Towards an optimal design for ecosystem-level ocean observatories

Four operational factors, together with high development cost, currently limit the use of ocean observatories in ecological and fisheries applications: 1) limited spatial coverage; 2) limited integration of multiple types of technologies; 3) limitations in the experimental design for in situ studies; and 4) potential unpredicted bias in monitoring outcomes due to the infrastructure’s presence and functioning footprint. To address these limitations, we propose a novel concept of a standardized “ecosystem observatory module” structure composed of a central node and three tethered satellite pods together with permanent mobile platforms. The module would be designed with a rigid spatial configuration to optimize overlap among multiple observation technologies each providing 360° coverage around the module, including permanent stereo-video cameras, acoustic imaging sonar cameras, horizontal multi-beam echosounders and a passive acoustic array. The incorporation of multiple integrated observation technologies would enable unprecedented quantification of macrofaunal composition, abundance and density surrounding the module, as well as the ability to track the movements of individual fishes and macroinvertebrates. Such a standardized modular design would allow for the hierarchical spatial connection of observatory modules into local module clusters and larger geographic module networks, providing synoptic data within and across linked ecosystems suitable for fisheries and ecosystem level monitoring on multiple scales.Peer ReviewedPostprint (author's final draft

The Hierarchic treatment of marine ecological information from spatial networks of benthic platforms

Measuring biodiversity simultaneously in different locations, at different temporal scales, and over wide spatial scales is of strategic importance for the improvement of our understanding of the functioning of marine ecosystems and for the conservation of their biodiversity. Monitoring networks of cabled observatories, along with other docked autonomous systems (e.g., Remotely Operated Vehicles [ROVs], Autonomous Underwater Vehicles [AUVs], and crawlers), are being conceived and established at a spatial scale capable of tracking energy fluxes across benthic and pelagic compartments, as well as across geographic ecotones. At the same time, optoacoustic imaging is sustaining an unprecedented expansion in marine ecological monitoring, enabling the acquisition of new biological and environmental data at an appropriate spatiotemporal scale. At this stage, one of the main problems for an effective application of these technologies is the processing, storage, and treatment of the acquired complex ecological information. Here, we provide a conceptual overview on the technological developments in the multiparametric generation, storage, and automated hierarchic treatment of biological and environmental information required to capture the spatiotemporal complexity of a marine ecosystem. In doing so, we present a pipeline of ecological data acquisition and processing in different steps and prone to automation. We also give an example of population biomass, community richness and biodiversity data computation (as indicators for ecosystem functionality) with an Internet Operated Vehicle (a mobile crawler). Finally, we discuss the software requirements for that automated data processing at the level of cyber-infrastructures with sensor calibration and control, data banking, and ingestion into large data portals.Peer ReviewedPostprint (published version

Boosting rare benthic macroinvertebrates taxa identification with one-class classification

Insect monitoring is crucial for understanding the consequences of rapid ecological changes, but taxa identification currently requires tedious manual expert work and cannot be scaled-up efficiently. Deep convolutional neural networks (CNNs), provide a viable way to significantly increase the biomonitoring volumes. However, taxa abundances are typically very imbalanced and the amounts of training images for the rarest classes are simply too low for deep CNNs. As a result, the samples from the rare classes are often completely missed, while detecting them has biological importance. In this paper, we propose combining the trained deep CNN with one-class classifiers to improve the rare species identification. One-class classification models are traditionally trained with much fewer samples and they can provide a mechanism to indicate samples potentially belonging to the rare classes for human inspection. Our experiments confirm that the proposed approach may indeed support moving towards partial automation of the taxa identification task.Comment: 5 pages, 1 figure, 2 table

Towards a multisensor station for automated biodiversity monitoring

Rapid changes of the biosphere observed in recent years are caused by both small and large scale drivers, like shifts in temperature, transformations in land-use, or changes in the energy budget of systems. While the latter processes are easily quantifiable, documentation of the loss of biodiversity and community structure is more difficult. Changes in organismal abundance and diversity are barely documented. Censuses of species are usually fragmentary and inferred by often spatially, temporally and ecologically unsatisfactory simple species lists for individual study sites. Thus, detrimental global processes and their drivers often remain unrevealed. A major impediment to monitoring species diversity is the lack of human taxonomic expertise that is implicitly required for large-scale and fine-grained assessments. Another is the large amount of personnel and associated costs needed to cover large scales, or the inaccessibility of remote but nonetheless affected areas. To overcome these limitations we propose a network of Automated Multisensor stations for Monitoring of species Diversity (AMMODs) to pave the way for a new generation of biodiversity assessment centers. This network combines cutting-edge technologies with biodiversity informatics and expert systems that conserve expert knowledge. Each AMMOD station combines autonomous samplers for insects, pollen and spores, audio recorders for vocalizing animals, sensors for volatile organic compounds emitted by plants (pVOCs) and camera traps for mammals and small invertebrates. AMMODs are largely self-containing and have the ability to pre-process data (e.g. for noise filtering) prior to transmission to receiver stations for storage, integration and analyses. Installation on sites that are difficult to access require a sophisticated and challenging system design with optimum balance between power requirements, bandwidth for data transmission, required service, and operation under all environmental conditions for years. An important prerequisite for automated species identification are databases of DNA barcodes, animal sounds, for pVOCs, and images used as training data for automated species identification. AMMOD stations thus become a key component to advance the field of biodiversity monitoring for research and policy by delivering biodiversity data at an unprecedented spatial and temporal resolution. (C) 2022 Published by Elsevier GmbH on behalf of Gesellschaft fur Okologie

