Highly resolved taphonomic variations within the Early Ordovician Fezouata Biota.

The Fezouata Biota (Morocco) is a Burgess Shale-type (BST) assemblage that provides a wealth of information on Early Ordovician ecosystems. Much work has been done to compare the preservation of the Fezouata Biota to other BSTs. However, studies investigating preservation variations within the Fezouata Biota are rare. Here, we use probabilities to investigate the preservation of various ecological categories of Fezouata eumetazoans. Complex taphonomic processes and phylum-specific constraints have led to the better preservation of predators/scavengers in this biota. However, no differences in preservation are observed between vagile and sessile taxa. Importantly, Tremadocian taxa are better preserved than Floian ones. As such, this study highlights the gradual closure of the BST window of preservation in the Zagora region of Morocco and constitutes a benchmark for future palaeoecological and evolutionary studies on the Fezouata Biota.

Deepdive: Leveraging Pre-trained Deep Learning for Deep-Sea ROV Biota Identification in the Great Barrier Reef.

Understanding and preserving the deep sea ecosystems is paramount for marine conservation efforts. Automated object (deep-sea biota) classification can enable the creation of detailed habitat maps that not only aid in biodiversity assessments but also provide essential data to evaluate ecosystem health and resilience. Having a significant source of labelled data helps prevent overfitting and enables training deep learning models with numerous parameters. In this paper, we contribute to the establishment of a significant deep-sea remotely operated vehicle (ROV) image classification dataset with 3994 images featuring deep-sea biota belonging to 33 classes. We manually label the images through rigorous quality control with human-in-the-loop image labelling. Leveraging data from ROV equipped with advanced imaging systems, our study provides results using novel deep-learning models for image classification. We use deep learning models including ResNet, DenseNet, Inception, and Inception-ResNet to benchmark the dataset that features class imbalance with many classes. Our results show that the Inception-ResNet model provides a mean classification accuracy of 65%, with AUC scores exceeding 0.8 for each class.

Two-year assessment of the effects of controlled sediment flushing on stream habitats and biota at reach scale.

Controlled sediment flushing operations (CSFOs) allow to recover reservoirs storage loss while rebalancing the sediment flux interrupted by dams but, at the same time, may cause unacceptable ecological impact. In this study, we investigated the responses of the food web of an upland stream to a CSFO, focusing on the effects of fine sediment deposition detected in three different mesohabitats, i.e., a pool, a riffle, and a step-pool. The field campaign lasted two years and included repeated measurements of fine sediment deposits, and sampling of periphyton, benthic macroinvertebrates and fishes. A moderate and patchy deposition occurred due to the CSFO with short and medium-term ecological impact on the lower trophic levels of the food web, which may affect the whole ecosystem functioning. The monitoring of all available mesohabitats in the investigated stream allowed to detect variations in the ecological response to CSFO, providing a more adequate assessment of the impact. As expected, sedimentation was larger in the pool but, in contrast to our hypotheses, the impact was lower and the recovery was longer for the benthic organisms inhabiting the riffle. In the case of fishes, no lethal impact of both brown trout and bullhead was recorded in the short term but the occurrence of longer lasting effects could not be excluded. To date, this is one of the few studies dealing with a detailed integrative assessment of the downstream impact of sediment management from reservoir on both abiotic and biotic components of stream ecosystem.

Pharmaceuticals in biota: The impact of wastewater treatment plant effluents on fish in Australia.

