Natural Beds Research Articles

Signatures of selection for bonamiosis resistance in European flat oyster (Ostrea edulis): New genomic tools for breeding programs and management of natural resources.

The European flat oyster (Ostrea edulis) is a highly appreciated mollusk with an important aquaculture production throughout the 20th century, in addition to playing an important role on coastal ecosystems. Overexploitation of natural beds, habitat degradation, introduction of non‐native species, and epidemic outbreaks have severely affected this important resource, particularly, the protozoan parasite Bonamia ostreae, which is the main concern affecting its production and conservation. In order to identify genomic regions and markers potentially associated with bonamiosis resistance, six oyster beds distributed throughout the European Atlantic coast were sampled. Three of them have been exposed to this parasite since the early 1980s and showed some degree of innate resistance (long‐term affected group, LTA), while the other three were free of B. ostreae at least until sampling date (naïve group, NV). A total of 14,065 SNPs were analyzed, including 37 markers from candidate genes and 14,028 from a medium‐density SNP array. Gene diversity was similar between LTA and NV groups suggesting no genetic erosion due to long‐term exposure to the parasite, and three population clusters were detected using the whole dataset. Tests for divergent selection between NV and LTA groups detected the presence of a very consistent set of 22 markers, located within a putative single genomic region, which suggests the presence of a major quantitative trait locus associated with B. ostreae resistance. Moreover, 324 outlier loci associated with factors other than bonamiosis were identified allowing fully discrimination of all the oyster beds. A practical tool which included the 84 highest discriminative markers for tracing O. edulis populations was developed and tested with empirical data. Results reported herein could assist the production of stocks with improved resistance to bonamiosis and facilitate the management of oyster beds for recovery production and ecosystem services provided by this species.

Size‐Independent Susceptibility to Transport in Aeolian Saltation

AbstractNatural wind‐eroded soils contain a mixture of particle sizes. However, models for aeolian saltation are typically derived for sediment bed surfaces containing only a single particle size. To nonetheless treat natural mixed beds, models for saltation and associated dust aerosol emission have typically simplified aeolian transport either as a series of noninteracting single particle size beds or as a bed containing only the median or mean particle size. Here we test these common assumptions underpinning aeolian transport models using measurements of size‐resolved saltation fluxes at three natural field sites. We find that a wide range of sand size classes experience “equal susceptibility” to saltation at a single common threshold wind shear stress, contrary to the “selective susceptibility” expected for treatment of a mixed bed as multiple single particle size beds. Our observation of equal susceptibility refutes the common simplification of saltation as a series of noninteracting single particle sizes. Sand transport and dust emission models that use this incorrect assumption can be both simplified and improved by instead using a single particle size representative of the mixed bed.

Quantifying hydrodynamic changes associated with bioengineered stabilization measures using numerical modelling

River bank stabilization is a common practise and can be observed on most rivers around the world, often using hard-engineering riprap. Increasingly, bioengineered approaches using vegetation-based constructive materials is promoted to alleviate some of the negative ecological stresses of bank stabilization. Because these stabilization projects use a variety of techniques to create a site-specific design, they can have unexpected morphological implications and variable ecological benefits which can be anticipated using numerical modelling. Bioengineered bank stabilization creates roughness elements on both micro and macro scales, where only macro-roughness can be captured by bathymetric adjustments. The definition of micro- and macro-roughness depends on the spatial resolution of the model domain, and may be considered analogous to skin and form friction when characterizing natural alluvial bed environments. The objectives of this research are to assess the hydrodynamic impact of the added micro- and macro-roughness associated with a bioengineering pilot project planned in Quebec, Canada and to use this case study to propose new techniques for integrating increased roughness due to bank stabilization into numerical models. The roughness of the stabilization project is assessed by adjusting bathymetry to simulate macro-roughness features, and roughness coefficients to simulate micro-roughness features. Results show a significant dampening interaction term that reduced the cumulative effect on resistance to flow when both roughness types were applied.

