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Blog - Bioenergetics for management and conservation

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Anglet, France

Bioenergetics for management and conservation is a section of the Evolutionary dynamics and management application course at University of Pau and Pays de l’Adour (Anglet, France). In this course, 2nd

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    • Can new ecosystems develop in metal contaminated soils?by Robin Brouat and Théo Garcia

      Published by Charlotte Recapet the December 2, 2019 on 1:38 PM

      A recent study revealed that gray birch has interesting characteristics in ecological restoration, which allow the tree to support high metal contaminated soils.

      What is the experiment?

      Whereas the majority of scientists were kept in their laboratory testing contaminant, a group of American biologists performed an experiment in the field, a full-scale exercise.  In Jersey City, they measured a lot of photosynthetic parameters, in gray birch (Betulia populifolia) in two different conditions in Liberty State Park: One with High trace Metal Loads (HML) and the second with Low trace Metal Loads (LML). It results that none measured biophysical parameters vary. The only parameter that varied significantly was the leaf mass per area which decreased when the tree was in contaminated soil. This result can have two main explications. The first is that photosynthesis will no longer be affiliated with leaves but with other organs such as roots. The second is the fact that the tree will renew its leaves more often and this will impact its growth rate.


      Photo by Charlie Hohn

      Photograph by Richtid

      What is the link with ecological restoration?

      Gray birch can capture trace metals through their leaves and roots. This allows partial decontamination of areas polluted by heavy metals. Nevertheless, it is necessary to seed the plots after contamination so that only trees with a genotype with a high tolerance for trace metal concentrations grow. However, this decontamination by trees will not be possible anywhere in the world because trees are less efficient to get trace metals pollution in areas of high temperature and drought.

      It’s wonderful, but where is the new ecosystem promised?

      Yes, we are coming here. We can see an ecosystem like a pyramid with at its base the plants (also called primary producer) which convert the solar energy in organic matter for the higher steps of the trophic chain. In the study, the scientists explain that the diminution of leaf mass per area in HML affects the energy in entrance to the ecosystem. If less energy enters in the ecosystem, the whole ecosystem will be affected.

      Pretty cool! So what species could we find here?

      In theory this will be happened. But in practice, it could be quite different. Indeed, the diminution of Leaf Mass per Area is significantly, but does it could have a really impact on the ecosystem? The diminution it’s approximately 10g.m-2 and it’s not very well documented in the paper how this diminution could have an impact. In addition, we have just information about one species of primary producer; in a temperate forest we can found several tens of species which can do photosynthesis housing an animal diversity. For having a better idea of what kind of forestall ecosystem we can obtain, it seems better study the whole vegetal community of the site, and not simply a unique species.

      Hum, so this forest is not different than another one… So bad…

      Nevertheless, this study is interesting, and allows us to see the adaptation capacity of a specific tree to contaminated conditions. The gray birch is commonly used in ecological restoration, and the study proves that the species is robust for this type of projects. In the future, it will be frequent to walk in a forest, in a place in which in the past there was an industrial zone, without realizing the past of this forest. When local people will tell you that, before, there were factories. You will see the forest with a different way. And for this it will be a different forest for you. And it’s the more important.

      Cited study: Salisbury, A.B., Gallagher, F.J., Caplan, J.S., and Grabosky, J.C. (2018) Maintenance of photosynthesis by Betula populifolia in metal contaminated soils, Science of The Total Environment 625,1615-1627, https://doi.org/10.1016/j.scitotenv.2017.12.279.

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    • What does the future has in store for red salmon in a context of global climate change?by Camille Sestac and Amandine Tauzin

      Published by Charlotte Recapet the November 1, 2019 on 1:18 PM

      Pacific salmon have extremely complex life histories and may be threatened by global climate change, as Peter S. Rand and colleagues investigate in their recent study.


      Life cycle of Sockeye Salmon

      Among all species, fishes must adapt to face disruptions caused by global climate change. Sockeye salmon (Oncorhyncus nerka), an anadromous species of salmon found in the Northern Pacific Ocean and rivers discharging into it, has a complex life cycle. As a migratory species, their energetic demands are high during spawning migration. Climate change might have important impacts on populations and their migration via variation of river discharge, increase of water temperature and decline of growth conditions. Aiming to better understand the impacts of these disruptions on the migratory performance of this species of salmon, Peter S. Rand from Wild Salmon Center teamed up with researchers from British Columbia. Their goal is to evaluate the effects of past and future trends in river discharge and temperature on the migratory performance of Sockeye Salmon in the Fraser River.

      In a context of global climate change, it is crucial to understand the effects of disruptions on ecosystems and the populations living in them. Indeed, it is important to know the impacts of these disruptions on every stage of their life cycle (the juvenile freshwater period, the estuarine period, and the subadult marine period) so that we can maintain the populations stock. It’s especially important for fishery management because the fishing quota has greatly increased over the last decades and has threatened populations of Pacific salmon, particularly during their spawning migration. That’s why with three main objectives, these scientists used analysis to improve the understanding of how changes in river conditions can affect the energy use and the mortality rate in Sockeye salmon population. To do so, they used several models: one to search a link between energetic conditions of individuals and en route mortality, one to simulate the energy use during spawning migration and one to hindcast and forecast energy use by simulating fish’s behaviour and migration conditions (for more information, a tip, read the article!).


