Large-scale Monitoring Programs Research Articles

Spatial variability in the abundance and prey selection of the corallivorous snail Drupella spp. in the southeastern Hainan Island, China

Global climate change has caused extensive loss of biodiversity and ecosystem function globally, particularly in coral reefs in shallow tropical waters. As the corallivorous snails represent considerable disturbances to coral reefs across Indo-Pacific region, it is becoming a threat to coral health and recovery in the Hainan Island, South China Sea, but current-knowledge gap remains on the spatial distribution, prey preferences, and the influence factors related. Thus, we investigated the abundance distribution of Drupella spp. in relation to coral-prey selectivity, availability, and nutritional value. The snail density was heterogeneously distributed in the study area with an average of 0.72 ± 0.32 ind m−2 (varying from 0.09 ± 0.03 to 1.78 ± 0.39 ind m−2), and the snail density was found generally higher in locations with higher coral cover, which resulted in much lower density where their preferred corals became scarce. Despite the snails showing a positive preference for Acroporidae corals, they displayed dietary plasticity by changing with prey abundance and availability. Further, we found the electivity index of the coral prey related to the substrate types, and the nutritional value of prey was an additional important determinant in the prey preference, suggesting that the specific reef habitat and environmental context may alter the prey preference of Drupella spp. Combined, these results provide preliminary evidence that Drupella spp. is among the common corallivories in the reef regions of Hainan Island, and we recommend that large-scale monitoring programs assess the spatial-temporal trends to better understand the dynamics of predation linked to both anthropogenic and natural impacts.

Using an acoustic complexity index to help monitor climate change effects on avian diversity

Passive recording technologies have become a valuable tool for ecologists to accumulate large data sets on vocalizing species assemblages and to study the response of biodiversity to regional and global environmental change. However, the process of interpreting these recordings and identifying species can be time-consuming. To automate this process, and to derive diversity metrics directly from the audio files, soundscape ecologists developed and published many bioacoustics indices, which are calculated using computer algorithms that mathematically summarize the acoustic energy in a recording. Of these indices, the acoustic complexity index (ACI) is perhaps the most widely proposed surrogate of bird species richness. Although several studies have shown the ACI to have positive correlations with species richness, it remains unknown how well the ACI will perform over large, habitat-diverse, regions. Our aim, here, was to examine whether site-level bird species richness (alpha diversity) correlated with the ACI across a large heterogenous mountain region. Further, we explored whether the elevational trends for alpha diversity and the ACI exhibited similar unimodal patterns with corresponding maximums and whether any shifts in the elevation of these maximums could be tracked over time in response to climate change. We deployed recording devices along two extensive transects on the Pacific Crest Trail in California, USA; these included a 689-km trail section in northern California and a 531-km section in southern California. Point counts for birds from the field were combined with the interpretation of the recordings to estimate alpha diversity using a Bayesian multispecies occupancy model. We found that alpha diversity exhibited a positive linear relationship with the ACI on both trail sections. However, these relationships were not strong (low R2 values). Similar mid-elevation maximums for alpha diversity and the ACI were observed along the northern trail section. Power analysis revealed that with repeated annual surveys using our protocols, we could detect an average shift in the elevation of either maximum species richness or ACI of approximately 100 m over 20 years (i.e., 5 m/yr), which could be improved in precision to 50 m (i.e., 2.5 m/yr) with a 5-fold increase in survey effort. Although there was considerable unexplained variation in our diversity- and ACI-elevation trends, which we suspect was due to microhabitat and microclimate effects, we concluded that the ACI was a useful, albeit coarse, surrogate of alpha diversity across large regions. The ACI warrants consideration by ecologists and land managers for application in large-scale monitoring programs.

A water quality barometer for Chesapeake Bay: Assessing spatial and temporal patterns using long-term monitoring data

This paper develops a barometer that indexes water quality in the Chesapeake Bay and summarizes quality over spatial regions and temporal periods. The barometer has a basis in risk assessment and hydrology, and is a function of three different metrics of water quality relative to numerical criteria: relative frequency of criterion attainment; magnitude of deviation from a numerical criterion; and duration of criterion attainment. Metrics associated with these features are calculated at the station level, allowing flexibility for simultaneously evaluating multiple stressors, different designated uses, and physical characteristics of the water. The barometer score is then created as a geometric mean of the three metrics. The water quality barometer (WQB) station scores may be spatially aggregated to report habitat scores across a spectrum of spatial resolutions (e.g., management segment, tidal subsystem, or the whole tidal bay). Dissolved oxygen measurements in the Chesapeake Bay collected during summer seasons of 1985 to 2020 are used to evaluate water quality. The WQB score and its bootstrapped confidence interval are reported at the station, segment, tidal subsystem and whole tidal bay levels. Notably, water quality interpreted through application of the WQB with dissolved oxygen concentration data and averaged over the 29-year period of record is good (i.e. protects aquatic living resources) in tributaries such as the James River, Rappahannock River and others; but is not as good in areas such as the Upper Tributaries and the York River. Recent summaries indicate that while the water quality is improving in much of the bay and its tidal tributaries, however, there is an indication of decline in quality in the period 20182020, especially in the upper regions of the Bay. The barometer is designed around using the time series data produced by the Chesapeake Bay Programs annual monitoring strategy; the approach has application to other large water bodies with large scale monitoring programs with extended time series or for integrating information from environmental sensor systems.

