Simulations of the flow in the Mahakam river–lake–delta system,Indonesia

Large rivers often present a river–lake–delta system, with a wide range of temporal and spatial scales of the flow due to the combined effects of human activities and various natural factors, e.g., river discharge, tides, climatic variability, droughts, floods. Numerical models that allow for simulating the flow in these river–lake–delta systems are essential to study them and predict their evolution under the impact of various forcings. This is because they provide information that cannot be easily measured with sufficient temporal and spatial detail. In this study, we combine one-dimensional sectional-averaged (1D) and two-dimensional depth-averaged (2D) models, in the framework of the finite element model SLIM, to simulate the flow in the Mahakam river–lake–delta system (Indonesia). The 1D model representing the Mahakam River and four tributaries is coupled to the 2D unstructured mesh model implemented on the Mahakam Delta, the adjacent Makassar Strait, and three lakes in the central part of the river catchment. Using observations of water elevation at five stations, the bottom friction for river and tributaries, lakes, delta, and adjacent coastal zone is calibrated. Next, the model is validated using another period of observations of water elevation, flow velocity, and water discharge at various stations. Several criteria are implemented to assess the quality of the simulations, and a good agreement between simulations and observations is achieved in both calibration and validation stages. Different aspects of the flow, i.e., the division of water at two bifurcations in the delta, the effects of the lakes on the flow in the lower part of the system, the area of tidal propagation, are also quantified and discussed.     

Bayesian analysis of Jolly-Seber type models

We propose the use of finite mixtures of continuous distributions in modelling the process by which new individuals, that arrive in groups, become part of a wildlife population. We demonstrate this approach using a data set of migrating semipalmated sandpipers (Calidris pussila) for which we extend existing stopover models to allow for individuals to have different behaviour in terms of their stopover duration at the site. We demonstrate the use of reversible jump MCMC methods to derive posterior distributions for the model parameters and the models, simultaneously. The algorithm moves between models with different numbers of arrival groups as well as between models with different numbers of behavioural groups. The approach is shown to provide new ecological insights about the stopover behaviour of semipalmated sandpipers but is generally applicable to any population in which animals arrive in groups and potentially exhibit heterogeneity in terms of one or more other processes.     

Sparse PCA and investigation of multi-elements compositional repositories: theory and applications

The geochemistry of floodplain sediments is fundamental to monitor environmental changes and to quantify their contribution to natural and anthropic processes. A floodplain sediment composition is a vector of positive elements which sum to a fixed constant. The analysis of high-dimensional compositions requires methods that produce results involving only a small portion of the original variables. On the other hand, the analysis must take into account the additional constraints specific to compositions. With the purpose of studying these problems, a new procedure for sparse PCA is proposed on European floodplain sediment samples.     

Photochemical indicators of ozone sensitivity: application in the Pearl River Delta,China

Surface O₃ production has a highly nonlinear relationship with its precursors. The spatial and temporal heterogeneity of O₃-NO _x -VOC-sensitivity regimes complicates the control-decision making. In this paper, the indicator method was used to establish the relationship between O₃ sensitivity and assessment indicators. Six popular ratios indicating ozone-precursor sensitivity, HCHO/NO _y , H₂O₂/ HNO₃, O₃/NO _y , O₃/NO _z , O₃/HNO₃, and H₂O₂/NO _z , were evaluated based on the distribution of NO_x- and VOC-sensitive regimes. WRF-Chem was used to study a serious ozone episode in fall over the Pearl River Delta (PRD). It was found that the south-west of the PRD is characterized by a VOCsensitive regime, while its north-east is NO _x -sensitive, with a sharp transition area between the two regimes. All indicators produced good representations of the elevated ozone hours in the episode on 6 November 2009, with H₂O₂/HNO₃ being the best indicator. The threshold sensitivity levels for HCHO/NO_y, H₂O₂/HNO₃, O₃/NO _y , O₃/NO _z , O₃/HNO₃, and H₂O₂/NO _z were estimated to be 0.41, 0.55, 10.2, 14.0, 19.1, and 0.38, respectively. Threshold intervals for the indicators H₂O₂/HNO₃, O₃/NO _y , O₃/NO _z , O₃/HNO₃, and H₂O₂/NO _z were able to identify more than 95% of VOC- and NO _x -sensitive grids. The ozone episode on 16 November 16 2008 was used to independently verify the results, and it was found that only H₂O₂/HNO₃ and H₂O₂/NO _z were able to differentiate the ozone sensitivity regime well. Hence, these two ratios are suggested as the most appropriate indicators for identifying fall ozone sensitivity in the PRD. Since the species used for indicators have seasonal variation, the utility of those indicators for other seasons should be investigated in the future work.