      Long-range forecasts of lower Fraser river temperature during the summer of 2018

      Using these friendly models, Rand and his colleagues proved that energy reserves and energy depletion of early Stuart Sockeye salmon are major factors that can affect their ability to reach their spawning grounds. They also stated that energy depletion is a function of both river temperature and discharge. Therefore, this population is structured by condition-dependant mortality. Nevertheless, this group of researchers brought to light a mechanism that allows fishes to cope with some environmental variability, providing a certain degree of resilience over time. Therefore, even if energetic demands and migration mortality increase as a result of exposure to warmer temperatures, it will be compensated by reduced time travel to the spawning ground as the river flow will be lower.

      However, increase of temperature means increase of diseases appearing and developing and that stress added may be a direct cause of increased mortality during migration. Finally, as if it wasn’t already bad enough for our salmons, ocean productivity can be affected by climate change and thus affect their river migration success. In fact, this can lead to a decrease of body size and body energy content. It implies that individuals will start their migration with lower energy densities and will be more likely to exhaust their energy stock before even reaching the spawning grounds.


      Salmon jumping over a weir
      According to the US-Canada Commission, a 21° C temperature spike was measured on the Fraser River in 2009. However, sockeye salmon show signs of physiological stress and migratory difficulties above 19°C and from 20°C, the first signs of illness and death appear. But migration of Sockeye salmon is not only threatened by climate change. In fact, migration of salmon specially is impacted by humans or natural obstacles. Dams and weirs form large obstacles for this migratory species and can be very difficult to cross. Many studies have already proved that this kind of obstacles, even when equipped with crossing devices, delay their migration and thus jeopardize their reproduction. This can lead to a decline of the population and in some cases to its extinction, as it happened in Belgium.

      So, whilst some questions have been answered, it seems that more studies need to be carried out to improve our knowledge about the impact of global change which seems to be another sword of Damocles hanging over the head of Sockeye salmon.

      Cited paper: Rand, P.S. et al. (2011) Effects of River Discharge, Temperature, and Future Climates on Energetics and Mortality of Adult Migrating Fraser River Sockeye Salmon. Trans. Am. Fish. Soc. 135(3), 655-667. https://doi.org/10.1577/T05-023.1

      Featured images: Life cycle of Sockeye salmon by Camille Sestac, graph from https://www.pac.dfo-mpo.gc.ca/science/habitat/frw-rfo/index-eng.html , Sockeye Salmon from www.ryanvolberg.com

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    • Organisms and their environment: Dangerous liaisonsby Marius Dhamelincourt and Charlie Sarran

      Published by Charlotte Recapet the October 14, 2019 on 9:15 AM

      Preface

              Whatever the incredulous think, organisms are necessarily linked to their environment to survive, science says. However, this relation, unstable, can be problematic for those concerned when variations overtake their acceptable thresholds. Although often natural, these variations can be exacerbated by anthropogenic actions, like putting fish on a grill.

              Global changes are often reduced to temperature increases, illustrated in the media with alarming news about ice melting and forest fires. While many people thus omit the complex mechanisms behind this black box, the necessity of a more “polar bear’s” respectful way of life is commonly accepted. In order to better understand how to respect such adorable creatures, scientists need to investigate their relationships with the environment.

      Chapter 1: Shells under investigation

              In order to scrutinize these relationships, selected species must be accessible, easy to catch/manipulate and in sufficient number. For instance, the study of the great white shark aggressivity over humans would require too many intern’s sacrifices. In response to this challenge, a valiant research team from Germany looked for the importance of these relations by studying in the Rhine a remarkable (body and soul), accessible, cheap and lovely species: Corbicula fluminea, a shell. This study is related to the mass mortalities events of this species, which occurred in the summer, especially in that of 2003. Their investigations aim to understand how these organisms are linked with their environment, and their reactions to changes.

      Chapter 2: Shells cooking in science

      Many tools exist to perform this type of search. Field searches can involve the scientist’s life (be bitten by a pigeon is a terrible experience…) and obstruct a long-term individual experiment. Now that researchers have selected the perfect organism, they must choose an appropriate way to analyse their problem. For this shell, scientists chose to use a modelling approach, a method dark and full of terrors. More precisely, they modelled several aspects of the metabolism of this organism at different scales: individual and population levels, using respectively DEBM (Dynamic Energy Budget Model) and PSPM (Physiologically Structured Population Model). This method, widespread in ecology, consists to “simulate the annual growth in length and mass and the reproductive success under different environmental scenarios”. This approach is suitable because an organism can respond differently relatively to their peers. Such fact can be proved by looking at many places and species, humans included… Ultimately, scientists aim to better understand the complex relation between the energy available in the environment and its utilization by shells.

      Chapter 3: Corbicula’s deadly summers

      Heat waves are often responsible for changes that every scientist can observe on living organisms. For instance, it is known that coral reefs are affected by increased temperatures, as shown in an article published in “Free Radical Biology and Medicine”. Many other examples such as lobster’s behavioural response to boiling water could be developed. Regarding our shellfish, scientists found an interesting pattern comforting our previous remark: temperature causes shell’s mortalities… Oh wait, no, it’s more complicated.

      In fact, mass mortalities events were probably related to a melting pot of many events like temperature increases and/or starvation. Moreover, these situations are also in relation with individual conditions. Indeed, researchers hypothesized that a combination of factors (biotic and/or abiotic), usually non-lethal under regular summers, can be problematic at high temperatures. Unfortunately, models developed were not able to explain completely the observed mass lethal events.

      Chapter 4: Life is not so simple

      Researchers finally enhance the comprehension of population dynamics, enlightening its complex mechanisms. However, in such cases, wishing to be exhaustive is useless and unproductive, like politics. That is why scientists look for compromise between easy-to-use and complicated (highly realistic) tools. For example, the authors of the Corbicula’s study proposed that it could be interesting to test other parameters, such as parasitism.

