Predicting the Location and Spatial Extent of Submerged Coral Reef Habitat in the Great Barrier Reef World Heritage Area,Australia

Aim

Coral reef communities occurring in deeper waters have received little research effort compared to their shallow-water counterparts, and even such basic information as their location and extent are currently unknown throughout most of the world. Using the Great Barrier Reef as a case study, habitat suitability modelling is used to predict the distribution of deep-water coral reef communities on the Great Barrier Reef, Australia. We test the effectiveness of a range of geophysical and environmental variables for predicting the location of deep-water coral reef communities on the Great Barrier Reef.

Location

Great Barrier Reef, Australia.

Methods

Maximum entropy modelling is used to identify the spatial extent of two broad communities of habitat-forming megabenthos phototrophs and heterotrophs. Models were generated using combinations of geophysical substrate properties derived from multibeam bathymetry and environmental data derived from Bio-ORACLE, combined with georeferenced occurrence records of mesophotic coral communities from autonomous underwater vehicle, remotely operated vehicle and SCUBA surveys. Model results are used to estimate the total amount of mesophotic coral reef habitat on the GBR.

Results

Our models predict extensive but previously undocumented coral communities occurring both along the continental shelf-edge of the Great Barrier Reef and also on submerged reefs inside the lagoon. Habitat suitability for phototrophs is highest on submerged reefs along the outer-shelf and the deeper flanks of emergent reefs inside the GBR lagoon, while suitability for heterotrophs is highest in the deep waters along the shelf-edge. Models using only geophysical variables consistently outperformed models incorporating environmental data for both phototrophs and heterotrophs.

Main Conclusion

Extensive submerged coral reef communities that are currently undocumented are likely to occur throughout the Great Barrier Reef. High-quality bathymetry data can be used to identify these reefs, which may play an important role in resilience of the GBR ecosystem to climate change.     

The good, the bad and the recovery in an assisted migration

Background

Assisted migration or translocation of species to ameliorate effects of habitat loss or changing environment is currently under scrutiny as a conservation tool. A large scale experiment of assisted migration over hundreds of kilometres was tested on a morph from a commercial fishery of southern rock lobster Jasus edwardsii, to enhance depleted populations, improve the yield and sustainability of the fishery, and test resilience to a changing climate.

Methodology and Principal Findings

Approximately 10,000 lower-valued, pale-coloured lobsters were moved from deep water to inshore sites (2 in Tasmania [TAS] and 2 in South Australia [SA]) where the high-value, red morph occurs. In TAS this was a northwards movement of 1° latitude. Growth was measured only in TAS lobsters, and reproductive status was recorded in lobsters from all locations. Pale females (TAS) grew 4 times faster than resident pale lobsters from the original site and twice as fast as red lobsters at their new location. Approximately 30% of translocated pale lobsters deferred reproduction for one year after release (SA and TAS), and grew around 1 mm yr⁻¹ less compared to translocated pale lobsters that did not defer reproduction. In spite of this stress response to translocation, females that deferred reproduction still grew 2–6 mm yr⁻¹ more than lobsters at the source site. Lobsters have isometric growth whereby volume increases as a cube of length. Consequently despite the one-year hiatus in reproduction, increased growth increases fecundity of translocated lobsters, as the increase in size provided a larger volume for producing and incubating eggs in future years.

Conclusions and Significance

Assisted migration improved egg production and growth, despite a temporary stress response, and offers a tool to improve the production, sustainability and resilience of the fishery.     

Use of Herring Bait to Farm Lobsters in the Gulf of Maine

Background

Ecologists, fisheries scientists, and coastal managers have all called for an ecosystem approach to fisheries management, yet many species such as the American lobster (Homarus americanus) are still largely managed individually. One hypothesis that has yet to be tested suggests that human augmentation of lobster diets via the use of Atlantic herring (Clupea harengus) as bait may contribute to recent increases in lobster landings. Currently 70% of Atlantic herring landings in the Gulf of Maine are used as bait to catch lobsters in traps throughout coastal New England.

