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Three molecular assays were used to detect and quantify white spot syndrome virus (WSSV) in DNA extracted from seston size-fractioned (0.02, 0.2, 1.2, and 20 μm) samples collected from a coastal lagoon and an adjacent shrimp farm. From 107 DNA extracts, only two from one sample tested positive for WSSV with nested PCR in the 1.2 and 20 μm fractions. These results were confirmed by a semi-quantitative (IQ2000TM WSSV Detection and Prevention System) and a quantitative (IQREALTM WSSV Quantitative System) detection system based, based, respectively, on nested PCR and real-time PCR. A first viral load reference value (6.54 × 104 WSSV copies/mL) was established in a seston size fraction (1.2−20 μm). The results suggest that WSSV could be associated with both resuspension of fine clays and silts, and nanoplankton and organic colloids during infectious events.

Extreme precipitation is occurring with greater frequency and intensity as a result of climate change. Such events boost the transport of allochthonous organic matter (allo-OM) to freshwater ecosystems, yet little is known about the impacts on dissolved organic matter (DOM) quality and seston elemental stoichiometry, especially for lakes in warm climates. A mesocosm experiment located in a Turkish freshwater lake was designed to simulate a pulse event leading to increased inputs of allo-OM by examining the individual effects of increasing water colour (HuminFeed®, HF), the direct effects of the extra energetic inputs (alder tree leaf leachate, L), and the interactions of the single treatment effects (combination of both sources, HFL), along with a comparison with unmanipulated controls. Changes in the DOM quality and nutrient stoichiometry of the allo-OM treatment additions was examined over the course of the experiments. Results indicated that there was an increase of high recalcitrant DOM components in the HF treatment, in contrast to an increase in less aromatic microbially derived molecules for the L treatment. Unexpectedly, seston C:P ratios remained below a severe P-limiting threshold for plankton growth and showed the same temporal pattern in all mesocosms. In contrast, seston N:P ratios differed significantly between treatments, with the L treatment reducing P-limiting conditions, whilst the HF treatment increased them. The effects of the combined HFL treatment indicated an additive type of interaction and chlorophyll-a was highest in the HFL treatment. Our results demonstrate that accounting for the optical and stoichiometric properties of experimental allo-OM treatments is crucial to improve the capacity to explain extrapolated conclusions regarding the effects of climate driven flooding on freshwater ecosystems in response to global climate change.

Advances in the analysis of amplicon sequence datasets have introduced a methodological shift in how research teams investigate microbial biodiversity, away from sequence identity-based clustering (producing Operational Taxonomic Units, OTUs) to denoising methods (producing amplicon sequence variants, ASVs). While denoising methods have several inherent properties that make them desirable compared to clustering-based methods, questions remain as to the influence that these pipelines have on the ecological patterns being assessed, especially when compared to other methodological choices made when processing data (e.g. rarefaction) and computing diversity indices. We compared the respective influences of two widely used methods, namely DADA2 (a denoising method) vs. Mothur (a clustering method) on 16S rRNA gene amplicon datasets (hypervariable region v4), and compared such effects to the rarefaction of the community table and OTU identity threshold (97% vs. 99%) on the ecological signals detected. We used a dataset comprising freshwater invertebrate (three Unionidae species) gut and environmental (sediment, seston) communities sampled in six rivers in the southeastern USA. We ranked the respective effects of each methodological choice on alpha and beta diversity, and taxonomic composition. The choice of the pipeline significantly influenced alpha and beta diversities and changed the ecological signal detected, especially on presence/absence indices such as the richness index and unweighted Unifrac. Interestingly, the discrepancy between OTU and ASV-based diversity metrics could be attenuated by the use of rarefaction. The identification of major classes and genera also revealed significant discrepancies across pipelines. Compared to the pipeline’s effect, OTU threshold and rarefaction had a minimal impact on all measurements.