A miniaturized passive sampling-based workflow for monitoring chemicals of emerging concern in water

The miniaturization of a full workflow for identification and monitoring of contaminants of emerging concern (CECs) is presented. Firstly, successful development of a low-cost small 3D-printed passive sampler device (3D-PSD), based on a two-piece methacrylate housing that held up to five separate 9 mm disk sorbents, is discussed. Secondly, a highly sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method reduced the need for large scale in-laboratory apparatus, solvent, reagents and reference material quantities for in-laboratory passive sampler device (PSD) calibration and extraction. Using hydrophilic-lipophilic balanced sorbents, sampling rates (Rs) were determined after a low 50 ng L−1 exposure over seven days for 39 pesticides, pharmaceuticals, drug metabolites and illicit drugs over the range 0.3 to 12.3 mL day−1. The high sensitivity LC-MS/MS method enabled rapid analysis of river water using only 10 μL of directly injected sample filtrate to measure occurrence of 164 CECs and sources along 19 sites on the River Wandle, (London, UK). The new 3D-PSD was then field-tested over seven days at the site with the highest number and concentration of CECs, which was down-river from a wastewater treatment plant. Almost double the number of CECs were identified in 3D-PSD extracts across sites in comparison to water samples (80 versus 42 CECs, respectively). Time-weighted average CEC concentrations ranged from 8.2 to 845 ng L−1, which were generally comparable to measured concentrations in grab samples. Lastly, high resolution mass spectrometry-based suspect screening of 3D-PSD extracts enabled 113 additional compounds to be tentatively identified via library matching, many of which are currently or are under consideration for the EU Watch List. This miniaturized workflow represents a new, cost-effective, and more practically efficient means to perform passive sampling chemical monitoring at a large scale. SynopsisMiniaturized, low cost, multi-disk passive samplers enabled more efficient multi-residue chemical contaminant characterization, potentially for large-scale monitoring programs.

A comparison of monitoring designs to assess wildlife community parameters across spatial scales.

Dedicated long-term monitoring at appropriate spatial and temporal scales is necessary to understand biodiversity losses and develop effective conservation plans. Wildlife monitoring is often achieved by obtaining data at a combination of spatial scales, ranging from local to broad, to understand the status, trends, and drivers of individual species or whole communities and their dynamics. However, limited resources for monitoring necessitates tradeoffs in the scope and scale of data collection. Careful consideration of the spatial and temporal allocation of finite sampling effort is crucial for monitoring programs that span multiple spatial scales. Here we evaluate the ability of five monitoring designs-stratified random, weighted effort, indicator unit, rotating panel, and split panel-to recover parameter values that describe the status (occupancy), trends (change in occupancy), and drivers (spatially varying covariate and an autologistic term) of wildlife communities at two spatial scales. Using an amphibian monitoring program that spans a network of US national parks as a motivating example, we conducted a simulation study for a regional community occupancy sampling program to compare the monitoring designs across varying levels of sampling effort (ranging from 10% to 50%). We found that the stratified random design outperformed the other designs for most parameters of interest at both scales and was thus generally preferable in balancing the estimation of status, trends, and drivers across scales. However, we found that other designs had improved performance in specific situations. For example, the rotating panel design performed best at estimating spatial drivers at a regional level. Thus, our results highlight the nuanced scenarios in which various design strategies may be preferred and offer guidance as to how managers can balance common tradeoffs in large-scale and long-term monitoring programs in terms of the specific knowledge gained. Monitoring designs that improve accuracy in parameter estimates are needed to guide conservation policy and management decisions in the face of broad-scale environmental challenges, but the preferred design is sensitive to the specific objectives of a monitoring program.

Detection of Ampelovirus and Nepovirus by Lab-on-a-Chip: A Promising Alternative to ELISA Test for Large Scale Health Screening of Grapevine.

