Phytoplankton assemblage characteristics in recurrently fluctuating environments

Annual variations in biogeochemical and physical processes can lead to nutrient variability and seasonal patterns in phytoplankton productivity and assemblage structure. In many coastal systems river inflow and water exchange with the ocean varies seasonally, and alternating periods can arise where the nutrient most limiting to phytoplankton growth switches. Transitions between these alternating periods can be sudden or gradual and this depends on human activities, such as reservoir construction and interbasin water transfers. How such activities might influence phytoplankton assemblages is largely unknown. Here, we employed a multispecies, multi-nutrient model to explore how nutrient loading switching mode might affect characteristics of phytoplankton assemblages. The model is based on the Monod-relationship, predicting an instantaneous growth rate from ambient inorganic nutrient concentrations whereas the limiting nutrient at any given time was determined by Liebig’s Law of the Minimum. Our simulated phytoplankton assemblages self-organized from species rich pools over a 15-year period, and only the surviving species were considered as assemblage members. Using the model, we explored the interactive effects of complementarity level in trait trade-offs within phytoplankton assemblages and the amount of noise in the resource supply concentrations. We found that the effect of shift from a sudden resource supply transition to a gradual one, as observed in systems impacted by watershed development, was dependent on the level of complementarity. In the extremes, phytoplankton species richness and relative overyielding increased when complementarity was lowest, and phytoplankton biomass increased greatly when complementarity was highest. For low-complementarity simulations, the persistence of poorer-performing phytoplankton species of intermediate R*s led to higher richness and relative overyielding. For high-complementarity simulations, the formation of phytoplankton species clusters and niche compression enabled higher biomass accumulation. Our findings suggest that an understanding of factors influencing the emergence of life history traits important to complementarity is necessary to predict the impact of watershed development on phytoplankton productivity and assemblage structure

Lumpy species coexistence arises robustly in fluctuating resource environments

The effect of life-history traits on resource competition outcomes is well understood in the context of a constant resource supply. However, almost all natural systems are subject to fluctuations of resources driven by cyclical processes such as seasonality and tidal hydrology. To understand community composition, it is therefore imperative to study the impact of resource fluctuations on interspecies competition. We adapted a well-established resource-competition model to show that fluctuations in inflow concentrations of two limiting resources lead to the survival of species in clumps along the trait axis, consistent with observations of “lumpy coexistence” [Scheffer M, van Nes EH (2006) Proc Natl Acad Sci USA 103:6230–6235]. A complex dynamic pattern in the available ambient resources arose very early in the self-organization process and dictated the locations of clumps along the trait axis by creating niches that promoted the growth of species with specific traits. This dynamic pattern emerged as the combined result of fluctuations in the inflow of resources and their consumption by the most competitive species that accumulated the bulk of biomass early in assemblage organization. Clumps emerged robustly across a range of periodicities, phase differences, and amplitudes. Given the ubiquity in the real world of asynchronous fluctuations of limiting resources, our findings imply that assemblage organization in clumps should be a common feature in nature

Changes in microbial (Bacteria and Archaea) plankton community structure after artificial dispersal in grazer-free microcosms

Microbes are considered to have a global distribution due to their high dispersal capabilities. However, our knowledge of the way geographically distant microbial communities assemble after dispersal in a new environment is limited. In this study, we examined whether communities would converge because similar taxa would be selected under the same environmental conditions, or would diverge because of initial community composition, after artificial dispersal. To this aim, a microcosm experiment was performed, in which the temporal changes in the composition and diversity of different prokaryoplankton assemblages from three distant geographic coastal areas (Banyuls-sur-Mer in northwest Mediterranean Sea, Pagasitikos Gulf in northeast Mediterranean and Woods Hole, MA, USA in the northwest Atlantic), were studied. Diversity was investigated using amplicon pyrosequencing of the V1-V3 hypervariable regions of the 16S rRNA. The three assemblages were grown separately in particle free and autoclaved Banyuls-sur-mer seawater at 18 °C in the dark. We found that the variability of prokaryoplankton community diversity (expressed as richness, evenness and dominance) as well as the composition were driven by patterns observed in Bacteria. Regarding community composition, similarities were found between treatments at family level. However, at the OTU level microbial communities from the three different original locations diverge rather than converge during incubation. It is suggested that slight differences in the composition of the initial prokaryoplankton communities, resulted in separate clusters the following days even when growth took place under identical abiotic conditions