Seaweed resources in India – current status of diversity and cultivation: prospects and challenges

Abstract Seaweeds are an integral part of coastal ecosystems and offer invaluable ecosystem services supporting the life of many marine forms. The economic value of seaweeds significantly contributes to the sustainable development of rural coastal regions. Seaweeds are consumed as food in some Asian countries, but their utilization for production of phycocolloids is widespread across the globe, with an estimated value of more than one billion US$. In India, seaweeds have been utilized exclusively for the production of phycocolloids but recently they are used for the production of plant growth stimulants for agricultural applications. The domestic agar and alginate industry totally depends on the supplies from natural seaweed beds with some occasional imports. The recent success achieved in both upstream and downstream technologies in production and processing of seaweeds has boosted the prospects for commercialization of seaweed resources in the country. The present article briefly appraises the current status of Indian seaweed resources and their utilization, as well as developments in seaweed farming technologies, the status of seaweed industry and recent efforts to transform seaweed farming into a social enterprise. It also highlights the challenges encountered for mainstreaming these resources so as to evolve into a marine industry.

Application of deep learning techniques for determining the spatial extent and classification of seagrass beds, Trang, Thailand

Abstract Few studies have investigated the long-term temporal dynamics of seagrass beds, especially in Southeast Asia. Remote sensing is one of the best methods for observing these dynamic patterns, and the advent of deep learning technology has led to recent advances in this method. This study examined the feasibility of applying image classification methods to supervised classification and deep learning methods for monitoring seagrass beds. The study site was a relatively natural seagrass bed in Hat Chao Mai National Park, Trang Province, Thailand, for which aerial photographs from the 1970s were available. Although we achieved low accuracy in differentiating among various densities of vegetation coverage, classification related to the presence of seagrass was possible with an accuracy of 80% or more using both classification methods. Automatic classification of benthic cover using deep learning provided similar or better accuracy than that of the other methods even when grayscale images were used. The results also demonstrate that it is possible to monitor the temporal dynamics of an entire seagrass area, as well as variations within sub-regions, located in close proximity to a river mouth.

A comparative analysis of capacity and non-capacity formulations for the simulation of unsteady flows over finite-depth erodible beds

Finite-depth sediment layers are common in natural water bodies. The presence of underlying bedrock strata covered by erodible bed layers is ubiquitous in rivers and estuaries. In the last years, the development of models based on the non-capacity sediment transport assumption, also called non-equilibrium assumption, has offered a new theoretical background to deal with complex non-erodible bed configurations and the associated numerical problems. Bedload non-capacity sediment transport models consider that the actual solid transport state can be different from the equilibrium state and depending on the temporal evolution of the flow. The treatment of finite-depth erodible bed layers, i.e. partially erodible beds, in bedload models based on the equilibrium approach has usually been made using numerical fixes, which correct the unphysical results obtained in some cases. Generally, the presence of a finite-depth erodible layer implies the introduction of a kind of non-equilibrium condition in the bedload transport state. Nevertheless, this common natural bed configuration has not been previously considered in the development of numerical models. In this work, a finite volume model (FVM) for bedload transport based on non-capacity approach and dealing with finite-depth erodible layers is proposed. New expressions for the actual bedload transport rate and the net exchange flux through the static-moving bed layers interface are used to develop a numerical scheme which solves the coupled shallow water and non-capacity bedload transport system of equations. The reconstruction of the intermediate states for the local Riemann problem at each intercell edge is designed to correctly model the presence of non-erodible strata, avoiding the appearance of unphysical results in the approximate solution without reducing the time step. The new coupled scheme is tested against laboratory benchmarking experiments in order to demonstrate its stability and accuracy, pointing out the properties of both equilibrium and non-equilibrium formulations.