Globally, pharmaceuticals and personal care products (PPCPs) are detected in surface waters receiving wastewater, yet their presence in biota, remain largely understudied. To address this, we conducted a study that measured 46 PPCPs in spot water samples and fish caught up- and downstream from wastewater treatment plants (WWTPs) in Victoria, Australia. We sampled 15 sites located along four waterways following a 3-site design: WWTP-discharge('hotspot'), 'upstream'(∼2 km) and 'downstream'(∼2 km). Spot water and fish were also sampled at reference sites >100 km from WWTP discharge (n = 3). Additionally, spot water samples were taken from WWTP effluent outflows (n = 3). From each locality, we analysed 3-12 fish (n = 131 total). In waterways, passive samplers (POCIS; ∼28d, n = 19 PPCPs) were also deployed. Individual fish (axial muscle) and water were analysed with LC-MS-MS. We found that PPCP concentrations in environmental surface water ranged from<0.02-0.97 µg/L. In WWTP effluent, the range was <0.02-1.4 µg/L. Of the 46 PPCPs analysed, 12 were detected in spot water samples and five in fish. In water, the highest concentration detected was for antidepressant venlafaxine (3 µg/L). The most frequently detected PPCPs: venlafaxine (54.9%), metoprolol (41.2%), propranolol (29.4%), carbamazepine (29.4%), caffeine (17.6%) and sulfamethoxazole (17.6%). Out of 131 fish analysed, 35 fish had detectable levels of PPCPs in the muscle tissue. The highest muscle concentrations were: venlafaxine (150 µg/kg, redfin perch), and sertraline (100 µg/kg, eel). Bioaccumulation factors ranged from 104 to 341L/kg for venlafaxine in redfins, 21-1,260L/kg for carbamazepine in redfins and eels, and 367-3,333L/kg for sertraline in eels. Based on our human health risk calculations for venlafaxine, carbamazepine, sertraline, triclosan, and caffeine, consumption of fish does not pose a significant risk to human health. Despite this, most of the detected PPCPs in surface waters exceeded 10 ng/L trigger value, which has led to further investigations by EPA. Our study highlights the need for using multiple lines of evidence for estimating risks of PPCPs.

An automated and high-throughput data processing workflow for PFAS identification in biota by direct infusion ultra-high resolution mass spectrometry.

The increasing recognition of the health impacts from human exposure to per- and polyfluorinated alkyl substances (PFAS) has surged the need for sophisticated analytical techniques and advanced data analyses, especially for assessing exposure by food of animal origin. Despite the existence of nearly 15,000 PFAS listed in the CompTox chemicals dashboard by the US Environmental Protection Agency, conventional monitoring and suspect screening methods often fall short, covering only a fraction of these substances. This study introduces an innovative automated data processing workflow, named PFlow, for identifying PFAS in environmental samples using direct infusion Fourier transform ion cyclotron resonance mass spectrometry (DI-FT-ICR MS). PFlow's validation on a bream liver sample, representative of low-concentration biota, involves data pre-processing, annotation of PFAS based on their precursor masses, and verification through isotopologues. Notably, PFlow annotated 17 PFAS absent in the comprehensive targeted approach and tentatively identified an additional 53 compounds, thereby demonstrating its efficiency in enhancing PFAS detection coverage. From an initial dataset of 30,332 distinct m/z values, PFlow thoroughly narrowed down the candidates to 84 potential PFAS compounds, utilizing precise mass measurements and chemical logic criteria, underscoring its potential in advancing our understanding of PFAS prevalence and of human exposure.

Long-distance Southern Ocean environmental DNA (eDNA) transect provides insights into spatial marine biota and invasion pathways for non-native species.

The Southern Ocean surrounding Antarctica harbours some of the most pristine marine environments remaining, but is increasingly vulnerable to anthropogenic pressures, climate change, and invasion by non-native species. Monitoring biotic responses to cumulative impacts requires temporal and spatial baselines and ongoing monitoring - traditionally, this has been obtained by continuous plankton recorder (CPR) surveys. Here, we conduct one of the longest environmental DNA (eDNA) transects yet, spanning over 3000 nautical miles from Hobart (Australia) to Davis Station (Antarctica). We evaluate eDNA sampling strategies for long-term open ocean biomonitoring by comparing two water volume and filter pore size combinations: large (12 l with 20 µm) and small (2 l with 0.45 µm). Employing a broad COI metabarcoding assay, we found the large sample/pore combination was better suited to open ocean monitoring, detecting more target DNA and rare or low abundance species. Comparisons with four simultaneously conducted CPR transects revealed that eDNA detections were more diverse than CPR, with 7 (4 unique) and 4 (1 unique) phyla detections respectively. While both methods effectively delineated biodiversity patterns across the Southern Ocean, eDNA enables surveys in the presence of sea-ice where CPR cannot be conducted. Accordingly, 16 species of concern were detected along the transect using eDNA, notably in the Antarctic region (south of 60°S). These were largely attributed to hull biofouling, a recognized pathway for marine introductions into Antarctica. Given the vulnerability of Antarctic environments to potential introductions in a warming Southern Ocean, this work underscores the importance of continued biosecurity vigilance. We advocate integrating eDNA metabarcoding with long-term CPR surveys in the Southern Ocean, emphasising the urgency of its implementation. We anticipate temporal and spatial interweaving of CPR, eDNA, and biophysical data will generate a more nuanced picture of Southern Ocean ecosystems, with significant implications for the conservation and preservation of Antarctic ecosystems.