Methodology/Principal Findings

We examined the effects of this herring bait on the diet composition and growth rate of lobsters at heavily baited vs. seasonally closed (i.e., bait free) sites in coastal Maine. Our results suggest that human use of herring bait may be subsidizing juvenile lobster diets, thereby enhancing lobster growth and the overall economic value and yield of one of the most valuable fisheries in the U.S.

Conclusions/Significance

Our study illustrates that shifting to an ecosystem approach to fisheries management should require consideration of cross-fishery interactions.     

Pharmacokinetics Study of Recombinant Hirudin in the Plasma of Rats Using Chromogenic Substrate,ELISA, and Radioisotope Assays

Aim

To compare the analytical methods used to study the pharmacokinetics of recombinant hirudin in the plasma of rats that had been injected with ¹²⁵I-recombinant hirudin.

Methods

2.0 mg/kg ¹²⁵I-recombinant hirudin were injected intravenously into rats. The recombinant hirudins in the plasma was analyzed by chromogenic substrate assay, enzyme-linked immunosorbent assay (ELISA), total radioisotope assay (RA) and trichloroacetic acid pre-treated total radioisotope assay (TCA-RA).

Results

The chromogenic substrate assay standard curve was linear over the concentration range from 3.12 to 40.00 ng/ml for the recombinant hirudin in plasma. The relative standard deviations (RSD) for the intra- and inter-day variation were 5.0 to 6.3% and 11.9 to 12.6%, respectively. The recoveries of recombinant hirudin was 89.8% to 100.7%. The limit of quantification (LOQ) was 3.12 ng/ml. The concentration-time curve of the recombinant hirudin in the plasma could be explained as a two-compartment model. Pharmacokinetic parameters, including the half-life of distribution phase (t_1/2 α), the half-life of elimination phase (t_1/2 β), volume of apparent distribution (Vd), and area under the concentration-time curve from zero to infinite time (AUC_0–t) were 7.59 min, 46.99 min, 0.17 L/kg, and 204.5 mg/L/min, respectively, as determined by chromogenic substrate assay; 6.41 min, 47.28 min, 1.24 L/kg, and 575.18 mg/L/min, respectively, as determined by ELISA; 3.69 min, 701.90 min, 0.04 L/kg, and 4189 mg/L/min, respectively as determined by RA; and 4.57 min, 724.9 min, 0.09 L/kg, and 2329 mg/L/min, respectively, as determined by TCA-RA.

Conclusions

The chromogenic substrate assay on the concentration dynamics of the recombinant hirudin in the plasma is a specific, sensitive, and accurate analytical method for pharmacokinetic studies. Moreover, the pharmacokinetic parameters determined by the chromogenic substrate assay and ELISA are congruent except for AUC.     

Prevailing negative soil biota effect and no evidence for local adaptation in a widespread Eurasian grass

Background

Soil biota effects are increasingly accepted as an important driver of the abundance and distribution of plants. While biogeographical studies on alien invasive plant species have indicated coevolution with soil biota in their native distribution range, it is unknown whether adaptation to soil biota varies among populations within the native distribution range. The question of local adaptation between plants and their soil biota has important implications for conservation of biodiversity and may justify the use of seed material from local provenances in restoration campaigns.

Methodology/Principal Findings

We studied soil biota effects in ten populations of the steppe grass Stipa capillata from two distinct regions, Europe and Asia. We tested for local adaptation at two different scales, both within (ca. 10–80 km) and between (ca. 3300 km) regions, using a reciprocal inoculation experiment in the greenhouse for nine months. Generally, negative soil biota effects were consistent. However, we did not find evidence for local adaptation: both within and between regions, growth of plants in their ‘home soil’ was not significantly larger relative to that in soil from other, more distant, populations.