      To put it in a nutshell (you got it, right?), things are not always what they seem to be, even in environmental studies. Main hypotheses are not always validated, and measures considered can be only a part of a more complex system, or sometimes even unappropriated. On the flip side, model’s development can help to understand the life cycle of organisms like Corbicula, thus helping to manage populations concerned.

      Cited study: Petter, G., Weitere, M., Richter, O., Moenickes, S., 2014. Consequences of altered temperature and food conditions for individuals and populations: a Dynamic Energy Budget analysis for Corbicula fluminea in the Rhine. Freshwater Biology 59, 832–846. https://doi.org/10.1111/fwb.12307

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    • Avoid predation or starvation: which strategy maximize rainbow trout juvenile survival?by Léa Bulon and Mylène Jury

      Published by Charlotte Recapet the September 9, 2019 on 7:12 AM

      Natural populations are increasingly exposed to a range of biotic stressors, such as predators, and abiotic environmental stressors such as environmental variations (seasonality -  Wingfield, 2013) or chemical pollution (Fisher et al., 2013). (We could think to grandma Margaret who throws away her bleach bucket directly into the river or grandpa George who loses all his plastic lures into the lack). The first year of life is complicated for all organisms because they are more sensitive to those kinds of stressors and their survival is highly impacted.

      In temperate zones, fry are subjected to high predation during the growing season and a nutritive resource deficit during winter. This is why juveniles need to find the best way to maximize their survival and make population viability durable through the time. Predators prefers a fry-up of little fish, it is why predation mortality is higher in small fish than large (Parkinson et al., 2004). However, growth itself may impose a significant energy mobilization which can drive trade-offs between growth and other metabolic processes. If you are really interested by the topic but not by fish, we recommend you to look at the article written by Mcleod et al., 2008, about birds.

      During winter, the metabolism needs some fuels like lipids and proteins to work because resources are often limited. Production of energy storage is energetically expensive, and energy contributes less to increasing their body-size.

      Is it better to allocate their energy into the growing season to avoid predators or into the lipid storage to survive during winter?

      Stephanie Morgensen and John R. Post, scientists from Canada, are been interested in this process. They led an experiment with juvenile rainbow trout (Oncorhynchus mykiss). They developed a mathematical model to determine the energy allocation strategy maximizing the first-year survival of rainbow trout.

      Rainbow trout juveniles are sampled from two sets of lakes in British Columbia in Canada. The first site is located on the Bonaparte Plateau and it corresponds to highly and cold lakes. The second site is located near the town of Merritt and it corresponds to low altitude and warm lakes. In warm lakes, the winter season is shorter than in cold lakes and there are more resources for juveniles.

      They found that juvenile growth is different between the two kinds of lakes: fish from the cold lakes growth more than fish from warm lakes. As we said before, production of lipid storage consumes more energy than growth and resources are more abundant in warm lakes. It is why, fish from warm lakes are more able to stock and fish from cold lakes, to growth. However, fish do not follow only one strategy. Indeed, they grow during the first part of the non-winter season and then they put their energy into the lipid storage to survive during winter. This switch between the strategies is controlled by environmental conditions and determined trout survival during winter.

      The juvenile survival trade-off influencing by environmental conditions such as temperature and resource availability would be important to understand population viability with the evolution of environmental conditions. Rainbow trout has been introduced into many streams and water bodies for recreational fishing because they are easy to catch and quite combative (fishing federation). They constitute an important economic interest it is why, it is one of the most studied species by biologists (INRA). This may lead to management measures to improve pisciculture conditions or to instore fishing quotas and a minimum size of capture. It could be also interesting to know if energy allocation strategies affect physiological processes like growth or reproduction.

      And you what would you choose to survive during winter?

      Cited study: Mogensen, S., & Post, J. R. (2011). Energy allocation strategy modifies growth–survival trade-offs in juvenile fish across ecological and environmental gradients. Oecologia, 168(4), 923–933. doi:10.1007/s00442-011-2164-0

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    • Zinc pollution of our rivers: shrimp on alertby Lucille Baron and Macha Joanin

      Published by Charlotte Recapet the August 12, 2019 on 10:03 AM

      No, we will not make an exhaustive catalog of the pollutants that affect our streams and boredom will not settle in your heads by reading us. Instead, we have chosen to discuss the effect of one of the very present emerging pollutants zinc on Gammarus pulex, through the study of Maltby and Naylor (1990).

      At present, world zinc production is over 13,000 kilotons (2018). Zinc is commonly used in metal corrosion coatings and for the manufacture of fertilizers and pesticides (European Commission, 2008b). Thanks to its physico-chemical properties, zinc melts particularly in fresh water, and it is absorbed on suspended solids and sediments (INERIS, 2014). All organisms living in these ecosystems are therefore exposed to this pollution and therefore, indirectly, we too, human.

      Thus, it is important to measure the risks of this exposure on organisms and especially to know the effects of zinc on populations in the long term. For this, researchers have studied, experimentally, the energy deployed in the reproductive mechanisms by aquatic organisms exposed to zinc at different concentrations. In additions, they sought to know if exposing females during a first brood (called current) could have an effect on their second brood unexposed (called subsequent).

      Gammarus pulex is a sentinel species, not only because this shrimp is abundant in fresh waters of England, but in addition it is fed with particulate matter which constitutes, in the natural environment, a large zinc stock. To measure the risks of maintaining the species and the genetic heritage of each individual under the effect of zinc, it is sufficient to study the offspring of females exposed to this compound at different concentrations. The number of individuals which hatched, and the size of each one give some indication of the energy allocated to reproduction. That's what researchers at the British Ecological Society did. If you haven’t understood anything about our attempt to explain the methods used to carry out the study experience, here is a summary diagram that you may be clearer!