Temporal asynchrony of plant and soil biota determines ecosystem multifunctional stability.

The role of plant biodiversity in stabilizing ecosystem multifunctionality has been extensively studied; however, the impact of soil biota biodiversity on ecosystem multifunctional stability, particularly under multiple environmental changes, remains unexplored. By conducting an experiment with environmental changes (adding water and nitrogen to a long-term grazing experiment) and an experiment without environmental changes (an undisturbed site) in semi-arid grasslands, our research revealed that environmental changes-induced changes in temporal stability of both above- and belowground multifunctionality were mainly impacted by plant and soil biota asynchrony, rather than by species diversity. Furthermore, changes in temporal stability of above- and belowground multifunctionality, under both experiments with and without environmental changes, were mainly associated with plant and soil biota asynchrony, respectively, suggesting that the temporal asynchrony of plant and soil biota has independent and non-substitutable effects on multifunctional stability. Our findings emphasize the importance of considering both above- and belowground biodiversity or functions when evaluating the stabilizing effects of biodiversity on ecosystem functions.

Phylogeny structures species' interactions in experimental ecological communities.

Species' traits and interactions are products of evolutionary history. Despite the long-standing hypothesis that closely related species possess similar traits, and thus experience stronger competition, measuring the effect of evolutionary history on the ecology of natural communities remains challenging. We propose a novel framework to test whether phylogeny influences patterns of coexistence and abundance of species assemblages. In our approach, phylogenetic trees are used to parameterize species' interactions, which in turn determine the abundance of species in a given assemblage. We use likelihoods to score models parameterized with a given phylogeny, and contrast them with models built using random trees, allowing us to test whether phylogenetic information helps to predict species' abundances. Our statistical framework reveals that interactions are indeed structured by phylogeny in a large set of experimental plant communities. Our results confirm that evolutionary history can help predict, and potentially manage or conserve, the structure and function of complex ecological communities.

Health risk assessment by consumption of commercial biota contaminated with heavy metals in Tampamachoco coastal lagoon, Gulf of Mexico.

Metal pollution is a significant environmental and health problem in aquatic ecosystems worldwide, particularly in coastal systems impacted by emissions from thermoelectric plants, as is the case of the Tampamachoco lagoon. To evaluate the seasonal contamination levels of Cd, Pb, Cr, and Cu in species of commercial interest in the Tampamachoco lagoon and estimate the health risk associated with their consumption, a total of 180 fish, 90 oysters (Crassostrea virginica), 27 crabs (Callinectes sapidus), and 24 shrimp (Litopenaeus setiferus) were sampled. Metal concentrations in the species analyzed were Cu > Pb > Cr > Cd. According to the Target Hazard Quotient and the health risk index, consumption of the marine species examined should be considered safe for human health, as both values are <1. However, Carcinogenic risk values for Pb and Cr indicated that consumers may be at risk of cancer (10-3), due to exposure from the thermoelectric emissions.

Suspect and non-target screening of chemicals of emerging Arctic concern in biota, air and human serum.

Contaminants of emerging concern receive increasing attention in the Arctic environment. The aim of this study was to screen for chemicals of emerging Arctic concern (CEACs) in different types of Arctic samples including biota, air and human serum. We used a combination of gas chromatography (GC) and liquid chromatography (LC) with high resolution mass spectrometry (HRMS) for suspect and non-target screening (NTS). Suspect screening of 25 CEACs was based on published in-silico approaches for the identification of CEACs and revealed tetrabromophthalic anhydride (TBPA) in pilot whale and air, albeit with low detection frequencies (17 and 33%, respectively). An NTS workflow detected 49, 42, 31 and 30 compounds in pilot whale, ringed seal, air, and human serum, respectively, at confidence level 2 and 3. Although legacy POPs still dominated the samples, 64 CEACs were tentatively identified and further assessed for persistence (P), bioaccumulation (B), mobility (M), toxicity (T), and long-range transport potential (LRTP). While four PBT compounds were identified, 37 PMT substances dominated among these 64 compounds. Our study indicated that many chemicals of potential risk might be present in Arctic samples and would benefit from confirmation and further studies of their transport to and accumulation in the Arctic environment.