Species extinctions strengthen the relationship between biodiversity and resource use efficiency

Evidence from terrestrial ecosystems indicates that biodiversity relates to ecosystem functions (BEF), but this relationship varies in its strength, in part, as a function of habitat connectivity and fragmentation. In primary producers, common proxies of ecosystem function include productivity and resource use efficiency. In aquatic primary producers, macroecological studies have observed BEF variance, where ecosystems with lower richness show stronger BEF relationships. However, aquatic ecosystems are less affected by habitat fragmentation than terrestrial systems and the mechanism underlying this BEF variance has been largely overlooked. Here, we provide a mechanistic explanation of BEF variance using a trait-based, numerical model parameterized for phytoplankton. Resource supply in our model fluctuates recurrently, similar to many coastal systems. Our findings show that following an extinction event, the BEF relationship can be driven by the species that are the most efficient resource users. Specifically, in species-rich assemblages, increased redundancy of efficient resource users minimizes the risk of losing function following an extinction event. On the other hand, in species-poor assemblages, low redundancy of efficient resource users increases the risk of losing ecosystem function following extinctions. Furthermore, we corroborate our findings with what has been observed from large-scale field studies on phytoplankton

Environmental DNA: a new low-cost monitoring tool for pathogens in salmonid aquaculture

Environmental DNA (eDNA) metabarcoding is a relatively new monitoring tool featuring in an increasing number of applications such as the facilitation of the accurate and cost effective detection of species in environmental samples. eDNA monitoring is likely to have a major impact on the ability of salmonid aquaculture industry producers and their regulators to detect the presence and abundance of pathogens and other biological threats in the surrounding environment. However, for eDNA metabarcoding to develop into a useful bio-monitoring tool it is necessary to (a) validate that sequence datasets derived from amplification of metabarcoding markers reflect the true species’ identity, (b) test the sensitivity under different abundance levels and environmental noise and (c) establish a low-cost sequencing method to enable the bulk processing of field samples. In this study, we employed an elaborate experimental design whereby different combinations of five biological agents were crossed at three abundance levels and exposed to sterile pre-filtered and unfiltered seawater, prior to coarse filtering and then eDNA ultrafiltration of the resultant material. We then benchmarked the low-cost, scalable, Ion Torrent sequencing method against the current gold-standard Illumina platform for eDNA surveys in aquaculture. Based on amplicon-seq of the 18S SSU rDNA v9 region, we were able to identify two parasites (Lepeophtheirus salmonis and Paramoeba perurans) to species level, whereas the microalgae species Prymnesium parvum, Pseudo-nitzschia seriata, and P. delicatissima could be assigned correctly only to the genus level. Illumina and Ion Torrent provided near identical results in terms of community composition in our samples, whereas Ion Torrent was more sensitive in detecting species richness when the medium was unfiltered seawater. Both methods were able to reflect the difference in relative abundance between treatments in 4 out of 5 species when samples were exposed to the unfiltered seawater, despite the significant amount of background noise from both bacteria and eukaryotes. Our findings indicate that eDNA metabarcoding offers significant potential in the monitoring of species harmful to aquaculture and for this purpose, the low-cost Ion Torrent sequencing is as accurate as Illumina in determining differences in their relative abundance between samples

Optimized classification predictions with a new index combining machine learning algorithms

Voting is a commonly used ensemble method aiming to optimize classification predictions by combining results from individual base classifiers. However, the selection of appropriate classifiers to participate in voting algorithm is currently an open issue. In this study we developed a novel Dissimilarity-Performance (DP) index which incorporates two important criteria for the selection of base classifiers to participate in voting: their differential response in classification (dissimilarity) when combined in triads and their individual performance. To develop this empirical index we firstly used a range of different datasets to evaluate the relationship between voting results and measures of dissimilarity among classifiers of different types (rules, trees, lazy classifiers, functions and Bayes). Secondly, we computed the combined effect on voting performance of classifiers with different individual performance and/or diverse results in the voting performance. Our DP index was able to rank the classifier combinations according to their voting performance and thus to suggest the optimal combination. The proposed index is recommended for individual machine learning users as a preliminary tool to identify which classifiers to combine in order to achieve more accurate classification predictions avoiding computer intensive and time-consuming search