The Logarithmic Law of the Wall in Flows over Mobile Lattice-Arranged Granular Beds

The purpose of the present paper is to provide further insights on the definition of the parameters of the log-law in open-channel flows with rough mobile granular beds. Emphasis is placed in the study of flows over cohesionless granular beds composed of monosized spherical particles in simple lattice arrangements. Potentially influencing factors such as grain size distribution, grain shape and density or cohesion are not addressed in this study. This allows for a preliminary discussion of the amount of complexity needed to obtain the log-law features observed in more realistic open-channel flows. Data collection included instantaneous streamwise and bed-normal flow velocities, acquired with a two-dimensional and two-component (2D2C) Particle Image Velocimetry (PIV) system. The issue of the non uniqueness of the definition of the parameters of the log-law is addressed by testing several hypotheses. In what concerns the von Kármán parameter, κ , it is considered as flow-independent or flow-dependent (a fitting parameter). As for the geometric roughness scale, k s , it results from a best fit procedure or is computed from a roughness function. In the latter case, the parameter B is imposed as 8.5 or is calculated from the best fit estimate. The analysis of the results reveals that a flow dependent von Kármán parameter, lower than the constant κ = 0.40 , should be preferred. Forcing κ = 0.40 leads to non-physical values of k s and would imply extending the inner layer up about 50% of the flow depth which is physically difficult to explain. Considering a flow dependent von Kármán parameter allows for coherent explanations for the values of the remaining parameters (the geometric roughness scale k s , the displacement height Δ , the roughness height z 0 ). In particular, for the same transport rate, the roughness height obtained in a natural sediment bed is much greater than in the case of bed made of monosized glass spheres, underlining the influence of the bed surface complexity (texture and self-organized bed forms, in the water-worked cases) on the definition of the log-law parameters.

Underwater Shell Middens: Excavation and Remote Sensing of a Submerged Mesolithic site at Hjarnø, Denmark

Shell middens, or shell-matrix deposits, occur in large numbers across the coastlines of the world from the mid-Holocene (ca. 6000–5000 cal BC) onwards, often forming substantial mounds. However, they become smaller, rarer or absent as one goes back into earlier periods, suggesting a world-wide process of economic intensification. Since sea level was generally much lower during these earlier periods, a critical question is the extent to which mounded shell middens could have accumulated on now-submerged palaeoshorelines, and if so, how they were affected by the potentially destructive impact of sea-level rise. Further, and important to modern practice, it is essential that archaeologists consider how such sites can be discovered through underwater investigation. Here we offer a proof of concept that shell middens can survive submergence and can be detected, using systematic investigation of a rare example of a confirmed underwater shell midden at the Mesolithic site of Hjarnø (ca. 5300–4300 cal BC) in Denmark. We compare the excavation results with the results of geophysical survey, explore the problems of distinguishing underwater cultural shell middens from natural shell beds and conclude that shell middens can survive inundation by sea-level rise and can be detected by remote sensing, but require at least minimally invasive sampling to establish their cultural status. We suggest the methods developed may be applicable to coastal and marine sites impacted by postglacial sea-level rise worldwide.

Environmental Problems Mining Industry in the Arctic

In this article characteristics and indicators of climatic conditions of a North taiga subzone where works on extraction of alluvial diamonds from alluvial deposits of the northern rivers are intensively carried out are considered. Mining works are conducted in the open career way with full transfer of the natural bed of the rivers. It is followed by pollution of the rivers and adjacent territories. For assessment of state of environment monitoring researches with studying of contents and migrations of minerals in a soil cover were conducted. Results of a condition of the chemical composition of soils before technogenic influence are given in work.

Idealisations of Dynamic Modelling for Railway Ballast in Flood Conditions

As the main component of a ballasted railway system, railway ballast is frequently used by the railway industry to enhance constructability and practicality. Numerous studies into train–track interactions focused on ballast modelling and idealisation in completely dry environments, but recent studies have found that, in extreme weather such as floods, water can clog natural ballast beds and change the initial state of their properties. Ballast models used in multi-body simulations have been mostly developed based on the instrumented impact hammering method considering the ballast as a spring/dashpot. The single degree of freedom (SDOF) idealization for ballast enables a non-destructive field testing technique for monitoring of railway components in practice. In this study, the suitability of the idealization of ballast for dynamic characteristics has been evaluated. A series of experiments have been performed with a variety of ballast conditions in flooding levels from 0 to 40 cm, with a frequency range of 0–500 Hz. The results clearly show that the increase in the flood level will result in increasing dynamic damping of more than 50% of dry natural ballast whilst reducing its stiffness and natural frequency. The novel insights are of great significance for exploring the non-linear dynamic traits of ballast in extreme environments, which can be integrated into the coupled train–track analysis that can better express more realistically the dynamic train–track interaction and load transfer mechanism of flooded railway tracks.