Open image in new window

     

The selective advantage of host feminization: a case study of the green crab Carcinus maenas and the parasitic barnacle Sacculina carcini

Male crabs infected by parasitic barnacles (Rhizocephala) are known to be morphologically feminized. Here, we investigate morphological chances in green crabs, Carcinus maenas, induced by the parasitic barnacle Sacculina carcini. Infected males acquire a broader, longer and segmented abdomen, fringed with marginal setae. Copulatory appendages and pereopods are reduced in length, and the chelae become smaller. The feminization show great individual variation. Males with scars from lost externae, the parasites reproductive organ situated under the abdomen, are less modified than males carrying an externa, and the feminization is more pronounced in smaller than in larger males. No super-feminization is evident in female crabs that remain morphologically unaffected by infection. The protective value of a parasitically induced enlargement of the male abdomen may constitute an adaptation that increases parasite longevity. The additional effects on male morphology are viewed as pleiotropic side effects of the main adaptive value of enlarging the abdomen.     

Evolution, radiation and chemotaxonomy of Lamellodysidea, a demosponge genus with anti-plasmodial metabolites

Sponges of the family Dysideidae (Dictyoceratida) are renowned for their diversity of secondary metabolites, and its genus Lamellodysidea, particularly Lamellodysidea herbacea, is the most studied taxon biochemically. Despite its importance, the taxonomic status of L. herbacea—whether it is a distinct species or a species complex—has never been assessed. Recent biochemical profiling revealed anti-plasmodial activity of brominated compounds in Lamellodysidea of the Pacific. Here, we present a comparative chemotaxonomic and molecular analysis of selected Dysideidae from the Pacific and the Indian Ocean (New Caledonia, Great Barrier Reef, Fiji, Mayotte, Guam, Palau). We investigated the phylogenetic relationships between the populations and assessed their bioactive (PBDE) compounds in order to unravel the taxonomic status of this commercially important group of sponges and assessed patterns of dispersal and biochemical variation. The molecular phylogeny was based on the internal transcribed ribosomal spacer and compared against a PBDE phylogeny for several specimens. Molecular data revealed a diversity of Indo-Pacific L. herbacea populations, also reflected by different PBDE compound profiles. Molecular and biochemical data also revealed a Lamellodysidea species new to science. Several specimens misidentified as Lamellodysidea were detected based on their position on different clades in the molecular phylogeny and their production of different halogenated compounds (brominated vs. chlorinated). The direct comparison of molecular and biochemical data also provided evidence for the occurrence of a host switch event and support for the theory that abiotic factors, such as sedimentation, affect the chemical constituents produced in L. herbacea.     

Degradation of methyl-phenanthrene isomers during bioremediation of soil contaminated by residual fuel oil

Phenanthrene and methyl-phenanthrenes are major aromatic pollutants originating in particular from fuel oil. Phenanthrene is usually degraded faster than methyl-phenanthrenes under geological and environmental conditions. Here, we report a preferential and accelerated biodegradation of methyl-phenanthrenes versus phenanthrene in soil contaminated by fuel oil. The polluted soil was mixed with sawdust and sand to form a homogenized biopile. The biopile was continuously sprayed with microbial consortia isolated from crude oil?Ccontaminated soil and treated by biosurfactants and nutritive substances for biostimulation. During a 6-month bioremediation experiment, a steady increase in the relative abundance of phenanthrene compared to methyl-phenathrenes was observed by gas chromatography?Cmass spectrometry. The increase was the highest for trimethyl-phenanthrenes, with a phenanthrene/trimethyl-phenanthrenes ratio increasing from 0.42 to 2.45. By contrast, the control, non-stimulated samples showed a ratio decrease from 0.85 to 0.11. Moreover, the results showed that the level of degradability depends on the number of methyl groups.     