      The results they obtained are surprising and show that exposure to zinc (even at low concentrations) significantly increases the number of broods aborted. This result is related to the decline of foods assimilated by females when they are exposed to zinc. The total energy drawn from food is no longer sufficient to sustain metabolic needs while maintaining the mechanisms of maturation and reproduction. Nevertheless, when exposed females carry her brood to term, the number of offspring of each does not seem to vary, despite of the difference in duration of exposure. So, a small criticism of the Figure which represent the percentage of broods aborted in function of the concentration of zinc (Figure 3) can be realize : we found in the control situation (not exposed to zinc), a great variability between the two categories tested. So, in science when the" control "already has significant variability, the results should be interpreted with caution thus it is difficult to conclude to a difference between the current and the subsequent.

      The results concerning the size variation of the descendants, bring a complementarity to this analysis because the researchers observe a reduction of the size in the generations following the exposure. It is the reduction of the available energy (females stopping feedings) which as a consequence the reduction of the size of the individuals of the next brood. Also, on this point, it is unfortunate that the study does not take into account the size of the female that could have an impact on the size of the offspring (Taïr-Abbaci K., 2016).

      The increase of the number of broods aborted and the decrease of the size can have a negative impact on the fitness of populations as exposure to zinc increases abortion. Also, the smallest offspring will take longer time to mature and under stress conditions, this phenomenon may be aggravated over generations and the snowball effect may strongly decreased fitness of individuals. Ultimately, these effects can have a profound impact on the entire population.

      The study seems relatively far from reality since it remains experimental, in the laboratory, and is not carried out in a natural environment and therefore with real conditions of experimentation and exposure to zinc. Thus, the adaptations set up or not by the organisms and the cocktail effects (potential combined effect of different compounds) are not taken into account.

      Nevertheless, the study above begins to be old, the latter dating back to 1990.Today, techniques allow to observe the embryonic development precisely and it turns out that during the different embryonic stages aberrations can appear (Bach et al., 2010). Then, it is difficult to think that abortion is the only response implemented by females when exposed to these chemical compounds. 

      In addition, reproductive success does not depend solely on embryonic development. It is important to consider the energy allocated to ovocyte development and the search for sexual partners to define the impact of zinc on the Gammarus pulex cohorts.

      It’s possible to reduce the production of zinc with recycling it.  However, the recycling of metals can sometimes be too expensive for small industries or privates companies. So, there are other ways than the installation of water decontamination mechanisms. Thus, bio-decontamination can be considered for these companies or industry but can also be useful to large industry in addition to their mechanisms for an exhaustive decontaminations and better water quality. Agriculture is also a source of metal pollution, so it is important to carry out hedgerows planting campaigns near fresh water since they have the function of absorbing a large part of the contaminants resulting from the leaching of flooded soils.

      Cited study: Maltby L. and Naylor C. (1990) Preliminary observations on the ecological relevance of the Gammarus ‘scope for growth’ assay: effect of zinc on reproduction, Functional Ecology. 4, 393-397.

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    • Albatrosses: the laziest ocean birds?by Manon Yerle

      Published by Charlotte Recapet the July 8, 2019 on 9:51 AM

      Movement ecology is a new scientific discipline that studies the movement paradigm in the animal kingdom. The fact is: How foragers choose their hunting technics? Foragers are animals that need searching in wild food resources. Since 1960s foraging theories are studied over the world. It’s known that free-handing animals must maximize their energy gain in order to spend as little as energy possible to find and catch their preys. To better understand how this works, some scientists conducted a study about the foraging strategy of the wandering albatross (Diomedea exulans). In this study they integrate instantaneous energy budgets within the movement ecology.


      Wandering albatross (Diomedea exulans) in sit-and-wait (SAW) foraging strategy. Credit: John Harrison

      Maybe, you have already heard “albatrosses are always sitting on water”, “albatrosses are lazy birds” …In fact when you see one, most of the time, it’s resting on surface of the water and does NOTHING! Why is it doing that whereas it could be attacked by sharks? Moreover, water is very cold! To answer at this primordial question, the foraging strategy of the wandering albatross was studied and well characterised in the Southern Indian Ocean. Four strategies are known: foraging-in-flight (FII), area-restricted-search (ARS), sit-and-wait (SAW) and resting (RES). Strategies depend on external conditions like weather features or wind, etc… In the study, between 2002 and 2005, during brooding periods, 45 birds were tracked but prey data capture were available only for 18 foraging trips. Over 18 birds, only 5 were studied because they were complete for all data.


      Albatross in FII foraging strategy. Credit: John Harrison

      Authors assumed that net energy gain equal to energy gain minus energy expenditure. Energy gain is estimated by prey capture data (stomach temperature and digestion time) and conversion factors corresponding to the diet of the wandering albatross. Energy expenditure is estimated with continuous measures of heart rates values during trips. Finally, total trip net energy is estimated by cumulating instantaneous net energy gain along the trip. Assuming external factors (wind speed and angle between flight and wind) affects foraging, they implement the flying cost model to provide energy expenditure estimates.

      The most used foraging strategy is sit-and-wait because this strategy is better for the brooding period; they obtained higher net energetic gain when foraging trips are short. So, albatrosses aren’t lazy, but they are searching for food. Are their results available regarding fewer numbers of individuals? In statistical analyses it is assumed that results are available if the number of individuals is higher than 30, which is not the case here.  Moreover, optimal models don’t work in wild life because there is always external factors that prevent it.

