2 and temperature on non-calcifying organisms: increasing the potential for phase shifts in kelp forests

Predictions about the ecological consequences of oceanic uptake of CO2 have been preoccupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks the direct effects of CO2 on non-calcareous taxa, particularly those that play critical roles in ecosystem shifts. We used two experiments to investigate whether increased CO2 could exacerbate kelp loss by facilitating non-calcareous algae that, we hypothesized, (i) inhibit the recovery of kelp forests on an urbanized coast, and (ii) form more extensive covers and greater biomass under moderate future CO2 and associated temperature increases. Our experimental removal of turfs from a phase-shifted system (i.e. kelp- to turf-dominated) revealed that the number of kelp recruits increased, thereby indicating that turfs can inhibit kelp recruitment. Future CO2 and temperature interacted synergistically to have a positive effect on the abundance of algal turfs, whereby they had twice the biomass and occupied over four times more available space than under current conditions. We suggest that the current preoccupation with the negative effects of ocean acidification on marine calcifiers overlooks potentially profound effects of increasing CO2 and temperature on non-calcifying organisms