The Ampelovirus Grapevine leafroll-associated virus 3 (GLRaV-3) and the Nepovirus Grapevine fanleaf virus (GFLV) are pathogens reported in many grapevine-growing areas all over the world, main causal agents of grapevine leafroll disease and grapevine fanleaf disease, respectively. Prevention of virus spread thanks to rapid diagnosis of infected plants is a key factor for control of both diseases. Although serological (e.g., enzyme-linked immunosorbent assay-ELISA test) and molecular methods are available to reveal the presence of the viruses, they turn out to be quite expensive, time-consuming and laborious, especially for large-scale health screening. Here we report the optimization of a lab-on-a-chip (LOC) for GLRaV-3 and GFLV detection, based on an electrochemical transduction and a microfluidic multichamber design for measurements in quadruplicate and simultaneous detection of both targets. The LOC detect GLRaV-3 and GFLV at dilution factors more than 15 times higher than ELISA, providing a higher sensitivity in the detection of both viruses. Furthermore, the platform offers several advantages as easy-to-use, rapid-test, portability and low costs, favoring its potential application for large-scale monitoring programs. Compared to other grapevine virus biosensors, our sensing platform is the first one to provide a dose-dependent calibration curve combined with a microfluidic module for sample analysis and a portable electronics providing an operator-independent read-out scheme.

Drones can reliably, accurately and with high levels of precision, collect large volume water samples and physio-chemical data from lakes

The rapid development and application of drone technology has included water sampling and collection of physiochemical data from lakes. Previous research has demonstrated the significant potential of drones to play a future pivotal role in the collection of such data from lakes that fulfil requirements of large-scale monitoring programmes. However, currently the utilisation of drone technology for water quality monitoring is hindered by a number of important limitations: i) the low rate of successful sample captured; ii) the relatively low volume of water sample retrieved for analyses of multiple water chemistry parameters; and critically iii) differences between water chemistry parameters when using a drone versus samples collected by boat.Here we present results comparing the water chemistry results of a large number of parameters (pH, dissolved oxygen concentration, temperature, conductivity, alkalinity, hardness, true colour, chloride, silica, ammonia, total oxidised nitrogen, nitrite, nitrate, ortho-phosphate, total phosphorous and chlorophyll) sampled via drone with samples collected by boat in a number of lakes. The drone water sampling method used here is the first to collect a sufficiently large volume of water to meet the monitoring requirements of large scale water monitoring programmes, 2 L, at a 100% success rate and most crucially, with water chemistry variables that are not significantly different to those taken using traditional boat water sampling. This study therefore shows that drone technology can be utilised to collect water chemistry data and samples from lakes in a reliable, more rapid and cost effective manner than traditional sampling using boats, that is safer for personnel and poses less of a biosecurity risk.

Rapid expansion of an aquatic invasive species (AIS) in Central-European surface waters; a case study of Achnanthidium delmontii

In this work the rapid expansion of a small-celled (<15 µm) monoraphid aquatic invasive species (AIS) along the Central European lotic systems is reported, using the integrated dataset of two large-scale monitoring programs, as supplemented by additional records. Achnanthidium delmontii Pérès, Le Cohu & Barthès 2012 (ADMO) was discovered in 2007 and formally described in 2012, on the basis of specimens from a French river. ADMO was first detected in the upper sections of River Danube in 2013, and has been detectable since 2013, and from 2015 onwards in Hungary. The abundance and the number of occupied habitat types by the species have gradually increased. In 2019, ADMO was found to be among the most abundant and the most frequent species in the River Danube, with a mean relative abundance of at least 5%, and a frequency of at least 10% in samples. To extend the Danubian dataset, the relative abundances of ADMO from 79 freshwater lotic samples were studied to assess their potential of the species as an indicator organism. Weighted average regression was employed to determine the species’ optima and tolerances for 18 environmental variables. ADMO has a wide ecological range, which serves to confirm its potential invasive behaviour. In the case of the following variables, the values were found to be consistent with previously published data on the requirements of the taxon. Despite ADMO prefers high temperatures (estimated optimum = 21.8 °C), its spread shows a downstream pattern of the main watercourses of Europe. The species was first found abundantly from the upper section of River Danube, then with increasing abundance in the middle section, while remaining rare in the lower section. This distribution demonstrates that the River Danube serves as an important linear route for the species' invasion. The results of the study will help improve the ecological classification of water bodies and inform water protection actions undertaken under the auspices of the Water Framework Directive (WFD).