Conclusions/Significance

Our study suggests that negative soil biota effects can prevail in different parts of a plant species'' range. Absence of local adaptation points to the possibility of similar rhizosphere biota composition across populations and regions, sufficient gene flow to prevent coevolution, selection in favor of plasticity, or functional redundancy among different soil biota. From the point of view of plant - soil biota interactions, our findings indicate that the current practice of using seeds exclusively from local provenances in ecosystem restoration campaigns may not be justified.     

Fishery-Independent Data Reveal Negative Effect of Human Population Density on Caribbean Predatory Fish Communities

Background

Understanding the current status of predatory fish communities, and the effects fishing has on them, is vitally important information for management. However, data are often insufficient at region-wide scales to assess the effects of extraction in coral reef ecosystems of developing nations.

Methodology/Principal Findings

Here, I overcome this difficulty by using a publicly accessible, fisheries-independent database to provide a broad scale, comprehensive analysis of human impacts on predatory reef fish communities across the greater Caribbean region. Specifically, this study analyzed presence and diversity of predatory reef fishes over a gradient of human population density. Across the region, as human population density increases, presence of large-bodied fishes declines, and fish communities become dominated by a few smaller-bodied species.

Conclusions/Significance

Complete disappearance of several large-bodied fishes indicates ecological and local extinctions have occurred in some densely populated areas. These findings fill a fundamentally important gap in our knowledge of the ecosystem effects of artisanal fisheries in developing nations, and provide support for multiple approaches to data collection where they are commonly unavailable.     

Verbal Memory Deficits Are Correlated with Prefrontal Hypometabolism in 18FDG PET of Recreational MDMA Users

Introduction

3,4-Methylenedioxymethamphetamine (MDMA, “ecstasy”) is a recreational club drug with supposed neurotoxic effects selectively on the serotonin system. MDMA users consistently exhibit memory dysfunction but there is an ongoing debate if these deficits are induced mainly by alterations in the prefrontal or mediotemporal cortex, especially the hippocampus. Thus, we investigated the relation of verbal memory deficits with alterations of regional cerebral brain glucose metabolism (rMRGlu) in recreational MDMA users.

Methods

Brain glucose metabolism in rest was assessed using 2-deoxy-2-(¹⁸F)fluoro-D-glucose positron emission tomography (¹⁸FDG PET) in 19 male recreational users of MDMA and 19 male drug-naïve controls. ¹⁸FDG PET data were correlated with memory performance assessed with a German version of the Rey Auditory Verbal Learning Test.

Results

As previously shown, MDMA users showed significant impairment in verbal declarative memory performance. PET scans revealed significantly decreased rMRGlu in the bilateral dorsolateral prefrontal and inferior parietal cortex, bilateral thalamus, right hippocampus, right precuneus, right cerebellum, and pons (at the level of raphe nuclei) of MDMA users. Among MDMA users, learning and recall were positively correlated with rMRGlu predominantly in bilateral frontal and parietal brain regions, while recognition was additionally related to rMRGlu in the right mediotemporal and bihemispheric lateral temporal cortex. Moreover, cumulative lifetime dose of MDMA was negatively correlated with rMRGlu in the left dorsolateral and bilateral orbital and medial PFC, left inferior parietal and right lateral temporal cortex.

Conclusions

Verbal learning and recall deficits of recreational MDMA users are correlated with glucose hypometabolism in prefrontal and parietal cortex, while word recognition was additionally correlated with mediotemporal hypometabolism. We conclude that memory deficits of MDMA users arise from combined fronto-parieto-mediotemporal dysfunction.     

Relative predation risk in two types of habitat for juvenile Australasian spiny lobsters,Jasus edwardsii

