Aquatic Ecosystem Research Research Articles

Towards Estimation of 3D Poses and Shapes of Animals from Oblique Drone Imagery

Abstract. Wildlife research in both terrestrial and aquatic ecosystems now deploys drone technology for tasks such as monitoring, census counts and habitat analysis. Unlike camera traps, drones offer real-time flexibility for adaptable flight paths and camera views, thus making them ideal for capturing multi-view data on wildlife like zebras or lions. With recent advancements in animals’ 3D shape & pose estimation, there is an increasing interest in bringing 3D analysis from ground to sky by means of drones. The paper reports some activities of the EU-funded WildDrone project and performs, for the first time, 3D analyses of animals exploiting oblique drone imagery. Using parametric model fitting, we estimate 3D shape and pose of animals from frames of a monocular RGB video. With the goal of appending metric information to parametric animal models using photogrammetric evidence, we propose a pipeline where we perform a point cloud reconstruction of the scene to scale and localize the animal within the 3D scene. Challenges, planned next steps and future directions are also reported.

Widespread Geographical Disparities in Phytoplankton Ecology Research in the Face of Climate Change: A Review

Climate change is a global threat that is better understood through global research spanning many regions, countries, and life-supporting ecosystems. This review focused on the bibliometric analysis of the distribution of a global research compendium on phytoplankton, an aquatic community that accounts for half of the carbon fixation in the global carbon cycle. A total of 716 primary research papers published in the immediate past decade (2012–2022) were reviewed. The articles were sampled from Web of Science and described field and laboratory experiments quantifying the impact of global climate change on phytoplankton from different climate zones (tropical, subtropical, temperate, subpolar, and polar) and ecosystems (freshwater, brackish, and marine). Analyses of these studies suggest that the bulk of the global research effort (80%) focused on high-latitude areas, and only a few (17%) were carried out in the tropics, largely led by four countries (Australia, Brazil, India, and Saudi Arabia), while Africa’s contribution was minuscule (<1%). In terms of ecosystems, the majority (76%) of the research was in marine waters, irrespective of the climate zone. Analyses of these studies also highlighted widespread disparities in phytoplankton research in tropical aquatic ecosystems, particularly in Africa. Strategic investment in terms of targeted funding, institutional networks, and partnerships between the global north and global south are necessary to increase phytoplankton research across different ecosystems in the tropics.

Nature reserves (zapovedniks) in the Volga catchment: protection, research and management

AbstractIn the Russian Federation, the protection category “Zapovednik” represents a strictly protected area, where the access is restricted and the aim is to keep the area “forever wild”. We provide an overview about the organization of these nature reserves and highlight their contribution to fundamental research. Aquatic ecosystems in zapovedniks provide pristine sites of great importance for long-term monitoring and research, which fosters process understanding regarding interannual variability and development of aquatic coenosis. We present a long term monitoring and research project about abiotic and biotic parameters in the Central Forest State Nature Biosphere Reserve. Examples from the Privolzhskaya Lesostep Nature Reserve include monitoring of invasive fish as well as analyses about the influence of beavers on fish. The Astrakhan Biosphere Nature Reserve in the Volga delta is a hotspot for fish biodiversity; thus, there the state nature reserve security service plays an important role to avoid poaching. Our case studies from the Volga Basin exemplify the structure and function of nature reserves and highlight their contribution to research, protection and management of aquatic ecosystems. Long-term datasets from the zapovedniks can (i) improve process understanding, (ii) ensure protection of aquatic systems and sustainable water management and (iii) support knowledge-based decisions.

Compact and modular autonomous surface vehicle for water research: The Naval Operating Research Drone Assessing Climate Change (NORDACC)

Research, monitoring, and management of marine and aquatic ecosystems often require surface water samples to measure biogeochemical and optical parameters. Traditional sampling with a boat and several personnel onboard can be labor-intensive and safety requirements limit sampling activities in high-risk environments. This paper describes the Naval Operating Research Drone Assessing Climate Change (NORDACC). NORDACC is an open source, light-weight, and portable autonomous surface vehicle that can acquire surface water samples while also measuring sea surface temperature and salinity for the duration of its deployment. NORDACC is ideal for operations in remote areas where resources and personnel are limited. Two sample bottles, each one liter in volume, can be filled, either at pre-programmed sampling stations or manually, using the remote control. A trimaran design provides buoyancy and stability, with hulls constructed of vacuum-formed acrylonitrile butadiene styrene (ABS) plastic. NORDACC can navigate autonomously between waypoints and features first person view capabilities for enhanced situational awareness. NORDACC’s performance was validated in Aarhus Bay, Denmark, collecting multiple surface water samples in winds in excess of 8 ms−1 and steep, choppy waves.