      Whereas previous studies (Weimerskirch et al. 2005) identified FII strategy as the most optimal for long trips, our study identified another strategy for shorts trips, SAW. In fact, birds need to provision chicks frequently and that requires more energy than during incubation. Breeding stage defines the foraging strategy used. Another study should be managed during the incubation period implementing an instantaneous energy-budget model. Moreover, they should implement internal factors as thermoregulation that is more important in SAW for example. Now, we know how wandering albatrosses choose their foraging strategies. We can ask if SAW really is a good foraging strategy because albatrosses are more vulnerable against predators like tiger sharks.

      Cited study: Louzao, M., Wiegand, T., Bartumeus, F. et al. (2014) Coupling instantaneous energy-budget models and behavioural mode analysis to estimate optimal foraging strategy: an example with wandering albatrosses. Mov Ecol 2, 8. doi:10.1186/2051-3933-2-8

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    • A damned energy loss for migratory fishes: dams!by Manon Salerno

      Published by Charlotte Recapet the June 10, 2019 on 9:42 AM

      Many species of fish grow in the sea and breed in rivers. These migratory fish are called anadromous. When a migratory fish is ready to breed, it leaves the sea and up a river to lay watershed upstream. It will find the optimum conditions to reproduce and allow the development of its offspring. But to do so, they spend a lot of energy on the upstream and sometimes, obstacles like dams in their path does not make it easy for them. This is the case of American Shad in the Connecticut River in the United States. Since the 1970s, 4 hydroelectric dams have been built in the river. Even if they are equipped with fish ladders, these obstacles require the Shad more energy to cross them than if they were not present. We know energy availability can be a limiting factor in migration. Thus, in 1999, scientists wanted to understand energy management in these fish, especially when it is modified by the presence of such.

      Any organism needs energy to perform the movements / migrations necessary for its life cycle. When they are heading into a period that will not allow them to feed (overwintering, migration), some species store energy, such as the bear before hibernating. For American Shad, this stock has to be created before migration because it will not feed during this move. First, scientists have found these are subcutaneous lipid reserves and skin constitute a special tissue for energy storage, which is rather unusual. Salmon, for example, usually mobilizes lipids from muscles and viscera. In contrast, for migration, somatic tissues (red and white muscles and skin) provide about 90% of the energy required in shad.

      According to this study, crossing dams is expensive in energy, especially for females. In fact, American Shad is a species able to reproduce itself several times in its life, but if migration requires too much energy, it will only happen once. It is therefore easy to understand a multitude of dams can have an influence on the reproduction of these fish and therefore on population size, even if they are equipped with systems allowing fish to pass. Not to mention some fish do not even find the fish ladder. These are more likely to be stressed, eaten by predators such as birds, or competing with other fish and unlikely to breed.

      Although fish ladders are quite efficient at the upstream for the American Shad, it is sometimes not suitable for other species. In addition, the outmigration can also present risks of mortality (water retention, drop height etc ...). It is therefore essential to remove the dams for which their function is not provided anymore. But in the United States, the erasure of small dams often meets opposition from local communities. Even though many dams have been removed, they represent a strong historical or landscape value for the inhabitants, creating tensions between the supporters of the restoration and the local communities. This situation reminds the context existing in France, where the aesthetic and historical arguments are very powerful. Many dams are attached to mills and water plants of olden times are therefore seen as a "living historical landscape" very characteristic of their landscape. Because of the local character of each operation, an opposition not necessarily collective but influential and well directed, is enough to block some sites.

      Cited study: J. B. K. Leonard and S. D. McCormick (1999) Effects of migration distance on whole-body and tissue-specific energy use in American shad (Alosa sapidissima). Canadian Journal of Fisheries and Aquatic Sciences 56(7), 1159-1171

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    • Pesticides and the power of earthwormsby Orane Becheler

      Published by Charlotte Recapet the May 10, 2019 on 6:04 PM

      We know that our current high use of some pesticides is harmful for the environment. For example, the controversy begun several years ago (National Geographic News, 2013 and Actu Environnement, 2018), about the disappearance of bees and the use of pesticides. Many of us have heard about this. In this context, assessing a priori the impacts of pesticides on environment can be helpful. This is why, five UK scientists have developed a model to anticipate the impacts of pesticides on the physiology of one species of earthworm, Eisenia fetida (A.S.A. Johnston and al., 2014).

      Why is it important?

                    The impact of pesticides on the growth and the reproduction of earthworms can lead to a huge decrease of their density and maybe to their disappearance. However, these organisms are very important for the soil quality. They provide good aeration and mixing of soil (call bioturbation) making it easier to absorb and keep water. Moreover, they greatly contribute to the degradation of organic matter making it accessible to other organisms. Indeed, a study of Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA, 2010) shows that, in a month, 1.5kg of earthworms (approximately 7,500 worms) can consume 30 days’ worth of a two-person household. In this way, plants growth better on a soil with earthworms than one without. This can be a great axis of reflexion about our way to produce vegetables. So, simulated impact of a pesticides on an area before destroy its ecosystem is a really good thing. Furthermore, we can see the importance of earthworms through their utilisation to evaluate the biodiversity in a participatory protocol (OPVT).

      In the video below, we can see the mix of soil by the earthworm’ displacements. Earthworms played a significant role in bioturbation.

      How did they do it?

                    These five UK scientists built complex model, call an energy-budget driven ABM. It consists of an interlocking of two model types: a huge one, an ABM (Agent Based Model), which contain many simple energy budget models. The first one allows to model how the population will progress, in other words the population’s dynamic. The second type allows to model life cycle processes for each earthworm from specified local conditions. Maybe the following picture can help you to understand.