Macrozoobenthos community structure in restored seagrass, natural seagrass and seagrassless areas around Badi Island, Indonesia

Seagrass ecosystems play an important role in providing food and protection to the organisms that live in and around seagrass meadows. However, due to heavy pressure from human activities, many seagrass beds have been degraded, with the loss or reduction of important ecological functions. Therefore, seagrass restoration needs to pay attention to the recovery of these ecological functions. This study aimed to determine the success of the seagrass restoration activities around Badi Island, South Sulawesi, Indonesia, in supporting the recovery of ecological functions, as viewed from the macrozoobenthos community structure. Data on macrozoobenthos community structure in transplanted seagrass areas was compared with the macrozoobentos community structure of nearby natural seagrass beds and seagrassless areas. The macrozoobenthos identified comprised 34 species from 3 classes in the seagrass restoration area, 73 species from 9 classes in natural seagrass beds, and 24 species from 4 classes in areas without seagrass. A one way ANOVA test indicated significant differences in macrozoobenthos density between the transplanted areas and natural seagrass beds but not sites without seagrass. Ecological indicators such as the diversity index and evenness index showed a higher level of macrozoobenthos community structure in all the sampling sites. We conclude that, as transplanted seagrasses become established, they can provide ecological functions and serve as habitat for a wider variety of other organisms, as reflected in the community structure of the associated macrozoobenthic organisms.

The Impact of Hydrologic Characteristics of Mountain Watersheds on Geometric and Hydraulic Parameters of Natural Torrent Beds

The Impact of Hydrologic Characteristics of Mountain Watersheds on Geometric and Hydraulic Parameters of Natural Torrent Beds

Baseline pathological data of the wedge clam Donax trunculus from the Tyrrhenian Sea (Mediterranean Basin).

In recent years, a collapse in Donax trunculus fishing yields has occurred in the Tyrrhenian Sea (Mediterranean Basin). There is little information available on the impact disease may have had on D. trunculus populations. For the first time, a pathological survey was performed on the natural beds of the bivalve on the Campania and Lazio coasts, western Italy. Detected pathogens and related diseases were analysed, and their prevalence and mean intensity values were calculated. Viral particles, Chlamydia-like organisms, ciliates, coccidians, microcells and trematodes were observed. An unknown ciliate was linked to severe inflammatory and necrotic lesions in the digestive gland. Metacercariae of the trematode Postmonorchis sp. were also strongly represented in almost all samples, reaching high levels of infection; however, none of the pathogens described required the World Organisation for Animal Health to be notified. Initial results indicated that further surveys related to environmental data are necessary in order to assess the relevance of these early observations in managing the declining D. trunculus population in the Tyrrhenian Sea.

Toxicity assessment of arsenic on common carp (Cyprinus carpio) and development of natural sorbents to reduce the bioconcentration by RSM methodology

The objective of the present study was firstly acute toxicity bioassay of arsenic on common carp (Cyprinus carpio) and then the development of natural sorbent beds (clinoptilolite and pumice) to reduce bioconcentration of arsenic in muscle tissue were considered in comparative evaluation. In this regard, the acute toxicity of arsenic on juvenile fish was assessed according to the OECD guideline (No. 203). Moreover, the efficacy of clinoptilolite and pumice as natural sorbents was assessed to reduce bioconcentration of arsenic in the fish muscle tissue during a 21 day by response surface methodology (RSM) under central composite design (CCD). The most important point of this study was to evaluate the interactions between independent variables (clinoptilolite and pumice as sorbents and arsenic as pollutant) and arsenic bioconcentration in fish muscle tissue as a dependent variable (response). In these regards, a total of 24 sets of experiments (12 sets for clinoptilolite and pumice separately) were designed by the software to achieve the best adsorption conditions. According to the arsenic toxicity test, results as estimated by Probit method, the 96 h LC50 was 9.48 ± 1.01 mg/L. Analysis of variance (ANOVA) which was applied to modeling and optimization of response revealed that the predicted values were in relatively good agreement with the experimental data. Additionally, the obtained value for model desirability by clinoptilolite and pumice were 0.932 and 0.958, respectively. Overall, the obtained results indicate that both adsorbents reduced the bioconcentration of As (V) in the muscle tissue of common carp, but clinoptilolite was more effective.