Clarifying water clarity: A call to use metrics best suited to corresponding research and management goals in aquatic ecosystems

Clarifying water clarity: A call to use metrics best suited to corresponding research and management goals in aquatic ecosystems

Fluid–structure interaction in a flexible vegetation canopy in an open channel

Submerged flexible vegetation occupies the core of aquatic ecosystem research. Hydrodynamics of submerged flexible vegetation and its interaction with the flow in an open channel are of great significance in studying the mass and momentum transports in the flow. In this study, a numerical model for highly flexible vegetation based on large eddy simulation and the immersed boundary method was used to simulate the flow–vegetation interaction. It is recognised that alternate vortices with opposite sense rotations appear at the flow–vegetation interface. These vortices prompt the vegetation canopy to have wave-like coherent waving motion, commonly called the monami phenomena. The spatial scale and the spreading velocity in the streamwise direction of these vortices determine the wavelength, frequency and amplitude of the vegetation coherent waving motion. In this study, the fast Fourier transform method was applied to analyse the factors affecting the characteristics of the vegetation coherent waving motion. It is revealed that, as the flow velocity increases, the wavelength of the coherent waving motion decreases, while the frequency and amplitude increase. Besides, as the vegetation spacing increases, the wavelength and amplitude of the coherent waving motion increase, but the frequency decreases. Furthermore, an increase in the relative density of vegetation magnifies the amplitude of coherent waving motion without affecting the wavelength and frequency.

The cell cycle of phytoplankton: A review

AbstractPhytoplankton play an enormously important role in ecology and serve as critical food for aquatic organisms. The phytoplankton population rapidly increases in number after continuous cell cycles. Thus, understanding the cell cycle of phytoplankton is fundamental to the aquatic ecosystem research. The eukaryotic cell cycle has been clarified; however, unique characteristics exist in phytoplankton. Their cell cycle progression either differs among species or varies with environmental changes. Here, we review the cell cycle progression of the eukaryotic phytoplankton and its response to environmental factors, introduce the cell cycle research methods, highlight the identified cell cycle regulatory proteins, and discuss prospects for future research directions.

Elena Alexandrovna Timofeeva-Resovskaya at the forefront of radiobiology in the XX century

Purpose. The purpose of the work was to show the outstanding contribution of Elena Alexandrovna Timofeeva-Resovskaya (1898-1973) to the development of radiobiology. Materials and methods. This article was prepared on the basis of the author's memoirs, using materials from the personal archive, as well as literary and electronic sources. Results and Conclusions. For the first time the autobiography of Elena A. Timofeeva-Resovskaya and the periods of her scientific activity are revealed. The priority in the radiobiology of aquatic ecosystems belongs to Elena A. Timofeeva-Resovskaya. The results of her work turned out to be important both for solving the problems of radioactive contamination of territories, and for the development of modern radioecology. Throughout her life, she worked with her husband Nikolay V. Timofeev-Resovsky (1900-1981), a great scientist and scientific enlightener of the world level. It was not the purpose of this article to describe the life of their family, full of exciting events, but it was not possible to avoid it. For young women planning a scientific career, Elena A. Timofeeva-Resovskaya is an example of a successful path in science even in turbulent times.

A review on aquatic ecosystem mesocosms.

Aquatic ecosystem mesocosm refers to an artificially constructed near-natural simulation facility in aquatic ecosystem. With aquatic ecosystem mesocosms, experiments on the responses of biological communities can be conducted by controlling physical, chemical and other habitat conditions. Mesocosm experiments can bridge the gap between laboratory experiments and field experiments. Laboratory experiment can only simulate a small number of simple factors, whereas field experimental systems are complex and difficult to conduct controlled experiments. By resear-ching into global long-term mesocosms, we classified them into four types, i.e. flowing type mesocosm, enclosure, land-based simulation pool and mobile experimental tank. The meoscosms gene-rally include physical-biological simulation system, automatic control system, monitoring and analysis system, and central control system. In recent years, aquatic ecosystem research in China has gradually changed from a single environmental factor to the whole ecosystem. We suggest that the construction of the mesocosms in China's aquatic ecosystem should increase the structural complexity and be combined with field in situ monitoring to support large scale simulation.