The decline in kelp habitat on coastal reefs resulting from changes in ocean climate and the distribution and abundance of herbivorous species is common in many temperate regions of the world. Kelp habitat is highly productive, biodiverse and provides a complex habitat into which many organisms recruit, including spiny lobsters, such as the Australasian red spiny lobster, Jasus edwardsii. The displacement of kelp habitat by less-complex barren reef habitat has the potential to influence the risk of predation for early juvenile lobsters. Therefore, relative predation risk on the juvenile spiny lobster, J. edwardsii, was compared for kelp and barren habitats on the northeast coast of New Zealand using juvenile lobsters held in transparent containers and recording predators with a video recorder. In total, 188 predation attempts were observed within 420?h of video recordings gathered over 3 weeks of sampling. There was an overall higher predation risk in barren habitats. Daytime predation attempts were higher in barren compared to kelp habitat; however, there was no difference between the habitats for night time, dawn or dusk observations, when juvenile lobsters are emergent from shelters and vulnerable to predation. Similar numbers of predatory species were identified in kelp (13) and barren habitat (12). Other factors, such as food availability and time spent away from shelter, especially during night and crepuscular periods, need consideration in future studies when investigating the cause of differences in juvenile lobster mortality among habitats.     

Water quality and herbivory interactively drive coral-reef recovery patterns in American Samoa

Background

Compared with a wealth of information regarding coral-reef recovery patterns following major disturbances, less insight exists to explain the cause(s) of spatial variation in the recovery process.

Methodology/Principal Findings

This study quantifies the influence of herbivory and water quality upon coral reef assemblages through space and time in Tutuila, American Samoa, a Pacific high island. Widespread declines in dominant corals (Acropora and Montipora) resulted from cyclone Heta at the end of 2003, shortly after the study began. Four sites that initially had similar coral reef assemblages but differential temporal dynamics four years following the disturbance event were classified by standardized measures of ‘recovery status’, defined by rates of change in ecological measures that are known to be sensitive to localized stressors. Status was best predicted, interactively, by water quality and herbivory. Expanding upon temporal trends, this study examined if similar dependencies existed through space; building multiple regression models to identify linkages between similar status measures and local stressors for 17 localities around Tutuila. The results highlighted consistent, interactive interdependencies for coral reef assemblages residing upon two unique geological reef types. Finally, the predictive regression models produced at the island scale were graphically interpreted with respect to hypothesized site-specific recovery thresholds.

Conclusions/Significance

Cumulatively, our study purports that moving away from describing relatively well-known patterns behind recovery, and focusing upon understanding causes, improves our foundation to predict future ecological dynamics, and thus improves coral reef management.     

Efficient 2,3-butanediol production from cassava powder by a crop-biomass-utilizer, Enterobacter cloacae subsp. dissolvens SDM

Background

2,3-Butanediol (BD) is considered as one of the key platform chemicals used in a variety of industrial applications. It is crucial to find an efficient sugar-utilizing strain and feasible carbon source for the economical production of BD.

Methodology/Principal Findings

Efficient BD production by a newly isolated Enterobacter cloacae subsp. dissolvens SDM was studied using crop-biomass cassava powder as substrate. The culture conditions and fermentation medium for BD production were optimized. Under the optimal conditions, 78.3 g l⁻¹ of BD was produced after 24 h in simultaneous saccharification and fermentation (SSF), with a yield of 0.42 g BD g⁻¹ cassava powder and a specific productivity of 3.3 g l⁻¹ h⁻¹. A higher BD concentration (93.9 g l⁻¹) was produced after 47 h in fed-batch SSF.

Conclusions/Significance

The results suggest that strain SDM is a good candidate for the BD production, and cassava powder could be used as an alternative substrate for the efficient production of BD.     

A Case-Control Study of Maternal Periconceptual and Pregnancy Recreational Drug Use and Fetal Malformation Using Hair Analysis

Objective

Maternal recreational drug use may be associated with the development of fetal malformations such as gastroschisis, brain and limb defects, the aetiology due to vascular disruption during organogenesis. Using forensic hair analysis we reported evidence of recreational drug use in 18% of women with a fetal gastroschisis. Here we investigate this association in a variety of fetal malformations using the same method.

Methods

In a multi-centre study, women with normal pregnancies (controls) and those with fetal abnormalities (cases) gave informed consent for hair analysis for recreational drug metabolites using mass spectrometry. Hair samples cut at the root were tested in sections corresponding to 3 month time periods (pre and periconceptual period).