Concerns are being raised that microplastic pollution can have detrimental effects on the feeding of aquatic invertebrates, including zooplankton. Both small plastic fragments (microplastics, MPs) produced by degradation of larger plastic waste (secondary MPs; SMPs) and microscopic plastic spheres used in cosmetic products and industry (primary MPs; PMPs) are ubiquitously present in the environment. However, despite the fact that most environmental MPs consist of weathered plastic debris with irregular shape and broad size distribution, experimental studies of organism responses to MP exposure have largely used uniformly sized spherical PMPs. Therefore, effects observed for PMPs in such experiments may not be representative for MP-effects in situ. Moreover, invertebrate filter-feeders are generally well adapted to the presence of refractory material in seston, which questions the potential of MPs at environmentally relevant concentrations to measurably affect digestion in these organisms. Here, we compared responses to MPs (PMPs and SMPs) and naturally occurring particles (kaolin clay) using the cladoceran Daphnia magna as a model organism. We manipulated food levels (0.4 and 9 μg C mL-1) and MP or kaolin contribution to the feeding suspension (<1 to 74%) and evaluated effects of MPs and kaolin on food uptake, growth, reproductive capacity of the daphnids, and maternal effects on offspring survival and feeding. Exposure to SMPs caused elevated mortality, increased inter-brood period and decreased reproduction albeit only at high MP levels in the feeding suspension (74% by particle count). No such effects were observed in either PMP or kaolin treatments. In daphnids exposed to any particle type at the low algal concentration, individual growth decreased by ~15%. By contrast, positive growth response to all particle types was observed at the high algal concentration with 17%, 54% and 40% increase for kaolin, PMP and SMP, respectively. When test particles comprised 22% in the feeding suspension, both MP types decreased food intake by 30%, while kaolin had no effect. Moreover, SMPs were found to homoaggregate in a concentration-dependent manner, which resulted in a 77% decrease of the ingested SMPs compared to PMPs. To better understand MP-processing in the gut, gut passage time (GPT) and evacuation rate of MPs were also assayed. SMPs and PMPs differed in their effects on daphnids; moreover, the particle effects were dependent on the MP: algae ratio in the suspension. When the MP contribution to the particle abundance in the medium changed from 1 to 4%, GPT for daphnids exposed to SMPs increased 2-fold. Our results suggest that MPs and, in particular, SMPs, have a greater capacity to negatively affect feeding in D. magna compared to naturally occurring mineral particles of similar size. Moreover, grazer responses observed in experiments with PMPs cannot be extrapolated to the field where SMPs dominate, because of the greater effects caused by the latter.

Rivers are a major source of microplastic particles (<5 mm) to oceans, but empirical measurements of microplastic movement in freshwater ecosystems are rare. The hard, buoyant surface of microplastic is a novel habitat that selects for unique microbial assemblages in rivers, especially downstream of wastewater treatment plant (WWTP) point sources. We measured microplastic in surface water and benthic habitats 50 m upstream and 50, 305, 1115, and 1900 m downstream of the effluent outfall from a large WWTP in an urban river. We used high-throughput sequencing to measure bacterial assemblages on microplastic from surface and benthic habitats and compared them to bacterial assemblages from seston, water, and sediment. Concentrations of total microplastic and microplastic types (fragment, pellet) in surface water did not change with distance downstream of the WWTP. Thus, microplastic transport showed no net deposition or resuspension. Microplastic concentrations were much higher in the benthic zone than surface water. Benthic deposition appears to be a plastic sink over longer time scales, but subsequent studies are needed to resolve microplastic transport dynamics by particle type, size, and habitat. Composition of microplastic-attached bacterial assemblages differed from that of assemblages in water, seston, and sediment and supports domestic wastewater as a point source of microplastic (e.g., gastrointestinal taxa). Shifts in microplastic assemblages with distance from the WWTP suggest succession toward a ‘stream-like’ bacterial assemblage. Future studies are required to quantify the metabolic capacity of microplastic-associated bacteria. Estimates of transport distance, microplastic storage, and microbial interactions are critical to include lotic ecosystems in accountings of global plastic budgets.

Shellfish reefs have been lost from bays and estuaries globally, including in the Swan-Canning Estuary in Western Australia. As part of a national program to restore the ecosystem services that such reefs once provided and return this habitat from near extinction, the mussel Mytilus galloprovincialis was selected for a large-scale shellfish reef construction project in this estuary. To assess the potential filtration capacity of the reef, estuary seston quality, mussel feeding behavior, and valve gape activity were quantified in the laboratory and field during winter and summer. In general, estuary water contained high total particulate concentrations (7.9–8.7 mg L−1). Standard clearance rates were greater in winter (1.9 L h−1; 17 °C) than in summer (1.3 L h−1; 25 °C), the latter producing extremely low absorption efficiencies (37%). Mussel valves remained open ~97% and ~50% of the time in winter and summer, respectively. They often displayed erratic behavior in summer, possibly due to elevated temperatures and the toxic microalgae Alexandrium spp. Despite numerous stressors, the reef, at capacity, was estimated to filter 35% of the total volume of the estuary over winter, incorporating 42.7 t of organic matter into mussel tissue. The reefs would thus make a substantial contribution to improving estuary water quality.