Fungi and viruses as important players in microbial mats.

Microbial mats are compacted, surface-associated microbial ecosystems reminiscent of the first living communities on early Earth. While often considered predominantly prokaryotic, recent findings show that both fungi and viruses are ubiquitous in microbial mats, albeit their functional roles remain unknown. Fungal research has mostly focused on terrestrial and freshwater ecosystems where fungi are known as important recyclers of organic matter, whereas viruses are exceptionally abundant and important in aquatic ecosystems. Here, viruses have shown to affect organic matter cycling and the diversity of microbial communities by facilitating horizontal gene transfer and cell lysis. We hypothesise fungi and viruses to have similar roles in microbial mats. Based on the analysis of previous research in terrestrial and aquatic ecosystems, we outline novel hypotheses proposing strong impacts of fungi and viruses on element cycling, food web structure and function in microbial mats, and outline experimental approaches for studies needed to understand these interactions.

Boundary element method to analyze acoustic scattering from a coupled swimbladder-fish body configuration

A model for computing acoustic scattering by swimbladdered fish is presented. The effect of acoustic coupling between the fish tissue and the swimbladder is included. The swimbladder is considered a gas-filled object whereas the fish tissue is assumed to behave as a homogeneous fluid. Mathematically, this corresponds to considering the problem of two penetrable scatterers immersed in a homogeneous medium, one of which is wholly embedded in the other. The model is formulated in the frame of boundary integral equations whose solution is achieved using the Boundary Element Method (BEM) for a planar triangle mesh. The numerical implementation is verified against benchmark solutions reported in the literature. The model is then applied to a specimen of Argentine hake (Merluccius hubbsi), whose morphometry was determined by CT scanning of a frozen sample, for evaluating its forward and backscattering responses. From the acoustic scattering viewpoint, the swimbladder is considered as a gas-filled object while the flesh constituting the fish body acts like a weak scatterer. The numerical results suggest the swimbladder and the fish body responses, when fully coupled, can lead to substantial differences with respect to the simplified models normally in use in the area of aquatic ecosystem research.

Beyond the trends: The need to understand multiannual dynamics in aquatic ecosystems

Beyond the trends: The need to understand multiannual dynamics in aquatic ecosystems

Chemical and microbial diversity covary in fresh water to influence ecosystem functioning

Invisible to the naked eye lies a tremendous diversity of organic molecules and organisms that make major contributions to important biogeochemical cycles. However, how the diversity and composition of these two communities are interlinked remains poorly characterized in fresh waters, despite the potential for chemical and microbial diversity to promote one another. Here we exploited gradients in chemodiversity within a common microbial pool to test how chemical and biological diversity covary and characterized the implications for ecosystem functioning. We found that both chemodiversity and genes associated with organic matter decomposition increased as more plant litterfall accumulated in experimental lake sediments, consistent with scenarios of future environmental change. Chemical and microbial diversity were also positively correlated, with dissolved organic matter having stronger effects on microbes than vice versa. Under our experimental scenarios that increased sediment organic matter from 5 to 25% or darkened overlying waters by 2.5 times, the resulting increases in chemodiversity could increase greenhouse gas concentrations in lake sediments by an average of 1.5 to 2.7 times, when all of the other effects of litterfall and water color were considered. Our results open a major new avenue for research in aquatic ecosystems by exposing connections between chemical and microbial diversity and their implications for the global carbon cycle in greater detail than ever before.

Current practices and future perspectives of microplastic pollution in freshwater ecosystems in China.

The pollution of marine and freshwater environments by plastic waste has attracted increasing public attention worldwide in recent years. China is the world's second largest economy and contributes the largest mass of mismanaged plastic waste. In this review, we collected accessible data on the abundance of microplastics in China's freshwater ecosystems, analyzing this pollutant in the samples of waters, sediments and biota. The results showed that microplastics are pervasive in surveyed freshwater environments, and a high abundance of microplastics was found in estuaries and inland waters located in populated urban areas. Moreover, many freshwater bivalve and fish have been found to uptake microplastics. Although similar sampling and laboratory processing methods were applied for microplastic research in different aquatic ecosystems, methods of investigation and units reported by different authors should be standardized. The characteristics of the detected microplastics showed that small size (<1 mm), fibers and transparency were the most common features in China's freshwater ecosystems and that PP and PE were the most common types of microplastics. The current situation of microplastic pollution in China is largely caused by inefficient administration and lack of applicable legislation and regulations. Therefore, we suggest that the Chinese government need to be more active in dealing with the plastic pollution issues, and increase education and publicity to promote people's awareness of environmental pollution caused by microplastics.