      What did they found?

                    The main results are a decrease of growth and reproduction for the use of two pesticides.


      Modelling dose-response curves of two pesticides on the growth and the reproduction of Eisenia fetida. Adapted from the article.

                   Pesticides tested in this study are copper oxychloride and chlorpyrifos. The first one is widely used as fungicide and repellent, is not biodegradable and is “toxic to mammals and most biodiversity” (IUPAC, 2018). The second one is a current insecticide, “moderately persistent in soil systems, […] is highly toxic to mammals, […] birds, fish[es], aquatic invertebrates and honey bees” and “is classified as a reproduction toxicant, an acetyl cholinesterase inhibitor and a neurotoxicant” (IUPAC, 2018). So, the use of these pesticides can have large consequences not only on earthworms’ populations and so modelling consequences on others species is great.

                    Another study, presented by the Institut National de la Recherche Agronomique (INRA, 2014), shows also a decrease of earthworm populations when the quantity of used pesticides increases and vice versa (Pelosi C. et al., 2013).

      They have input local conditions of experimental data from literature. Their outputs fit great with the literature’s results, for non-toxic environments and for toxic ones, both individual life cycle processes and population dynamics.

      What is good and what is not?

                    Their model seems extremely complete because they incorporate varying food availability, use three steps of life with different parameters, for the adult stage they consider each step of processes under different feeding conditions and they consider interactions between individuals.

      In the ABM, they use a model landscape of 0.01 m2 patches of soil. It’s 10 cm2. I find this very small for a model which would simulate what it’s happening in the field. Moreover, further work is required to apply this approach to others species, maybe more ecologically relevant, and to implement the “heterogeneous distribution of chemicals in the soil and their degradation with time”. But this model can be useful to help to extrapolate data from laboratory to field or from species to species.

      Cited study: A.S.A. Johnston, M.E. Hodson, P. Thorbek and al. (2014) An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides. Ecological Modelling 280, 5-17.

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    • A new approach of modeling dissolved organic matter release by phytoplankton. Is it an improvement?by Bastien Mourguiart and Thomas Panarotto

      Published by Charlotte Recapet the April 12, 2019 on 6:53 PM

      Phytoplankton is playing key roles in marine ecosystems. These microscopic plants are known, in particular, to be a part of the “Biological Pump”. Using photosynthesis as metabolism, it fixes carbon of the atmosphere to produce energy. This process reduces atmospheric concentration of CO2 and limits the greenhouse effect. It also produces oxygen indispensable to the life of many organisms.

      Phytoplankton forms the basis of the marine food chain. Autotrophic organisms, they convert sunlight energy into chemical energy (food). This food constituted by molecules with carbon (organic matter) can pass directly along the food chain when zooplankton eats the phytoplankton and in turn are consumed by larger animals such as fishes, whales, squids, shellfishes and birds. Organic matter (OM) can also be released by phytoplankton in a dissolved form named dissolved organic matter (DOM). Organic matter can then be absorbed by bacteria and enter the main food chain when bacteria are eaten by zooplankton.


      Marine food web

      Heterotrophic prokaryotes (all animals) use carbon contained in DOM as a major source of energy.  So, products excreted by phytoplankton are really important in the functioning of marine ecosystems and understand how DOM is released in the environment is essential.

      Livanou et al. present in their article “A DEB-based approach of modeling dissolved organic matter release by phytoplankton” a new model to calculate DOM release by phytoplankton. They apply Dynamic Energy Budget (DEB) theory on phytoplankton cells for that. In this study, the metabolism theory leads to describe DOM fluxes, based on assumptions about energy uptake, storage, and utilization of N and C. The authors are mainly interested in how DOM is excreted by phytoplankton under different nitrate concentrations.

      They calibrate and test the goodness of fit of the model using past laboratory data. In this previous experiment, others scientists (Flynn et al. 2008), measured DOM released by one species of phytoplankton with two phase of nutrient concentration: one with enough nitrate for all the individuals and one with nitrate in limitation. The results of DEB-Model fit well to experimental data according to Livanou et al. even it does not explain all the information: in the figure below, lines (the model) do not fit exactly the points (experimental data).


      Figure 2 in Livanou et al.

      To conclude, they explain quickly that their model permit to describe how DOM is released. In no N-limitation condition, passive mode is used and DOM excreted is more accessible for bacteria. For N-limitation condition, DOM released cannot be used by bacteria and it tends to accumulate.

      This study is maybe a step forward in comprehension of phytoplankton physiological mechanisms. However, in our opinion, it is not really useful to improve our understanding of energetic flows in the oceans. Moreover, the model was calibrated for only one of the thousand species of phytoplankton existing in nature. It should be calibrated for others species to catch up more processes which can change between species. The model can be more accurate catching up all the processes in this particular species too: the fitting test shows some differences from the experimental data (Figure 2). There is also limiting by the fact that only one nutrient is used as limiting nutrient: in reality, there can be more (Moore et al. 2013). To summarize, it needs very lot of work on this model to employ it in real ecosystems and be an improvement.

      Cited study: Livanou E. et al. (2019). A DEB-based approach of modeling dissolved organic matter release by phytoplankton. Journal of Sea Research 143, 140-151.

      Other references:

      Flynn, K. J., Clark, D. R., and Xue, Y., (2008). Modeling the release of dissolved organic matter by phytoplankton, J. Phycol., 44, 1171–1187, https://doi.org/10.1111/j.1529- 8817.2008.00562.x

      Moore, C. M. et al. (2013). Processes and patterns of oceanic nutrient limitation. Nature geoscience, 6(9), 701.