The Changing Exploitation of Oysters (Ostrea edulis L. 1758) in Late Medieval and Early Modern England: A Case Study from Dudley Castle, West Midlands

ABSTRACTAnalysis of over 4000 complete left oyster valves from late medieval and post-medieval Dudley Castle reveals the changing role of this perishable luxury over a 700-year period. Throughout the occupation, it seems that oysters were used as ingredients rather than served raw in the shell. A greater reliance on oyster consumption is apparent in the later fourteenth century, perhaps reflecting a more diverse diet amongst the aristocracy in the wake of the Black Death. An increased preference for mussels and whelks is also attested in the Tudor and early modern periods, reflecting changing perceptions of these foods.Overall, it is likely that natural beds were exploited throughout the time that oysters were being brought to Dudley Castle; however, the evidence demonstrates a shift from limited exploitation of natural inter-tidal sources in the eleventh century towards the dredging of sub-littoral beds in later periods, with some possible translocation of oyster stock. Changes in the shape, size and appearance of the oyster shells suggest the source locales from which the oysters derived changed through time. A notable shift occurred in the fourteenth century, which could reflect changes in supply brought about by altered tenancy at Dudley Castle and/or disruptions to trade brought about by the Black Death. Future biochemical analyses are recommended to provide greater clarity on the origin of those sources.

Drastic difference in cadmium concentration in mussels (Mytilus chilensis) observed between seasons in natural bed and aquaculture systems in Chile.

Globally, Chile is the second largest producer of mussels, with 99% of production concentrated in the inland sea of the Los Lagos Region, Southern Chile. This study reveals that seasons produce a drastic difference in the cadmium concentration (Cd) in marine mussels in bay, channel, and fjord ecosystems in this area. As the global mussel industry continues its rapid expansion, a complete understanding of cadmium pathways is critical in order to minimize the cadmium content in harvests. In this study, biweekly sampling was conducted in Chiloé (Southern Chile), during five consecutive seasons from June 2014 to November 2015. Cadmium in the soft tissues (ST) and in the content of the digestive gland (CDG) of Mytilus chilensis were investigated, in addition to resuspensions and seston to determine the effect of the seasons on metal bioassimilation capacity. In spring, the (Cd) between CDG and ST varied by approximately 2mg Cd kg-1 dry mass (DM). In summer and autumn, the (Cd) in CDG increased from 3 to 6mg Cd kg-1 while the (Cd) in ST decreased from 2.5 to 1.5mg Cd kg-1 DM. The three ecosystems showed the same cadmium bioconcentration trends in all seasons, revealing coherent global trends. These findings should caution the industry and coastal populations about the seasonal variability and intensity of cadmium metal transfer to biofilters, especially because of the adverse effects of cadmium consumption on human health. Additionally, this study found that mussels in natural beds concentrate more Cd (> 1mg Cd kg-1 DM) than in industrial facilities. Multiregression analysis showed and explained the cadmium in CDG for three ecosystems: channel (R2 0.9537), bay (R2 0.5962), and fjord (R2 0.4009). The independent variable nocturnal seston was able to explain the increase in cadmium.