Results

Women whose fetus had gastroschisis, compared to women with a normal control fetus, were younger (mean age 23.78±SD4.79 years, 18–37 vs 29.79±SD6 years, 18–42, p = 0.00001), were more likely to have evidence of recreational drug use (15, 25.4% vs 21, 13%, OR2.27, 95^thCI 1.08–4.78, p = 0.028), and were less likely to report periconceptual folic acid use (31, 53.4% vs 124, 77.5%, OR0.33, 95^thCI 0.18–0.63, p = 0.001). Age-matched normal control women were no less likely to test positive for recreational drugs than women whose fetus had gastroschisis. After accounting for all significant factors, only young maternal age remained significantly associated with gastroschisis. Women with a fetus affected by a non-neural tube central nervous system (CNS) anomaly were more likely to test positive for recreational drugs when compared to women whose fetus was normal (7, 35% vs 21, 13%, OR3.59, 95^th CI1.20–10.02, p = 0.01).

Conclusions

We demonstrate a significant association between non neural tube CNS anomalies and recreational drug use in the periconceptual period, first or second trimesters, but we cannot confirm this association with gastroschisis. We confirm the association of gastroschisis with young maternal age.     

Coverage,Diversity, and Functionality of a High-Latitude Coral Community (Tatsukushi,Shikoku Island,Japan)

Background

Seawater temperature is the main factor restricting shallow-water zooxanthellate coral reefs to low latitudes. As temperatures increase, coral species and perhaps reefs may move into higher-latitude waters, increasing the chances of coral reef ecosystems surviving despite global warming. However, there is a growing need to understand the structure of these high-latitude coral communities in order to analyze their future dynamics and to detect any potential changes.

Methodology/Principal Findings

The high-latitude (32.75°N) community surveyed was located at Tatsukushi, Shikoku Island, Japan. Coral cover was 60±2% and was composed of 73 scleractinian species partitioned into 7 functional groups. Although only 6% of species belonged to the ‘plate-like’ functional group, it was the major contributor to species coverage. This was explained by the dominance of plate-like species such as Acropora hyacinthus and A. solitaryensis. Comparison with historical data suggests a relatively recent colonization/development of A. hyacinthus in this region and a potential increase in coral diversity over the last century. Low coverage of macroalgae (2% of the benthic cover) contrasted with the low abundance of herbivorous fishes, but may be reasonably explained by the high density of sea urchins (12.9±3.3 individuals m⁻²).

Conclusions/Significance

The structure and composition of this benthic community are relatively remarkable for a site where winter temperature can durably fall below the accepted limit for coral reef development. Despite limited functionalities and functional redundancy, the current benthic structure might provide a base upon which a reef could eventually develop, as characterized by opportunistic and pioneer frame-building species. In addition to increasing seawater temperatures, on-going management actions and sea urchin density might also explain the observed state of this community. A focus on such ‘marginal’ communities should be a priority, as they can provide important insights into how tropical corals might cope with environmental changes.     

Present,past and future of the European rock fern Asplenium fontanum: combining distribution modelling and population genetics to study the effect of climate change on geographic range and genetic diversity

Background and Aims

Climate change is expected to alter the geographic range of many plant species dramatically. Predicting this response will be critical to managing the conservation of plant resources and the effects of invasive species. The aim of this study was to predict the response of temperate homosporous ferns to climate change.

Methods

Genetic diversity and changes in distribution range were inferred for the diploid rock fern Asplenium fontanum along a South–North transect, extending from its putative last glacial maximum (LGM) refugia in southern France towards southern Germany and eastern-central France. This study reconciles observations from distribution models and phylogeographic analyses derived from plastid and nuclear diversity.

Key Results

Genetic diversity distribution and niche modelling propose that genetic diversity accumulates in the LGM climate refugium in southern France with the formation of a diversity gradient reflecting a slow, post-LGM range expansion towards the current distribution range. Evidence supports the fern''s preference for outcrossing, contradicting the expectation that homosporous ferns would populate new sites by single-spore colonization. Prediction of climate and distribution range change suggests that a dramatic loss of range and genetic diversity in this fern is possible. The observed migration is best described by the phalanx expansion model.