      Image source: Maggy Wassilieff, 'Plankton - Animal plankton', Te Ara - the Encyclopedia of New Zealand, http://www.TeAra.govt.nz/en/diagram/5137/marine-food-chain (accessed 8 February 2019)

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    • High throughput screening methods to assess pollutants effects: A relevant technique?by Alexandre Bijaye and Melody Fernandez

      Published by Charlotte Recapet the March 12, 2019 on 6:43 PM

      The purpose of the paper written by Miller et al. in 2016 is to assess the effectiveness of HTS (High Throughput Screening) techniques to predict the effects of metal nanoparticles on a population of Isochrysis Galbana, a common species of phytoplankton. 

      High Throughout Screening is one of the newest techniques used in toxicology and which is planned to be implemented in biological and chemical sciences in the near future. Their technology is based on the analyzes of chemical compounds to be conducted in a short time. The affinity of biological structures which is related to the toxicity to be defined. 

      In this article, we’ll focus on nanoparticles: Engineered nanoparticles (ENPs) are actually an emerging form of metal contamination. These particles are widely used in biochemistry, engineering,… Four elements are studied in this paper: Ag, ZnO, CeO2 and CuO. The studied concentrations of each compound chosen were known to affect phytoplankton populations.


      Silver nanoparticules (T. Theivasanthi/Wikimedia)

      The results showing a decline of the photosynthetic activity (PSII) are compared to the HTS tests results. DEBtox models are energycally and toxycodynamically balanced modelling techniques (DEBtox and TD) and are here used to evaluate the impact of ENPs.

      First, the decline in photosynthetic activity is a good predictor. Phytoplankton are vulnerable to pollution, particularly because of their aptitude to accumulate contaminants. As a result, such a bioaccumulation can impact food webs integrity.

      Isochrysis Galbana populations were cultured at 20°C in sterile seawater (at 34 per thousand of salinity). In these conditions, HTS techniques measured cellular lesions responding to a toxic agent, permitting here to measure the potential impacts of ENPs on organisms. 

      Four HTS tests were undertaken (based on the mitochondrial membrane potential, ROS occurence, (3) cellular efflux pump action and cell membranes permeability). These tests are based on fluorescence and cell health. The impact of metallic nanoparticles was also measured. However, the results obtained were not consistent enough to highlight responses to ENP exposure:

      Non-HTS tests were performed by the measurement of the impact on photosynthetic efficiency. The metal concentrations were measured using the graphite furnace atomic absorption.

      Fluorescence kinetics of chlorophyll was also measured with an amplitude modulated pulsed fluorometer. Then the maximum fluorescence yield was computed using WinControl Software. This  the maximum fluorescence variation is assumed to be a measurement of the potential quantum yield of the PSII.

      A clear decrease in the performance of the PSII was observed for all the ENP’s:

      1. A greater decrease was observed for ZnO
      2. Also, a notable decrease was measured for CuO, at low concentrations
      3. Finally, the presence CeO and Ag decreased the performances as well even though the decrease was the smoothest.

      According to the authors, these results linked with the different dissolution rates that are specific to each compound. In this direction, Zn has a high dissolution rate, CuO and Ag dissolve very slowly and CeO has an undetectable dissolution rate. 

      As a conclusion by the authors, HTS methods can not be used to measure the impacts of metal particles because of their poor predictive power. So far, traditional ecotoxicological methods must be used.

      With such results in mind, we also agree on this statement: the four tests led by the authors all brought different conclusions. As HTS methods rely on the affinity of biological structures which is often related to toxicity to be defined, the presence of cellular compensatory mechanisms could have masked cellular responses to ENPs expositions.

      In conclusion, although HTS methods offer promising opportunities in the biological sciences (such as ecotoxicology), there are need for further investigation in this area before these techniques can be commonly adopted and used.

      Cited study: Miller, Robert J., et al. (2016) Photosynthetic efficiency predicts toxic effects of metal nanomaterials in phytoplankton, Aquatic toxicology 183, 85-93.

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    • Identifying the optimal depth for mussel suspended culture in shallow and turbid environments.by Yann Godard and Louna Riem

      Published by Charlotte Recapet the February 1, 2019 on 4:52 PM

      Bivalve aquaculture is commonly carried out in shallow water where there is an important influence of winds, tide and currents. These factors can lead to the remobilization of particulate matter which is an important source of food for bivalves. However, the concentration of the particulate matter in water can be minimized by the filtration capacity of high density cultured bivalves. In order to improve the productivity of cultured bivalves, it is important to take into account these different parameters. Indeed, it will help to know where is the best place for bivalve’s growth.


      Skive Fjord mussel farms - https://northsearegion.eu/watercog/pilot-projects/skive-fjord-dk/

      A study conducted in a Fjord in Denmark suggests that the TPM (Total Paticulate Matter) in the environment of culture is very important for the growth of mussel. The autors have built two models to understand the mechanism:

      • The first model try to give a pattern of the vertical distribution of resuspended materiel by including, among others, the particles concentration at 1m above the seafloor
      • The second model allows seeing the growth mussel at different height in the water column and calculates growth rates. This is made under different scenario of food availability.

      Both of these models allow determining the optimal localization of mussel in the water column for the better production.