Soil biodiversity: functions, threats and tools for policy makers

Human societies rely on the vast diversity of benefits provided by nature, such as food, fibres, construction materials, clean water, clean air and climate regulation. All the elements required for these ecosystem services depend on soil, and soil biodiversity is the driving force behind their regulation. With 2010 being the international year of biodiversity and with the growing attention in Europe on the importance of soils to remain healthy and capable of supporting human activities sustainably, now is the perfect time to raise awareness on preserving soil biodiversity. The objective of this report is to review the state of knowledge of soil biodiversity, its functions, its contribution to ecosystem services and its relevance for the sustainability of human society. In line with the definition of biodiversity given in the 1992 Rio de Janeiro Convention, soil biodiversity can be defined as the variation in soil life, from genes to communities, and the variation in soil habitats, from micro-aggregates to entire landscapes. Bio Intelligence Service, IRD, and NIOO, Report for European Commission (DG Environment

Kohalike ja invasiivsete röövtoiduliste suurselgrootute elupaigakasutus ja toitumissuhted Läänemere põhjaosas

Väitekirja elektrooniline versioon ei sisalda publikatsiooneRöövtoidulised suurselgrootud, peamiselt vähilaadsed, on rannikumere toitumisvõrgustikes oluliseks lüliks põhjaelustiku ja kalade vahel ning ühtlasi nad reguleerivad väiksemate selgrootute arvukust. Läänemere põhjaosas elas selle rühma esindajaid seni ainult kaks liiki – läänemere krevett (Palaemon adspersus) ja põhjamere garneel (Crangon crangon). Hiljuti lisandusid neile kohalikele liikidele kaks võõrliiki – elegantne krevett (Palaemon elegans) ja rändkrabi (Rhithropanopeus harrisii). Kohalike ja võõrliikidest röövtoiduliste suurselgrootute leviku, elupaigaeelistuste ja toitumise uurimiseks kasutati olemasolevaid põhjaelustiku leviku andmeid, spetsiaalselt uuritavatele liikidele suunatud proovide kogumist loodusest ja laborikatseid, kus rakendati muuhulgas loomade raadiomärgistamist. Võõrliigist kreveti levik oli ulatuslikum kui kohalike krevettide levik. Võõrliik oli kohalike krevettidega võrreldes enam seotud elupaikadega, millele on iseloomulikud etrofeerumise tunnused (kõrge toitainete kontsentratsioon, lühiealiste niitjate vetikate suur hulk). Krevettide toitumisuuringud näitasid, et uuritud Palaemon liikide toitumisintensiivsus ja toidu kooseis ei erinenud. Seega on kohaliku ja võõrkreveti roll rannikumere toiduvõrkudes sarnane, ent võõrliik võib troofilisi suhteid ümber kujundada piirkondades, kus kohalikud krevetid puuduvad. Kõige kitsama elupaigakasutusega oli põhjamere garneel ja Palaemon liikidest oli võõrliigi P. elegans spetsialiseerumise tase mõnevõrra kõrgem kui kohalikul liigil. R. harrisii eelistas põisadruga (Fucus vesiculosus) elupaika mis viitab sellele, et põisadruga elupaik pakub krabile aastaringset stabiilset elupaika ja et mitmekesine põhjakooslus võib saada seetõttu krabidest oluliselt mõjutatud. Doktoritöö tulemused näitasid, et elupaikade iseloom ja seisund mõjutab kohalike ja võõrliikide levikumustreid ning võõrliikidest selgrootute kiskjate saabumine ja kiire levila laienemine Läänemere põhjaosas toovad kaasa täiesti uue ökoloogilise funktsiooni (suuremõõtmeline kiskja) või juba varem regionaalselt esinenud funktsiooni leviku piirkondadesse, kus see varem puudus.Decapod crustaceans, such as crabs and shrimps play an important role in coastal ecosystems as they prey on small benthic invertebrates and at the same time they are an important food item for fishes. Until recently, this group of macroinvertebrates consisted of only a few species in the northern Baltic Sea, including only two species of native shrimps – Crangon crangon and Palaemon adspersus. However, very recently two non-native crustacean predators arrived – the shrimp Palaemon elegans and the crab Rhithropanopeus harrisii. Data from available databases were used together with field sampling and laboratory experiments (incl. radio frequency positioning technology) to describe the geographical distribution, habitat selection, and feeding of native and invasive predatory crustaceans in the coastal areas of the northern Baltic Sea. The distribution of the non-native P. elegans was wider than that of native species. P. elegans was associated with lower salinity, higher concentrations of nutrients and higher proportions of ephemeral filamentous algae, relative to P. adspersus. According to results of the experiment on feeding activity, P. elegans performs a similar role in the coastal food web as the native congener, although it may rearrange trophic interactions and introduce new ecological function in the most eutrophicated areas previously lacking any native shrimp. Among the studied shrimps, C. crangon had the highest habitat specialization. The non-native P. elegans showed slightly higher habitat specialization compared to the native P. adspersus. The invasive crab R. harrisii preferred habitats with bladder wrack where the diverse native community may become heavily impacted by this novel large-bodied predator. This thesis showed that the successful establishment of non-native predatory invertebrates can introduce new ecological functions (large-bodied predators) or considerably strengthen already existed ones, while the heterogeneity of habitats has varying effects on the distribution patterns of native and invasive species