Evaluation of existing equations for temporal scour depth around circular bridge piers

Scour is defined as the processes of removal of sediment particles from water stream bed by the erosive action of activated water, and also carries sediment away from the hydraulic structures. Scour is the main cause of pier failure. Numerous equations are available for estimating temporal and equilibrium scour depth. The present study describes the phenomenon of temporal scour depth variation at bridge piers and deals with the methods for its estimation. The accuracy of six temporal scour depth equations are also checked in this study. After graphical and statistical analysis, it was found that the relationship proposed by Oliveto and Hager (J Hydraul Eng (ASCE) 128(9):811–520, 2002) predicts temporal scour depth better than other equations. Three equations of equilibrium time of scour are also used for computing equilibrium time. Equilibrium time equation proposed by Choi and Choi (Water Environ J 30(1–2):14–21, 2016) gives better agreements with observed values.     

Simulation of dam/levee-break hydrodynamics with a three-dimensional implicit unstructured-mesh finite element model

Dam failures usually cause huge economic and life losses , especially in urban areas where there is a high concentration of inhabitants and economic actors. In order to understand the physical mechanisms of the formation and development of dam-break flooding, lots of efforts have been put into different types of modelling techniques. However, most of existing models are 1D (one-dimensional) or 2D models based on the shallow water equations. In this paper, we present a 3D numerical modelling investigation of dam-break flow hydrodynamics in an open L-shape channel. A newly developed 3D unstructured mesh finite element model is used here. An absorption-like term is introduced to the Navier–Stokes equations in order to control the conditioning of the matrix equation in the numerical solution process and thus improve the stability. A wetting and drying algorithm is used here to allow the free surface height to be treated with a high level of implicitness and stability. The 3D model has been validated by comparing the results with the published experimental data. Good agreement has been achieved at six selected locations. This study shows that the 3D unstructured mesh model is capable of capturing the 3D hydraulic aspects and complicated local flows around structures in simulation of dam-break flows.     

Energetic cost of development through metamorphosis for the seastar<Emphasis Type="Italic"> Mediaster aequalis</Emphasis> (Stimpson)

Rates of oxygen consumption were measured for embryos, larvae and juveniles of the seastar Mediaster aequalis for 76 days post-fertilization. The rate increased from 0.65 nmol O₂ ind^–1 h^–1 at 6 h after fertilization to 2.8 nmol O₂ ind^–1 h^–1 at day 35. Larvae became competent to metamorphose around day 35 post-fertilization and began to decrease their metabolic rate after this time. Metamorphosed juveniles consumed 0.74 nmol O₂ ind^–1 h^–1. Eggs contained 138.6 µg lipid ind^–1 and 12.1 µg protein ind^–1. Lipid levels decreased in concentration throughout development while protein levels increased slightly. The lipid levels decreased by 88.5 µg from eggs to day 76 larvae, accounting for 3.5 J of energy. Total oxygen consumption to this point was 3.74 µmol O₂ ind^–1, accounting for 1.84 J. The energetic demand up to day 76 was met completely through the use of lipid reserves. Metamorphosed juveniles expended 0.5 J more than larvae at the same age. Tubes of the polychaete Phyllochaetopterus prolifica were able to induce metamorphosis in M. aequalis larvae and a non-polar extract of these tubes also triggered metamorphosis. Larvae that are delayed to metamorphose can sustain their metabolic rate with lipid reserves for a limited, yet undetermined, period.Communicated by P.W. Sammarco, Chauvin