      Firstly, the authors have determined the characterization of seston in the long-term and in the short-term. They observe that there was important correlation between wind and TPM but with a lag of 9 hours. Thus, they say that the remobilization of particles is not depending of the wind in the farm but of the remobilization in another place in the fjord for the short-term seston characterization. These particles are then transported by water current until the Fjord. Moreover, a correlation is also observed between the chlorophyll concentration and the TPM but not between the water velocity and TPM.

      For the long-term, they were able to highlight that the repartition of seston, and particulary phytoplankton in the water column was not homogeneous. There is a difference in concentration at the bottom and at the top with more phytoplankton at the surface (because of the lightening).

      Secondly, the authors wanted to characterize the growth of mussels under different conditions of availability of food with the hypothesis that the concentration of phytoplankton is homogeneous in the water column. The results say that in reality, there is more phytoplankton in the surface, then, the growth in the top is not very well implemented in the model. They conclude that it is important to consider the position of bivalves in the water column for an optimal growth.

      The dynamic energetic budget model shows that it is important to have a lot of phytoplankton and less detritus in order to get a better growth whatever the position of the culture. Moreover, this model allows showing that the variation of growth between the top and the bottom is only 2.6% which is negligible. They conclude this part by suggesting that “The reduced impact of height above the seafloor on mussel growth is related to the small contribution of resuspended material compared to the high background concentration of detrital matter”.

      This study takes place in a Fjord where the conditions are highly variable (changes in the tide, current, wind…). This is not implemented in the model. Therefore, it could be interesting to add some hydrodynamics parameters in the model in order to adjust it. Moreover, to improve the model, it would be wise to include some biological mussel parameter like the energetic costs of pre-ingestive sorting and pseudofaeces production. This model could be experimented in different places and different moment to validate it.

      Cited study: Filgueira, R., Grant, J., and Petersen, J. K. (2018). Identifying the optimal depth for mussel suspended culture in shallow and turbid environments. Journal of Sea Research 132, 15-23.

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    • Global change and climate-driven invasion of the Pacific oyster along European coasts: a bioenergetics modelling approachby Mélanie Gouaux and Lise Guégniard

      Published by Charlotte Recapet the January 8, 2019 on 3:20 PM

      Environmental changes such as seawater warming, and coastal eutrophication have an impact on breeding, larval survival and recruitment of marine benthic species. Global change induces changes in the natural distributions of native species and facilitates the spread of non-native species. Nowadays, the spread of non-native species in marine ecosystems around the world is one of the most serious environmental concerns. In receiving ecosystems, consequences of biological invasions are readily identifiable when invasive species are ecosystem engineers such as polychaetes or bivalves.

      Scientists of the French Research Institute for the Exploitation of the Sea and of the university of Nantes investigated how global change relates to the invasion of European coasts by a non-native marine invertebrate, the Pacific oyster Crassostrea gigas.

      This species was introduced on the European coasts of the Atlantic at the end of the 19th century for shellfish culture purposes and is the main oyster species farmed in Europe today. In recent decades, the Pacific oyster has acquired invasive species status with the expansion of its biogeographic distribution along the northwestern European coast beyond its initial zone of introduction into sites breeding. Bourgneuf Bay on the French Atlantic coast was considered as the northern boundary of C. gigas expansion at the time of its introduction to Europe in the 1970s. From this latitudinal reference, variations in the spatial distribution of the C. gigas  reproductive niche were analysed along the northwestern European coast from Gibraltar to Norway.


      A bed of Pacific oyster Crassostrea gigas in the Netherlands - Bas Kers - CC BY-NC-SA 2.0

      Mechanistic models are valuable tools for this purpose, and modelling approaches are useful for gaining a quantitative understanding of the effects of environmental changes on marine communities, and predicting their responses to projected climatic trends.

      The use of the IBM and DEB models has shown results at different scales, at the individual scale, at the Bourgneuf Bay scale and at the European scale.

      At the individual level, the results showed interannual variability of the dry flesh mass (DFM). A loss of DFM is explained by a spawning event. There has been a significant increase in DFM and the number of oocytes in recent years. To explain these results, they studied the relationship between the environmental conditions in late spring and the characteristics of the oyster. Then they achieved positive relationships between DFM and phytoplankton. Likewise, between the number of accumulated oocytes and phytoplankton. Here, phytoplankton seems to be the cause of this increase of DFM and the number of oocytes in recent years for this species of oyster. Here, phytoplankton seems to be the cause of this increase of DFM and the number of oocytes in recent years for this species of oyster. Moreover, according to the individual model, the higher the temperature of the sea surface, the earlier the clutches (June-July). While a cooler sea surface temperature will result in late laying (August-September).

      Then, they applied the same models to the bay of Bourgneuf. The results showed an increase in the temperature of the sea surface in the bay, but also the effects of the temperature of the water on the laying. Indeed, as at the individual scale, the high-water temperatures lead to prose spits and vice versa.

      Results at the European level showed a change in the geographic limit of spawning habitat, regardless of phytoplankton concentration. In 1986, the limit was located at the level of the Loire estuary with a south-north spawning gradient, earlier in the south of Europe. In 2003, this limit moved completely to the north of Europe. This change can be explained by the global warming of the waters.

      Other studies have highlighted other results. Indeed, using a Degree / day model, Ifermer has demonstrated the importance of the nutrient pool for egg laying. Indeed, in recent years, laying is actually late because of the low nutritional value of phytoplankton. The warming of the waters would therefore cause the loss of the oyster's nutrient pool and thus a delay in laying eggs.

      Cited study: Yoann, T., et al. (2016). Global change and climate-driven invasion of the Pacific oyster (Crassostrea gigas) along European coasts: a bioenergetics modelling approach. Journal of Biogeography 43(3), 568-579.

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