Conclusions

The results suggest that homosporous ferns reproducing preferentially by outcrossing accumulate genetic diversity primarily in LGM climate refugia and may be threatened if these areas disappear due to global climate change.     

Effects of light, food availability and temperature stress on the function of photosystem II and photosystem I of coral symbionts

Background

Reef corals are heterotrophic coelenterates that achieve high productivity through their photosynthetic dinoflagellate symbionts. Excessive seawater temperature destabilises this symbiosis and causes corals to “bleach,” lowering their photosynthetic capacity. Bleaching poses a serious threat to the persistence of coral reefs on a global scale. Despite expanding research on the causes of bleaching, the mechanisms remain a subject of debate.

Methodology/Principal Findings

This study determined how light and food availability modulate the effects of temperature stress on photosynthesis in two reef coral species. We quantified the activities of Photosystem II, Photosystem I and whole chain electron transport under combinations of normal and stressful growth temperatures, moderate and high light levels and the presence or absence of feeding of the coral hosts. Our results show that PS1 function is comparatively robust against temperature stress in both species, whereas PS2 and whole chain electron transport are susceptible to temperature stress. In the symbiotic dinoflagellates of Stylophora pistillata the contents of chlorophyll and major photosynthetic complexes were primarily affected by food availability. In Turbinaria reniformis growth temperature was the dominant influence on the contents of the photosynthetic complexes. In both species feeding the host significantly protected photosynthetic function from high temperature stress.

Conclusions/Significance

Our findings support the photoinhibition model of coral bleaching and demonstrate that PS1 is not a major site for thermal damage during bleaching events. Feeding mitigates bleaching in two scleractinian corals, so that reef responses to temperature stresses will likely be influenced by the coinciding availabilities of prey for the host.     

Topography and Land Cover of Watersheds Predicts the Distribution of the Environmental Pathogen Mycobacterium ulcerans in Aquatic Insects

Background

An understanding of the factors driving the distribution of pathogens is useful in preventing disease. Often we achieve this understanding at a local microhabitat scale; however the larger scale processes are often neglected. This can result in misleading inferences about the distribution of the pathogen, inhibiting our ability to manage the disease. One such disease is Buruli ulcer, an emerging neglected tropical disease afflicting many thousands in Africa, caused by the environmental pathogen Mycobacterium ulcerans. Herein, we aim to describe the larger scale landscape process describing the distribution of M. ulcerans.

Methodology

Following extensive sampling of the community of aquatic macroinvertebrates in Cameroon, we select the 5 dominant insect Orders, and conduct an ecological niche model to describe how the distribution of M. ulcerans positive insects changes according to land cover and topography. We then explore the generalizability of the results by testing them against an independent dataset collected in a second endemic region, French Guiana.

Principal Findings

We find that the distribution of the bacterium in Cameroon is accurately described by the land cover and topography of the watershed, that there are notable seasonal differences in distribution, and that the Cameroon model does not predict the distribution of M. ulcerans in French Guiana.

Conclusions/Significance

Future studies of M. ulcerans would benefit from consideration of local structure of the local stream network in future sampling, and further work is needed on the reasons for notable differences in the distribution of this species from one region to another. This work represents a first step in the identification of large-scale environmental drivers of this species, for the purposes of disease risk mapping.     

Caribbean corals in crisis: record thermal stress, bleaching, and mortality in 2005

Background

The rising temperature of the world''s oceans has become a major threat to coral reefs globally as the severity and frequency of mass coral bleaching and mortality events increase. In 2005, high ocean temperatures in the tropical Atlantic and Caribbean resulted in the most severe bleaching event ever recorded in the basin.