Effects of long-term exposure to microfibers on ecosystem services provided by coastal mussels

The biofiltration capacity of bivalve populations is known to alleviate the effects of coastal eutrophication. However, this important ecosystem service could potentially be impaired by the increasing microplastic abundance in near shore environments. It is known that relatively large microplastics (∼500 μm) impair the filtration capacity of bivalves, however, the effect of smaller microplastics, and specifically microfibers, is not known even though they are more common in many natural systems and similar in size to phytoplankton, the main food source of mussels. Here, we investigated the effects of long-term exposure to microfibers (MFs), which are smaller than 100 μm, on the biofiltration capacity of the blue mussel, Mytilus edulis. Our findings show that long-term exposure (here 39 days) to microfibers significantly reduced (21%) the clearance of phytoplankton (Tetraselmis sp). While previous studies have shown that larger microplastics can decrease the filtration capacity of mussels after short-term exposure, our findings suggest that, for smaller MFs, mussel's clearance capacity is significantly affected after long-term exposure (39 days in this study). This may be due to the accumulation of MFs in the digestive system. In addition, the most efficient phytoplankton consumers were more susceptible to MF accumulation in the digestive system. This suggests that prolonged exposure to MF of coastal mussels could negatively impact the biofiltration of more potent individuals, thus decreasing the ecosystem service potential of the population as a whole

Interplay between r- and K-strategists leads to phytoplankton underyielding under pulsed resource supply

Fluctuations in nutrient ratios over seasonal scales in aquatic ecosystems can result in overyielding, a condition arising when complementary life-history traits of coexisting phytoplankton species enables more complete use of resources. However, when nutrient concentrations fluctuate under short-period pulsed resource supply, the role of complementarity is less understood. We explore this using the framework of Resource Saturation Limitation Theory (r-strategists vs. K-strategists) to interpret findings from laboratory experiments. For these experiments, we isolated dominant species from a natural assemblage, stabilized to a state of coexistence in the laboratory and determined life-history traits for each species, important to categorize its competition strategy. Then, using monocultures we determined maximum biomass density under pulsed resource supply. These same conditions of resource supply were used with polycultures comprised of combinations of the isolated species. Our focal species were consistent of either r- or K-strategies and the biomass production achieved in monocultures depended on their efficiency to convert resources to biomass. For these species, the K-strategists were less efficient resource users. This affected biomass production in polycultures, which were characteristic of underyielding. In polycultures, K-strategists sequestered more resources than the r-strategists. This likely occurred because the intermittent periods of nutrient limitation that would have occurred just prior to the next nutrient supply pulse would have favored the K-strategists, leading to overall less efficient use of resources by the polyculture. This study provides evidence that fluctuation in resource concentrations resulting from pulsed resource supplies in aquatic ecosystems can result in phytoplankton assemblages' underyielding

Everything is not everywhere: can marine compartments shape phytoplankton assemblages?

The idea that ‘everything is everywhere, but the environment selects' has been seminal in microbial biogeography, and marine phytoplankton is one of the prototypical groups used to illustrate this. The typical argument has been that phytoplankton is ubiquitous, but that distinct assemblages form under environmental selection. It is well established that phytoplankton assemblages vary considerably between coastal ecosystems. However, the relative roles of compartmentalization of regional seas and site-specific environmental conditions in shaping assemblage structures have not been specifically examined. We collected data from coastal embayments that fall within two different water compartments within the same regional sea and are characterized by highly localized environmental pressures. We used principal coordinates of neighbour matrices (PCNM) and asymmetric eigenvector maps (AEM) models to partition the effects that spatial structures, environmental conditions and their overlap had on the variation in assemblage composition. Our models explained a high percentage of variation in assemblage composition (59–65%) and showed that spatial structure consistent with marine compartmentalization played a more important role than local environmental conditions. At least during the study period, surface currents connecting sites within the two compartments failed to generate sufficient dispersal to offset the impact of differences due to compartmentalization. In other words, our findings suggest that, even for a prototypical cosmopolitan group, everything is not everywhere