Insights into the harmful algal flora in northwestern Mediterranean coastal lagoons revealed by pyrosequencing metabarcodes of the 28S rRNA gene

This study investigated the genetic diversity of phytoplankton communities in six shallow lagoons located on the French coast of the northwestern Mediterranean Sea that represented a trophic gradient ranging from oligotrophic to hypereutrophic. The phytoplankton communities were sampled once a month from spring (May) to the beginning of autumn (September/early October) in 2012 and fractionated by size. Metabarcodes were generated from cDNAs by targeting the D1-D2 region of the 28S rRNA gene and pyrosequenced using Roche 454 technology. Examination of the annotated barcodes revealed harmful algal species not previously documented in these lagoons. Three ichthyotoxic species belonging to Pfiesteriaceae were detected: Luciella masanensis was relatively widespread and abundant in many samples, whereas Pfiesteria piscicida and Stoeckeria changwonensis were found as single barcode sequences. Furthermore, a phylogenetic analysis of barcodes annotated as belonging to Pfiesteriaceae suggested the existence of two previously undescribed clades. The other toxic or potentially harmful dinoflagellates detected through rare barcodes were Dinophysis acuminata, Vulcanodinium rugosum, Alexandrium andersonii and A. ostenfeldii. The two most abundant dinoflagellate taxa were Gymnodinium litoralis and Akashiwo sanguinea with respect to sequence numbers. Four diatom species from the genus Pseudo-nitzschia that potentially produce domoic acid were identified (P. galaxiae, P. delicatissima, P. brasiliana and P. calliantha). These observations are discussed in terms of the literature and monitoring records related to the identified taxa in this Mediterranean area.     

Tropical ant communities are in long-term equilibrium

Communities change with time. Studying long-term change in community structure permits deeper understanding of community dynamics, and allows us to forecast community responses to perturbations at local (e.g. fire, secondary succession) and global (e.g. desertification, global warming) spatial scales. Monitoring efforts exploring the temporal dynamics of indicator taxa are therefore a critical part of conservation agendas. Here, the temporal dynamics of the Otongachi leaf litter ant community, occurring in a cloud forest in coastal Ecuador, were explored. By sampling this community six times over eleven years, I assessed how the ant fauna caught by Winkler traps (more diverse and cryptic fauna) and caught by pitfall traps (larger, more mobile fauna) changed over time. The Otongachi leaf litter ant community was dynamic. Although species richness in the community remained constant, temporal turnover of species was high: on average, 51% of the ant species in Winkler traps, and 56% of those in pitfall traps, were replaced with other ant species from one year to the other. Shifts in the rank abundance of species in the community were also large across the eleven years and, on average, shifts in the rank abundance of species collected by Winkler traps doubled those occurring in pitfall traps from one census to the other. In spite of these trends, the Otongachi ant fauna showed no (Winkler) or weak (pitfall) evidence of directional change (towards a new community). Thus, this tropical ant community can be divided in two community compartments. The Winkler compartment composed by a more diverse and cryptic ant fauna appears to be resilient and stable in time. The pitfall compartment composed by larger and more mobile ants may be prone to respond to disturbance. This study suggests that 1) species appearing/disappearing from a site may be rather the rule, difficult to separate from responses to ecological stress. 2) Conclusions made in short-term studies, or studies comparing two (e.g. before and after) snapshots of a community, should thus be revisited. Finally, 3) the ant fauna caught by pitfall traps (a rather simple and cheap survey method) is the most likely community compartment to indicate ecological perturbation. This study adds to the growing evidence that using ants as ecological indicators should incorporate long-term temporal dynamics.     

EMAP-Wetlands: A sampling design with global application

The U.S. Environmental Protection Agency (EPA) initiated the Environmental Monitoring and Assessment Program (EMAP) in 1988. The wetland component (EMAP-Wetlands) is designed to provide quantitative assessments of the current status and long-term trends in the ecological condition of wetland resources. EMAP-Wetlands will develop a wetland monitoring network and will identify and evaluate indicators that describe and quantify wetland condition. The EMAP-Wetlands network will represent a probability sample of the total wetland resource. The EMAP sample is based on a triangular grid of approximately 12,600 sample points in the conterminous U.S. The triangular grid adequately samples wetland resources that are common and uniformly distributed in a region, such as the prairie pothole wetlands of the Midwest. However, the design is flexible and allows the base grid density to be increased to adequately sample wetland resources, such as the coastal wetlands of the Gulf of Mexico, which are distributed linearly along the coast. The Gulf sample network required a 49-fold increase in base grid density. EMAP-Wetlands aggregates the 56 U.S. Fish and Wildlife Service's (FWS) National Wetland Inventory (NWI) categories (Cowardin et al. 1979) into 12 functionally similar groups (Leibowitz et al. 1991). Both the EMAP sample design and aggregated wetland classes are suitable for global inventory and assessment of wetlands.The research described in this report has been funded by the U.S. Environmental Protection Agency. This document has been prepared at the EPA Environmental Research Laboratory in Corvallis, OR, through contract No. 68-C8-0006 to Man Tech Environmental Technology, Inc. This paper has been subjected to the Agency's peer and administrative review and approved for publication. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.     