Methodology/Principal Findings

Satellite-based tools provided warnings for coral reef managers and scientists, guiding both the timing and location of researchers'' field observations as anomalously warm conditions developed and spread across the greater Caribbean region from June to October 2005. Field surveys of bleaching and mortality exceeded prior efforts in detail and extent, and provided a new standard for documenting the effects of bleaching and for testing nowcast and forecast products. Collaborators from 22 countries undertook the most comprehensive documentation of basin-scale bleaching to date and found that over 80% of corals bleached and over 40% died at many sites. The most severe bleaching coincided with waters nearest a western Atlantic warm pool that was centered off the northern end of the Lesser Antilles.

Conclusions/Significance

Thermal stress during the 2005 event exceeded any observed from the Caribbean in the prior 20 years, and regionally-averaged temperatures were the warmest in over 150 years. Comparison of satellite data against field surveys demonstrated a significant predictive relationship between accumulated heat stress (measured using NOAA Coral Reef Watch''s Degree Heating Weeks) and bleaching intensity. This severe, widespread bleaching and mortality will undoubtedly have long-term consequences for reef ecosystems and suggests a troubled future for tropical marine ecosystems under a warming climate.     

Fatty acid composition indicating diverse habitat use in coral reef fishes in the Malaysian South China Sea

Background

In order to understand feeding ecology and habitat use of coral reef fish, fatty acid composition was examined in five coral reef fishes, Thalassoma lunare, Lutjanus lutjanus, Abudefduf bengalensis, Scarus rivulatus and Scolopsis affinis collected in the Bidong Island of Malaysian South China Sea.

Results

Proportions of saturated fatty acids (SAFA) ranged 57.2% 74.2%, with the highest proportions in fatty acids, the second highest was monounsaturated fatty acids (MUFA) ranged from 21.4% to 39.0% and the proportion of polyunsaturated fatty acids (PUFA) was the lowest ranged from 2.8% to 14.1%. Each fatty acid composition differed among fishes, suggesting diverse feeding ecology, habitat use and migration during the fishes’ life history in the coral reef habitats.

Conclusions

Diets of the coral fish species might vary among species in spite of that each species are living sympatrically. Differences in fatty acid profiles might not just be considered with respect to the diets, but might be based on the habitat and migration.     

Ecological Meltdown in the Firth of Clyde,Scotland: Two Centuries of Change in a Coastal Marine Ecosystem

Background

The Firth of Clyde is a large inlet of the sea that extends over 100 km into Scotland''s west coast.

Methods

We compiled detailed fisheries landings data for this area and combined them with historical accounts to build a picture of change due to fishing activity over the last 200 years.

Findings

In the early 19^th century, prior to the onset of industrial fishing, the Firth of Clyde supported diverse and productive fisheries for species such as herring (Clupea harengus, Clupeidae), cod (Gadus morhua, Gadidae), haddock (Melanogrammus aeglefinus, Gadidae), turbot (Psetta maxima, Scophthalmidae) and flounder (Platichthys flesus, Pleuronectidae). The 19^th century saw increased demand for fish, which encouraged more indiscriminate methods of fishing such as bottom trawling. During the 1880s, fish landings began to decline, and upon the recommendation of local fishers and scientists, the Firth of Clyde was closed to large trawling vessels in 1889. This closure remained in place until 1962 when bottom trawling for Norway lobster (Nephrops norvegicus, Nephropidae) was approved in areas more than three nautical miles from the coast. During the 1960s and 1970s, landings of bottomfish increased as trawling intensified. The trawl closure within three nautical miles of the coast was repealed in 1984 under pressure from the industry. Thereafter, bottomfish landings went into terminal decline, with all species collapsing to zero or near zero landings by the early 21^st century. Herring fisheries collapsed in the 1970s as more efficient mid-water trawls and fish finders were introduced, while a fishery for mid-water saithe (Pollachius virens, Gadidae) underwent a boom and bust shortly after discovery in the late 1960s. The only commercial fisheries that remain today are for Nephrops and scallops (Pecten maximus, Pectinidae).