Seagrass ecosystems rank amongst the most efficient natural carbon sinks on earth, sequestering CO 2 through photosynthesis and storing organic carbon (C org ) underneath their soils for millennia and thereby, mitigating climate change. However, estimates of C org stocks and accumulation rates in seagrass meadows (blue carbon) are restricted to few regions, and further information on spatial variability is required to derive robust global estimates. Here we studied soil C org stocks and accumulation rates in seagrass meadows across the Colombian Caribbean. We estimated that Thalassia testudinum meadows store 241 ± 118 Mg C org ha −1 (mean ± SD) in the top 1 m-thick soils, accumulated at rates of 122 ± 62 and 15 ± 7 g C org m −2  year −1 over the last ~ 70 years and up to 2000 years, respectively. The tropical climate of the Caribbean Sea and associated sediment run-off, together with the relatively high primary production of T. testudinum , influencing biotic and abiotic drivers of C org storage linked to seagrass and soil respiration rates, explains their relatively high C org stocks and accumulation rates when compared to other meadows globally. Differences in soil C org storage among Colombian Caribbean regions are largely linked to differences in the relative contribution of C org sources to the soil C org pool (seagrass, algae Halimeda tuna , mangrove and seston) and the content of soil particles < 0.016 mm binding C org and enhancing its preservation. Despite the moderate areal extent of T. testudinum in the Colombian Caribbean (661 km 2 ), it sequesters around 0.3 Tg CO 2 year −1 , which is equivalent to ~ 0.4% of CO 2 emissions from fossil fuels in Colombia. This study adds data from a new region to a growing dataset on seagrass blue carbon and further explores differences in meadow C org storage based on biotic and abiotic environmental factors, while providing the basis for the implementation of seagrass blue carbon strategies in Colombia.

The combination of an efficient sampling method and high‐throughput analysis of environmental DNA (eDNA) can be a powerful approach for characterising biodiversity across aquatic ecosystems. Plankton net tows are one of the oldest, simplest, and least expensive methods for seston and eDNA collection, but require laborious filtration steps which often lead to clogging and/or the introduction of contaminants. In this study, we used a cruising speed net (CSN) device enabling the collection of seston‐derived eDNA at 5 knots speed combined with a novel modified cod‐end with 20 μm nylon mesh inserts enabling eDNA capture while towing. We compared the performance of the CSN sampling protocol with the original conventional filtration of water sample versus the modified cod‐end. Samples were collected in parallel horizontal tows along New Zealand's North‐Eastern coastline. Concentrated water was filtered on conventional 5 μm cellulose acetate membranes, while the 20 μm nylon mesh inserts were immediately isolated post‐towing. Metabarcoding of bacterial 16S rRNA, eukaryotic nuclear 18S rRNA and mitochondrial COI genes, revealed no significant difference in alpha diversity between filtration techniques. In terms of community composition, a clear and significant shift could be observed between sampling sites and environments. Significant differences could be detected between filtration methods for 16S and COI markers, likely driven by fine‐scale differences at more turbid sheltered sites. Nonetheless, each technique could detect shifts in communities between sites and environments with similar sensitivity. Our results demonstrate the promising potential of the modified cod‐end to enable practical and cost‐effective isolation of eDNA‐derived biodiversity data from any vessel types (at ≤5 knots) across a large range of aquatic ecosystems and biogeographic scales. La combinaison d'une méthode d'échantillonnage efficace et d'une analyse à haut débit de l'ADN environnemental (ADNe) peut être une approche puissante pour caractériser la biodiversité dans les écosystèmes aquatiques. Les dragages au filet planctonique sont l'une des méthodes les plus anciennes, les plus simples et les moins coûteuses pour la collecte de seston et d'ADNe, mais nécessitent des étapes de filtration laborieuses qui conduisent souvent à des obstructions et/ou à l'introduction de contaminants. Dans cette étude, nous avons utilisé un dispositif de filet à vitesse de croisière (CSN) permettant la collecte d'ADNe dérivé du seston à une vitesse de 5 nœuds, combiné à un nouveau cod‐end modifié avec filtre inséré en maille de nylon de 20 μm permettant la capture de l'ADNe pendant le remorquage. Nous avons comparé les performances du protocole d'échantillonnage CSN avec la filtration conventionnelle originale de l'échantillon d'eau par rapport au cod‐end modifié. Les échantillons ont été collectés lors de remorquages horizontaux parallèles le long de la côte nord‐est de la Nouvelle‐Zélande. L'eau concentrée a été filtrée sur des membranes d'acétate de cellulose de 5 μm, tandis que les inserts en maille de nylon de 20 μm étaient immédiatement isolés après le remorquage. Le métabarcodage des gènes de l'ADNr 16S bactérien, de l'ADNr nucléaire 18S eucaryote et du Cytochrome mitochondrial (COI) n'a révélé aucune différence significative de diversité alpha entre les techniques de filtration. En ce qui concerne la composition de la communauté, un changement clair et significatif a pu être observé entre les sites d'échantillonnage et les environnements. Des différences significatives ont pu être détectées entre les méthodes de filtration pour les marqueurs 16S et COI, probablement dues à des différences à échelle fine sur des sites plus troubles et abrités. Néanmoins, chaque technique a pu détecter des changements dans les communautés entre les sites et les environnements avec une sensibilité similaire. Nos résultats démontrent le potentiel prometteur du cod‐end modifié pour permettre l'isolement pratique et rentable de données de biodiversité dérivées de l'ADNe à partir de tous les types de navires (à ≤5 nœuds) dans une large gamme d'écosystèmes aquatiques et d'échelles biogéographiques.