Stable isotopes of zooplankton and their applications in the research of aquatic ecosystems

Zooplankton plays a mediating role in the food web of aquatic ecosystems, the stable carbon and nitrogen isotopes (δ13C and δ15N) of which have been widely used to study the utilization of food resources, material cycling pathways, and trophic relationships. The δ13C and δ15N values of zooplankton have been used to predict primary productivity, sources and sinks of pollutants and environmental changes. To better use δ13C and δ15N of zooplankton as ecological and environmental indicators, it is particularly important to understand their temporal and spatial variations and the influencing factors. Based on related literature, we synthesized spatial and temporal variations in δ13C and δ15N of zooplankton in different aquatic ecosystems and taxa groups, and the use of δ13C and δ15N indicators for ecological processes and environmental changes. The δ13C and δ15N of zooplankton are largely affected by its food sources, and its stable isotope compositions are in turn affected by primary productivity and nitrogen sources. We proposed that the combination of δ13C and δ15N in zooplankton with transportation and transformation of emerging pollutants would form a multi-means, multi-disciplinary and multi-scale research direction in the fields of earth science and biology.

Detection and characterisation of deep-sea benthopelagic animals from an autonomous underwater vehicle with a multibeam echosounder: A proof of concept and description of data-processing methods

Benthopelagic animals are an important component of the deep-sea ecosystem, yet are notoriously difficult to study. Multibeam echosounders (MBES) deployed on autonomous underwater vehicles (AUVs) represent a promising technology for monitoring this elusive fauna at relatively high spatial and temporal resolution. However, application of this remote-sensing technology to the study of small (relative to the sampling resolution), dispersed and mobile animals at depth does not come without significant challenges with respect to data collection, data processing and vessel avoidance. As a proof of concept, we used data from a downward-looking RESON SeaBat 7125 MBES mounted on a Dorado-class AUV to detect and characterise the location and movement of backscattering targets (which were likely to have been individual fish or squid) within 50 m of the seafloor at ~800 m depth in Monterey Bay, California. The targets were detected and tracked, enabling their numerical density and movement to be characterised. The results revealed a consistent movement of targets downwards away from the AUV that we interpreted as an avoidance response. The large volume and complexity of the data presented a computational challenge, while reverberation and noise, spatial confounding and a marginal sampling resolution relative to the size of the targets caused difficulties for reliable and comprehensive target detection and tracking. Nevertheless, the results demonstrate that an AUV-mounted MBES has the potential to provide unique and detailed information on the in situ abundance, distribution, size and behaviour of both individual and aggregated deep-sea benthopelagic animals. We provide detailed data-processing information for those interested in working with MBES water-column data, and a critical appraisal of the data in the context of aquatic ecosystem research. We consider future directions for deep-sea water-column echosounding, and reinforce the importance of measures to mitigate vessel avoidance in studies of aquatic ecosystems.

Index to Titles and Authors/Editors of Books Reviewed Volume 92 (2017)

Index to Titles and Authors/Editors of Books Reviewed Volume 92 (2017)

Development of cultures of the marine sponge Hymeniacidon perleve for genotoxicity assessment using the alkaline comet assay.

Sponges are a potential alternative model species to bivalves in pollution biomonitoring and environmental risk assessment in the aquatic ecosystem. In the present study, a novel in vivo exposure sponge culture model was developed from field-collected and cryopreserved sponge (Hymeniacidon perleve) cells to investigate the genotoxic effects of environmentally relevant metals in the laboratory. Sponge cell aggregates were cultured and exposed to noncytotoxic concentrations (0-0.4 mg/L) of cadmium chloride, nickel chloride, and sodium dichromate as quantified by the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and DNA-strand breaks assessed by the comet assay. Reactive oxygen species (ROS) formation was quantified by oxidation of 2',7'-dichlorofluorescin diacetate in sponge cell aggregates exposed to the same concentrations of Cd, Cr, and Ni. There was a statistically significant (p < 0.05) concentration-dependent increase in the level of DNA-strand breaks and ROS formation in all of the metals investigated. To the best of our knowledge, we have utilized for the first time the alkaline comet assay to detect DNA-strand breaks in marine sponge cells and demonstrated that exposure to noncytotoxic concentrations of Cd, Cr, and Ni for 12 h results in a concentration-dependent increase in DNA damage and levels of ROS production. In conclusion, we have developed a novel in vivo model based on culture of cryopreserved sponge cells that is compatible with the alkaline comet assay. Genotoxicity in marine sponges measured by the comet assay technique may be a useful tool for biomonitoring research and risk assessment in aquatic ecosystems. Environ Toxicol Chem 2017;36:3314-3323. © 2017 SETAC.