In and out: Effects of shoot- vs. rooted-presence sampling methods on plant diversity measures in mountain grasslands

Plant diversity measures (e.g., alpha- and beta-diversity) provide the basis for a number of ecological indication and monitoring methods. These measures are based on species counts in sampling units (plots or quadrats). However, there are two alternative conventions for defining a vascular plant species as “present” in a plot, i.e. “shoot presence” (a species is recorded if the vertical projection of any above-ground part falls within the plot) and “rooted presence” (a species is recorded only when an individual is rooted inside the plot). Very few studies addressed the effects of the two sampling conventions on species richness and diversity indices. We sampled mountain dry grasslands in Italy across different plot sizes and vegetation types to assess how large is the difference in alpha- and beta-diversity values and in sample-based rarefaction curves between the two methods. We found that the difference is greatly dependent on plot size, being more relevant, both in absolute and percentage values, at smaller grain; it is also dependent on habitat type, being larger in shallow-soil communities, as they have a sparser vegetation structure and host life-form types with a larger lateral spread. At fine spatial scales (<1 m²) the difference is large enough to bias statistical inference, and we conclude that at such scales one should not attempt to compare plant diversity indices if they were not obtained with the same sampling convention.     

Evaluation of three field test kits to detect microcystins from a public health perspective

Cyanobacteria blooms may present a public health concern in sources of drinking water and recreational water due to the production of toxins by some species, microcystins being the most commonly found. It is possible to detect microcystins using instrumental analyses and field test kits. While instrumental analysis methods are accurate, they are also costly, and in regions with a high incidence of blooms the time to report is lengthy (days). On the other hand, the use of commercially available test kits may provide quicker results at a lower cost. The purpose of this work was to evaluate three commercially available kits: the Immunochromatographic Strip Test for the Detection of Microcystins and Nodularins in Source Drinking Water at 1 μg/L (Abraxis strip test), the Abraxis Microcystin Tube Kit and the Envirologix QualiTube Kit. The evaluation of each kit focussed on the interpretation of the results by the end-user and the validity of a test kit was based on four indices: sensitivity, specificity, positive predictive rate (PPR) and negative predictive rate (NPR) (false positive/negative) based on the manufacturer's specifications. The results indicate that there are challenges in the visual interpretation of the results at levels close to the threshold value for each kit. The scope of each kit must be understood: free vs. total, qualitative vs. semiquantitative. For instance, the Envirologix Qualitube Kit does not provide a lysing agent, therefore it will underestimate the levels of total microcystin if a lysing step is not included. In the case of the Abraxis strip test, the kit provides information on the absence/presence of microcystin at a threshold value of 1 μg/L, but false positives were encountered.     

An Ecosystem Health Index for a large and variable river basin: Methodology,challenges and continuous improvement in Queensland’s Fitzroy Basin

Report cards are an increasingly popular method for summarising and communicating relative environmental performance and ecosystem health, including in aquatic environments. They are usually underpinned by an Ecosystem Health Index (EHI) that combines various individual indicators to produce an overall ecosystem health “score”. As a result of public water quality concerns, an integrated means of monitoring and reporting on aquatic ecosystem health was needed for the Fitzroy Basin in central Queensland, Australia. The Fitzroy Partnership for River Health was formed to address this need, and developed an EHI and report card for the Basin using existing monitoring data collected from various third parties including regulated companies operations and government. At 142,000 square kilometres, the Fitzroy Basin is the largest catchment draining to the World Heritage Listed Great Barrier Reef. The Fitzroy Basin provides an example of how to deliver an effective aquatic ecosystem health reporting system in a large and complex river basin. We describe the methodology used to develop an adaptive EHI for the Fitzroy Basin that addresses variability, complexity and scale issues associated with reporting across large areas. As well, we report how to manage the design and reporting stages given limitations in data collection and scientific understanding.     

Interpreting coral reef monitoring data: A guide for improved management decisions

Coral reef monitoring programmes exist in all regions of the world, recording reef attributes such as coral cover, fish biomass and macroalgal cover. Given the cost of such monitoring programs, and the degraded state of many of the world’s reefs, understanding how reef monitoring data can be used to shape management decisions for coral reefs is a high priority. However, there is no general guide to understanding the ecological implications of the data in a format that can trigger a management response. We attempt to provide such a guide for interpreting the temporal trends in 41 coral reef monitoring attributes, recorded by seven of the largest reef monitoring programmes. We show that only a small subset of these attributes is required to identify the stressors that have impacted a reef (i.e. provide a diagnosis), as well as to estimate the likely recovery potential (prognosis). Two of the most useful indicators, turf algal canopy height and coral colony growth rate are not commonly measured, and we strongly recommend their inclusion in reef monitoring. The diagnosis and prognosis system that we have developed may help guide management actions and provides a foundation for further development as biological and ecological insights continue to grow.     

Recording relative water table depth using PVC tape discolouration: Advantages and constraints in fens

Question: Recognizing water table dynamics in wetlands is crucial for understanding species‐environment relationships, ecosystem function and changes during restoration. The PVC tape discolouration method enables spatially and temporally extensive studies of reductive conditions associated with long‐term water table dynamics in peat soils. The reliability of the method has been verified only for ombrotrophic bogs, even though wide usage can be expected in minerotrophic fens. Location: T?reboň basin, Czech Republic. Methods: Using data from 49 plots in six poor and moderately rich fens, we correlated the directly measured lowest, highest and mean water table depths and the same variables indicated by discolouration of PVC tape attached to green bamboo stakes installed vertically in the soil profile. Results: The depth to the first sign of PVC discolouration was highly correlated with the directly measured position of the highest water table, the correlation between the depth of complete discolouration and the directly measured position of the lowest water table was poorer. The accuracy of the minimum water table measurement depended on the depth of the peat layer. Surprisingly, the depth at which the green bamboo stakes turned brown correlated highly with the minimum water table. Conclusions: The PVC tape discolouration method reliably indicates water table maxima in fens, but minima are not accurately indicated. The depth of the green bamboo discolouration is suggested as a new alternative indicator of the minimum water table, even in fens and mineral soils. Combining both methods enables efficient monitoring of water table dynamics at a large number of mire sites.