Time is of the essence: A general framework for uncovering temporal structures of communities.

Ecological communities are inherently dynamic: species constantly turn over within years, months, weeks or even days. These temporal shifts in community composition determine essential aspects of species interactions and how energy, nutrients, information, diseases and perturbations 'flow' through systems. Yet, our understanding of community structure has relied heavily on static analyses not designed to capture critical features of this dynamic temporal dimension of communities. Here, we propose a conceptual and methodological framework for quantifying and analysing this temporal dimension. Conceptually, we split the temporal structure into two definitive features, sequence and duration, and review how they are linked to key concepts in ecology. We then outline how we can capture these definitive features using perspectives and tools from temporal graph theory. We demonstrate how we can easily integrate ongoing research on phenology into this framework and highlight what new opportunities arise from this approach to answer fundamental questions in community ecology. As climate change reshuffles ecological communities worldwide, quantifying the temporal organization of communities is imperative to resolve the fundamental processes that shape natural ecosystems and predict how these systems may change in the future.

Beyond the rootzone: Unveiling soil property and biota gradients around plants.

Although the effects of plants on soil properties are well known, the effects of distance from plant roots to root-free soil on soil properties and associated soil organisms are much less studied. Previous research on the effects of distance from a plant explored specific soil organisms and properties, however, comparative studies across a wide range of plant-associated organisms and multiple model systems are lacking. We conducted a controlled greenhouse experiment using soil from two contrasting habitats. Within each soil type, we cultivated two plant species, individually and in combination, studying soil organisms and properties in the root centre, the root periphery, and the root-free zones. We showed that the distance from the cultivated plant (representing decreasing amount of plant roots) had a significant impact on the abiotic properties of the soil (pH and available P and N) and also on the composition of the fungal, bacterial, and nematode communities. The specific patterns, however, did not always match our expectations. For example, there was no significant relationship between the abundance of fungal pathogens and the distance from the cultivated plant compared to a strong decrease in the abundance of arbuscular mycorrhizal fungi. Changes in soil chemistry along the distance from the cultivated plant were probably one of the important drivers that affected bacterial communities. The abundance of nematodes also decreased with distance from the cultivated plant, and the rate of their responses reflected the distribution of their food sources. The patterns of soil changes along the gradient from plant to root-free soil were largely similar in two contrasting soil types and four plant species or their mixtures. This suggests that our results can be generalised to other systems and contribute to a better understanding of the mechanisms of soil legacy formation.

The topology of spatial networks affects stability in experimental metacommunities.

Understanding the drivers of community stability has been a central goal in ecology. Traditionally, emphasis has been placed on studying the effects of biotic interactions on community variability, and less is understood about how the spatial configuration of habitats promotes or hinders metacommunity stability. To test the effects of contrasting spatial configurations on metacommunity stability, I designed metacommunities with patches connected as random or scale-free networks. In these microcosms, two prey and one protist predator dispersed, and I evaluated community persistence, tracked biomass variations, and measured synchrony between local communities and the whole metacommunity. After 30 generations, scale-free metacommunities had lower global biomass variability and higher persistence, suggesting higher stability. Synchrony between patches was lower in scale-free metacommunities. Patches in scale-free metacommunities showed a positive relationship between variability and patch connectivity, indicating higher stability in isolated communities. No clear relationship between variability and patch connectivity was observed in random networks. These results suggest the increased heterogeneity in connectivity of scale-free networks favours the prevalence of isolated patches of the metacommunity, which likely act as refugia against competition-the dominant interaction in this system-resulting in higher global stability. These results highlight the importance of accounting for network topology in the study of spatial dynamics.

The interplay between abiotic and biotic factors in dispersal decisions in metacommunities.