Significance

The Firth of Clyde is a marine ecosystem nearing the endpoint of overfishing, a time when no species remain that are capable of sustaining commercial catches. The evidence suggests that trawl closures helped maintain productive fisheries through the mid-20^th century, and their reopening precipitated collapse of bottomfish stocks. We argue that continued intensive bottom trawling for Nephrops with fine mesh nets will prevent the recovery of other species. This once diverse and highly productive environment will only be restored if trawl closures or other protected areas are re-introduced. The Firth of Clyde represents at a small scale a process that is occurring ocean-wide today, and its experience serves as a warning to others.     

Dynamic Locomotor Capabilities Revealed by Early Dinosaur Trackmakers from Southern Africa

Background

A new investigation of the sedimentology and ichnology of the Early Jurassic Moyeni tracksite in Lesotho, southern Africa has yielded new insights into the behavior and locomotor dynamics of early dinosaurs.

Methodology/Principal Findings

The tracksite is an ancient point bar preserving a heterogeneous substrate of varied consistency and inclination that includes a ripple-marked riverbed, a bar slope, and a stable algal-matted bar top surface. Several basal ornithischian dinosaurs and a single theropod dinosaur crossed its surface within days or perhaps weeks of one another, but responded to substrate heterogeneity differently. Whereas the theropod trackmaker accommodated sloping and slippery surfaces by gripping the substrate with its pedal claws, the basal ornithischian trackmakers adjusted to the terrain by changing between quadrupedal and bipedal stance, wide and narrow gauge limb support (abduction range = 31°), and plantigrade and digitigrade foot posture.

Conclusions/Significance

The locomotor adjustments coincide with changes in substrate consistency along the trackway and appear to reflect ‘real time’ responses to a complex terrain. It is proposed that these responses foreshadow important locomotor transformations characterizing the later evolution of the two main dinosaur lineages. Ornithischians, which shifted from bipedal to quadrupedal posture at least three times in their evolutionary history, are shown to have been capable of adopting both postures early in their evolutionary history. The substrate-gripping behavior demonstrated by the early theropod, in turn, is consistent with the hypothesized function of pedal claws in bird ancestors.     

Profiling of substrate specificities of 3C-like proteases from group 1, 2a, 2b, and 3 coronaviruses

Background

Coronaviruses (CoVs) can be classified into alphacoronavirus (group 1), betacoronavirus (group 2), and gammacoronavirus (group 3) based on diversity of the protein sequences. Their 3C-like protease (3CL^pro), which catalyzes the proteolytic processing of the polyproteins for viral replication, is a potential target for anti-coronaviral infection.

Methodology/Principal Findings

Here, we profiled the substrate specificities of 3CL^pro from human CoV NL63 (group 1), human CoV OC43 (group 2a), severe acute respiratory syndrome coronavirus (SARS-CoV) (group 2b) and infectious bronchitis virus (IBV) (group 3), by measuring their activity against a substrate library of 19×8 of variants with single substitutions at P5 to P3'' positions. The results were correlated with structural properties like side chain volume, hydrophobicity, and secondary structure propensities of substituting residues. All 3CL^pro prefer Gln at P1 position, Leu at P2 position, basic residues at P3 position, small hydrophobic residues at P4 position, and small residues at P1'' and P2'' positions. Despite 3CL^pro from different groups of CoVs share many similarities in substrate specificities, differences in substrate specificities were observed at P4 positions, with IBV 3CL^pro prefers P4-Pro and SARS-CoV 3CL^pro prefers P4-Val. By combining the most favorable residues at P3 to P5 positions, we identified super-active substrate sequences ‘VARLQ↓SGF’ that can be cleaved efficiently by all 3CL^pro with relative activity of 1.7 to 3.2, and ‘VPRLQ↓SGF’ that can be cleaved specifically by IBV 3CL^pro with relative activity of 4.3.

Conclusions/Significance

The comprehensive substrate specificities of 3CL^pro from each of the group 1, 2a, 2b, and 3 CoVs have been profiled in this study, which may provide insights into a rational design of broad-spectrum peptidomimetic inhibitors targeting the proteases.