Diagnóstico de degradação do Rio Santa Bárbara no trecho urbano do município de São Gonçalo do Rio Abaixo (MG)

No decorrer da história verifica-se que o surgimento das cidades está vinculado à proximidade de um curso hídrico. Neste contexto insere-se o município de São Gonçalo do Rio Abaixo (MG) que surgiu e se desenvolveu às margens do Rio Santa Bárbara. Dessa forma, este trabalho objetivou elaborar o diagnóstico de degradação de um trecho de 5,35 km deste rio e a proposição de medidas visando sua restauração. Para tal, foi utilizada a pesquisa de campo para a observação das condições fluviais e ambientais, tais como morfologia e diversidade de habitats; além da análise de documentos referentes à qualidade da água e de imagens de satélite obtidas nos anos de 2007 a 2017 para avaliação do uso do solo no trecho analisado. Considerando a análise das imagens de satélite, notou-se a expansão da área urbanizada e a supressão da vegetação em alguns trechos do Rio Santa Bárbara. Além disso, verificou-se, de maneira geral, uma degradação considerada “média” para o trecho analisado, uma vez que o curso hídrico, apesar de estar em leito natural, recebe efluentes in natura. Com relação às técnicas de restauração propostas, visto que há localmente assoreamento e deslizamento das margens, podem ser utilizadas estacas vivas e biomantas para controle destes. Por fim, mostra-se necessária uma preservação contínua do curso hídrico, para isso, além de técnicas adequadas visando a mitigação dos impactos ambientais negativos identificados, as ações a serem implementadas devem envolver a sensibilização e participação da população local.

The prevalence of parasitic pea crab Afropinnotheres monodi in mussels depending on the degree of exposure of habitats: implications for mussel culture

XX Iberian Symposium on Marine Biology Studies (SIEBM XX) , Braga, Portugal, 9 Sep - 12 Sep, 2019.

The seaweed resources of Chile over the period 2006–2016: moving from gatherers to cultivators

AbstractChile, located in the southeastern Pacific, possess a high richness of seaweed species, some of which have been traditionally extracted from natural beds for the production of hydrocolloids (e.g. agar, carrageenan and alginates), but still a high proportion of the biomass is being exported as dried material to processors in Asia and Europe. During the period 2006–2016, this tendency has been maintained, but has also started to show signs of changing towards a more sustainable, localized seaweed industry as new actions by the Chilean government provided subsidies to seaweed farming activities and also to investments in local valorization of the resources. This “sea change” has been further supported by an increase in the number of localized scientific and technical studies related to Chilean seaweed resources which has prepared the foundation required in order to move to more advanced stages of local seaweed farming and development of local processing.

Spatio-temporal variability of strandings of the southern bull kelp Durvillaea antarctica (Fucales, Phaeophyceae) on beaches along the coast of Chile—linked to local storms

Availability of floating seaweeds may depend on the seasonal cycles of benthic populations, but our ability to predict temporal patterns of stranded biomasses is still limited. Season-dependent, local storms favor detachment of seaweeds from the substratum, which can be reflected in the stranded biomasses on adjacent beaches after these events. Hence, we hypothesized that seaweed strandings are positively correlated with storm intensity. Using as a model the southern bull kelp Durvillaea antarctica (Chamisso) Hariot, a species frequently found in seaweed strandings in Chile, bimonthly surveys were carried out on three beaches: Pichicuy (32° S), Itata Norte (36° S), and Curinanco (39° S) for 3 years (2014 to 2017). Stranded biomass, total length, and wet weight of specimens were quantified and related to local storms (using the Douglas sea scale). Stranded biomasses decreased in the spring months of each year, being higher in Pichicuy and Curinanco than Itata Norte. Regression models showed a better fit with recent storms in Curinanco compared to other beaches. An interannual decrease of beach-cast raft size was observed, showing smaller specimens in Itata Norte than those in Pichicuy and Curinanco. Reduced habitat availability and the exploitation of natural beds in the central zone (34°–37° S) might explain the decrease of biomasses and sizes of stranded bull kelps. Also, oceanographic features at intermediate (i.e., local winds and currents) and large scales (i.e., El Nino) can help to explain the temporal variability, particularly in spring and summer. Our results suggest that harvesting of stranded bull kelps might be most favorable in summer and autumn.