Where technology meets ecology: acoustic telemetry in contemporary Australian aquatic research and management

Acoustic telemetry is used to investigate a diverse suite of questions regarding the biology and ecology of a range of aquatic species, and is an important tool for fisheries and conversation management. Herein we present a brief review of the Australian acoustic telemetry literature in the context of key areas of progress, drawing from several recent studies and identifying areas for future progress. Acoustic telemetry has been increasingly used in Australia over the past decade. This has included substantial investment in a national acoustic array and the associated development of a national acoustic telemetry database that enables tag deployment and detection data to be shared among researchers (the Integrated Marine Observing System Animal Tracking Facility). Acoustic telemetry has contributed to important areas of management, including public safety, design and management of marine protected areas, the use of closures in fisheries management, informing environmental flow regimes and the impacts of fisheries enhancements, and is most powerful when used as a complementary tool. However, individual variability in movement often confounds our ability to draw general conclusions when attempting to characterise broad-scale patterns, and more work is required to address this issue. This overview provides insight into the important role that acoustic telemetry plays in the research and management of Australian aquatic ecosystems. Application of the technology transcends aquatic environments and bureaucracies, and the patterns revealed are relevant to many of the contemporary challenges facing decision makers with oversight of aquatic populations or ecosystems.

Biotic hotspots in mangrove-dominated estuaries: macro-invertebrate aggregation in unvegetated lower intertidal flats

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 556:31-43 (2016) - DOI: https://doi.org/10.3354/meps11860 Biotic hotspots in mangrove-dominated estuaries: macro-invertebrate aggregation in unvegetated lower intertidal flats Marcus Sheaves, Liliana Dingle, Carlo Mattone* Centre for Tropical Water & Aquatic Ecosystem Research (TropWATER), Estuary and Coastal Wetland Ecosystem Research Group, College of Marine and Environmental Sciences, James Cook University, Queensland 4811, Australia *Corresponding author: carlo.mattone@my.jcu.edu.au ABSTRACT: Macro-benthic invertebrates are important components of estuarine communities providing links between primary producers and higher trophic levels. In temperate regions, abundance and biomass peak in the mid-intertidal, giving this zone substantial functional importance. In tropical estuaries, the higher intertidal is generally occupied by mangrove forests, potentially influencing the way intertidal invertebrate assemblages are structured. We investigated the distribution and richness of benthic invertebrates across intertidal sand- and mud-flats seaward of mangrove forest to quantify the extent and location of areas of high benthic richness, abundance and biomass. Four estuaries in tropical north Queensland and 2 habitat types, sand and mud, were sampled using a van Veen grab. Macro-invertebrate richness, abundance and biomass peaked with a ‘hotspot’ in the lower low-intertidal, with patterns of distribution similar among substrate types. However, substantial differences in biotic and abiotic contexts between tropical estuaries and the temperate systems, where models of intertidal macro-invertebrate distribution were developed, mean that the variables influencing tropical macro-invertebrate hotspots are likely to differ from those that operate in temperate regions. The high concentration of benthic biomass in the lower low-intertidal means this zone probably regulates many of the ecological processes occurring in the intertidal regions of tropical estuaries. Consequently, any damage or modification to this zone is likely to severely impact estuarine function. KEY WORDS: Benthos · Tropical estuary · Nutrients · Invertebrate distribution Full text in pdf format Supplementary material PreviousNextCite this article as: Sheaves M, Dingle L, Mattone C (2016) Biotic hotspots in mangrove-dominated estuaries: macro-invertebrate aggregation in unvegetated lower intertidal flats. Mar Ecol Prog Ser 556:31-43. https://doi.org/10.3354/meps11860 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 556. Online publication date: September 08, 2016 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2016 Inter-Research.