Aim: The average carbon-to-nitrogen-to-phosphorus ratio (C:N:P) of marine algae is known to be tightly coupled to that of the inorganic pools of C, N and P in the ocean interior (i.e. the Redfield ratio), and therefore plays a key role in regulating the C and N cycles in the ocean. The C:N:P ratio of algae also varies substantially, both within and among taxa, in response to variation in the abiotic environment, raising the possibility that biogeochemical controls on the marine C and N cycles may shift as a result of climate change. Howerer, the role of temperature in driving phenotypic variation in stoichiometry within algal taxa, as well as biogeographic variation in particulate C, N and P among oceanic regions, remains largely unresolved. Location: Global. Methods: To assess the extent to which temperature controls algal stoichiometry we performed two complementary meta-analyses. First, we characterized the global temperature dependence of algal stoichiometry by analysing field data that encompassed 767 estimates of C:N:P from 22 oceanic sites spanning over 130° of latitude. Second, we characterized the within-species acclimation responses of C:N:P stoichiometry to temperature by analysing data that encompassed 17 experiments, 9 species and 4 taxonomic classes. Results: The geographic analyses demonstrated that the N:P and C:P ratios of marine algae were best predicted by latitudinal variation in average sea-surface temperature, and that both ratios increased 2.6-fold from 0 to 30 °C. These global-scale temperature responses, which largely reflect geographic variation in the species compositions of algal assemblages, were of similar magnitude to the average within-species response of the N:P and C:P ratios to experimental temperature manipulations. Main conclusions: The congruence between field and experimental observations suggests that temperature-dependent physiological mechanisms operating at the subcellular level play an important role in determining the stoichiometry of algae in the world's oceans.

The planktonic cladocerans Ceriodaphnia richardi, Daphnia gessneri, and Daphnia birgei inhabit the limnetic and littoral zones of Lake Monte Alegre, where the former species tends to be abundant. Laboratory experiments were carried out to investigate the competition for seston of the limnetic and littoral zones in cladocerans using life table data. In experiment 1, the species C. richardi and D. gessneri were fed seston from the limnetic zone (1–1.29 mg C L−1); in experiment 2, the species C. richardi and D. birgei were fed seston from the littoral zone. Despite the relatively high concentration of sestonic algae (0.96–1 mg C L−1), with predominance of nanoplankton, C. richardi outcompeted D. gessneri in the experiment with the limnetic seston. The species C. richardi and D. birgei benefited from the presence of each other in the experiment with littoral seston, where nanoplankton predominated, with increases in some parameters of the life table. D. birgei, however, showed better reproductive performance than C. richardi. A comparison between the results of the experiments suggests that the seston of the limnetic zone, in terms of quantity and quality, is better for C. richardi than the littoral seston.