Suitable conditions for species to survive and reproduce constitute their ecological niche, which is built by abiotic conditions and interactions with conspecifics and heterospecifics. Organisms should ideally assess and use information about all these environmental dimensions to adjust their dispersal decisions depending on their own internal conditions. Dispersal plasticity is often considered through its dependence on abiotic conditions or conspecific density and, to a lesser extent, with reference to the effects of interactions with heterospecifics, potentially leading to misinterpretation of dispersal drivers. Here, we first review the evidence for the effects of and the potential interplays between abiotic factors, biotic interactions with conspecifics and heterospecifics and phenotype on dispersal decisions. We then present an experimental test of these potential interplays, investigating the effects of density and interactions with conspecifics and heterospecifics on temperature-dependent dispersal in microcosms of Tetrahymena ciliates. We found significant differences in dispersal rates depending on the temperature, density and presence of another strain or species. However, the presence and density of conspecifics and heterospecifics had no effects on the thermal-dependency of dispersal. We discuss the causes and consequences of the (lack of) interplay between the different environmental dimensions and the phenotype for metacommunity assembly and dynamics. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

The evolution of passive dispersal versus habitat selection have differing emergent consequences in metacommunities.

Dispersal among local communities is fundamental to the metacommunity concept but is only important to the metacommunity structure if dispersal causes distortions of species abundances away from what local ecological conditions favour. We know from much previous work that dispersal can cause such abundance distortions. However, almost all previous theoretical studies have only considered one species alone or two interacting species (e.g. competitors or predator and prey). Moreover, a systematic analysis is needed of whether different dispersal strategies (e.g. passive dispersal versus demographic habitat selection) result in different abundance distortion patterns, how these distortion patterns change with local food web structure, and how the dispersal propensities of the interacting species might evolve in response to one another. In this article, we show using computer simulations and analytical models that abundance distortions occur in simple food webs with both passive dispersal and habitat selection, but habitat selection causes larger distortions. Additionally, patterns in the evolution of dispersal propensity in interacting species are very different for these two dispersal strategies. This study identifies that the dispersal strategies employed by interacting species critically shape how dispersal will influence metacommunity structure. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

The biotic and abiotic contexts of ecological selection mediate the dominance of distinct dispersal strategies in competitive metacommunities.

While the influence of dispersal on ecological selection is the subject of intense research, we still lack a thorough understanding of how ecological selection operates to favour distinct dispersal strategies in metacommunities. To address this issue, we developed a model framework in which species with distinct quantitative dispersal traits that govern the three stages of dispersal-departure, movement and settlement-compete under different ecological contexts. The model identified three primary dispersal strategies (referred to as nomadic, homebody and habitat-sorting) that consistently dominated metacommunities owing to the interplay of spatiotemporal environmental variation and different types of competitive interactions. We outlined the key characteristics of each strategy and formulated theoretical predictions regarding the abiotic and biotic conditions under which each strategy is more likely to prevail in metacommunities. By presenting our results as relationships between dispersal traits and well-known ecological gradients (e.g. seasonality), we were able to contrast our theoretical findings with previous empirical research. Our model demonstrates how landscape environmental characteristics and competitive interactions at the intra- and interspecific levels can interact to favour distinct multivariate and context-dependent dispersal strategies in metacommunities. This article is part of the theme issue 'Diversity-dependence of dispersal: interspecific interactions determine spatial dynamics'.

Altering operational conditions during protein fermentation to volatile fatty acids modifies the associated bacterial community.

In recent years, the production of volatile fatty acids (VFA) through mixed culture fermentation (MCF) has been gaining attention. Most authors have focused on the fermentation of carbohydrates, while other possible substrates, such as proteins, have not been considered. Moreover, there is little information about how operational parameters affect the microbial communities involved in these processes, even though they are strongly related to reactor performance and VFA selectivity. Hence, this study aims to evaluate how microbial composition changes according to three different parameters (pH, type of protein and micronutrient addition) during anaerobic fermentation of protein-rich side streams. For this, two continuous stirred tank reactors (CSTR) were fed with two different proteins (casein and gelatine) and operated at different conditions: three pH values (5.0, 7.0 and 9.0) with only macronutrients supplementation and two pH values (5.0 and 7.0) with micronutrients' supplementation as well. Firmicutes, Proteobacteria and Bacteroidetes were the dominant phyla in the two reactors at all operational conditions, but their relative abundance varied with the parameters studied. At pH 7.0 and 9.0, the microbial composition was mainly affected by protein type, while at acidic conditions the driving force was the pH. The influence of micronutrients was dependent on the pH and the protein type, with a special effect on Clostridiales and Bacteroidales populations. Overall, this study shows that the acidogenic microbial community is affected by the three parameters studied and the changes in the microbial community can partially explain the macroscopic results, especially the process selectivity.

Nuclear power plant biological complications on marine biota from a probabilistic accident - A case study.

An accident at the Barakah Nuclear Power Plant (BNPP) would result in a significant radionuclide release into the semi-closed marine environment. In this research, the released radionuclide distribution pattern and dose rate in the Persian/Arabian (Gulf) were calculated using a combined hydrodynamic/radiobiological model. Simulations of the dispersion of artificial radionuclide concentrations were conducted using a HYSPLIT model. To assess prospective hazards in case of an incident, environmental risk from ionizing contaminants: assessment and management (ERICA) tools were used. Using the Fukushima nuclear power accident as a model, the scenario source term profile was developed. The volumetric concentrations levels of pollutants ranged between 1 × 104 mBq m-3 to 1 × 1010 mBq m-3 in the radius of 200 km after 48 h. Based on the dose rates of the various marine biotas, Polychaete worms, and Pelagic fish, they had the highest and lowest dose contribution.

Anaerobic treatment removing tetrabromobisphenol A and biota safety: How do tropical aquatic species respond to effluent toxicity over short- and long-term exposures?

Wastewater containing tetrabromobisphenol A (TBBPA), a commonly used flame retardant found in wastewater, can present significant toxic effects on biota, yet its impact on tropical freshwater environments is not well understood. This study explores the effectiveness of two independent anaerobic treatment systems, the acidogenic reactor (AR) and the methanogenic reactor (MR), for the ecotoxicity reduction of TBBPA-rich wastewater in four tropical freshwater species. Despite presenting good physicochemical performance and reduced toxicity of the influent for most species, AR and MR treatments remain acute and chronic toxicity. Overall, MR exhibited greater efficacy in reducing influent toxicity compared with AR. TBBPA bioaccumulation was observed in Chironomus sancticaroli after short-term exposure to 100% MR effluent. Multigenerational exposures highlighted changes in the wing length of C. sancticaroli, showing decreases after influent and AR exposures and increases after MR exposures. These findings underscore the need for ecotoxicological tools in studies of new treatment technologies, combining the removal of emerging contaminants with safeguarding aquatic biota. PRACTITIONER POINTS: Acidogenic and methanogenic reactors reduced the acute and chronic toxicity of wastewater containing tetrabromobisphenol A. Both treatments still exhibit toxicity, inducing short- and long-term toxic effects on four native tropical species. The aquatic species Pristina longiseta was most sensitive to effluents from acidogenic and methanogenic reactors. TBBPA concentrations recovered from Chironomus sancticaroli bioaccumulation analysis ranged from 1.07 to 1.35 µg g-1. Evaluating new treatment technologies with multiple species bioassays is essential for a comprehensive effluent toxicity assessment and ensuring aquatic safety.

The Stability of Competitive Metacommunities Is Insensitive to Dispersal Connectivity in a Fluctuating Environment.

AbstractMaintaining the stability of ecological communities is critical for conservation, yet we lack a clear understanding of what attributes of metacommunity structure control stability. Some theories suggest that greater dispersal promotes metacommunity stability by stabilizing local populations, while others suggest that dispersal synchronizes fluctuations across patches and leads to global instability. These effects of dispersal on stability may be mediated by metacommunity structure: the number of patches, the pattern of connections across patches, and levels of spatiotemporal correlation in the environment. Thus, we need theory to investigate metacommunity dynamics under different spatial structures and ecological scenarios. Here, we use simulations to investigate whether stability is primarily affected by connectivity, including dispersal rate and topology of connectivity network, or by mechanisms related to the number of patches. We find that in competitive metacommunities with environmental stochasticity, network topology has little effect on stability on the metacommunity scale even while it could change spatial diversity patterns. In contrast, the number of connected patches is the dominant factor promoting stability through averaging stochastic fluctuations across more patches, rather than due to more habitat heterogeneity per se. These results broaden our understanding of how metacommunity structure changes metacommunity stability, which is relevant for designing effective conservation strategies.