Decadal beach-dune profile monitoring along a 230-km high-energy sandy coast: Aquitaine, southwest France

Large-scale coastal monitoring programs are challenging to maintain over time but are necessary to understand and further predict complex coastal evolution and resilience. The 230 km-long Aquitaine coast is a high-energy meso-macrotidal coast composed of beach-dune systems showing dramatic morphological changes at seasonal and interannual scales. This study investigates the alongshore variability in beach-dune response based on a unique 11-year dataset of 41 spaced transects surveyed yearly in spring. The dataset is completed by interspersed autumn LiDAR surveys for seasonal analysis. Several beach-dune morphological descriptors are developed, such as beach-dune volume, beach width and different shoreline proxies delimiting the intertidal zone, the beach face and the dune face. The Aquitaine beach-dune system is characterised by a north-south gradient, from chronically eroding dunes backing low-elevation dissipative beaches in the north, to slowly accreting dunes backing wide beaches in the south, through a range of intermediate beach-dune states. Time- and spatially-averaged shoreline (dune foot position) trend is −0.5 m/year (erosion), with local variations ranging from −5.9 m/year to +2.1 m/year. During the 2013–2014 winter widespread erosion was observed, with the shoreline eroding by 13 m and 8 m on average along the Gironde and Landes coasts, respectively. This dataset provides insight into the timing, magnitude and spatial variability of beach-dune recovery from the outstandingly erosive 2013–2014 winter. We also show that local beach-dune volume is a good proxy for long-term shoreline trend. It is advocated that such large-scale coastal monitoring by means of single beach profiles spaced and distributed along 10–100 km of coast is a cheap and efficient approach to address coastal changes at regional scale, which can bring complementary information to aerial photographs interpretation to determine long-term shoreline evolution trend and thus contribute to support sustainable coastal management and planning.

Selection of a density separation solution to study microplastics in tropical riverine sediment.

Microplastics (MPs) are small (< 5mm) plastic particles that are widely found in marine, freshwater, terrestrial and atmospheric environments. Due to their prevalence and persistence, MPs are considered an emerging contaminant of environmental concern. The separation and quantitation of MPs from freshwater sediments is a challenging and critical issue. It is necessary to identify the fate and sources of MPs in the environment, minimise their release and adverse effects. Compared to marine sediments, standardised methods for extracting and estimating the amount of MPs in freshwater sediments are relatively limited. The present study focuses on MP recovery efficiency of four commonly used salt solutions (NaCl, NaI, CaCl2 and ZnCl2) for isolating MPs during the density separation step from freshwater sediment. Known combinations of artificial MP particles (PS, PE, PVC, PET, PP and HDPE) were spiked into standard river sediment. Extraction using NaI, ZnCl2 and NaCl solutions resulted in higher recovery rates from 37 to 97% compared to the CaCl2 solution (28-83%) and varied between polymer types. Low-density MPs (PE, HDPE, PP and PS) were more effectively recovered (> 87%) than the denser polymers (PET and PVC: 37 to 88.8%) using NaCl, NaI and ZnCl2 solutions. However, the effective flotation of ZnCl2 and NaI solutions is relatively expensive and unsafe to the environment, especially in the context of developing countries. Therefore, considering the efficiency, cost and environmental criteria, NaCl solution was selected. The protocol was then tested by extracting MPs from nine riverine sediment samples from the Red River Delta. Sediments collected from urban rivers were highly polluted by MPs (26,000 MPs items·kg-1 DW) compared to sediments located downstream. Using a NaCl solution was found to be effective in this case study and might also be used in long-term and large-scale MP monitoring programmes in Vietnam.

Bleaching in sponges on temperate mesophotic reefs observed following marine heatwave events

Climate change driven extreme events such as marine heatwaves (MHWs) can have dramatic impacts on ecosystems, with thermal stress often resulting in localised die-offs and visible signs of impacts such as bleaching of organisms. Such impacts are reported widely in shallower ecosystems but are less studied on deeper mesophotic ecosystems (MEs) where collecting data is more expensive. However, these deeper ecosystems are often biodiverse and play important ecological roles, and so understanding climate change impacts at these depths is important. Here we use benthic imagery collected as part of a large-scale monitoring program to explore bleaching in a cup sponge ‘morphospecies’ (i.e. morphologically distinct organisms readily identified in imagery) in MEs across eastern Tasmania, a region experiencing rapid ocean warming. We find an increased incidence of bleaching in surveys following MHWs, but currently no evidence for mass mortality following bleaching. Our results suggest that this cup sponge morphospecies may be useful for tracking climate change impacts on MEs in the region. Future efforts should be directed towards a better understanding of the physiological limits of this morphospecies across its range and timing surveys to more closely follow MHW events. Sponges form an important and dominant component of temperate MEs and monitoring the impacts of climate change on sponges across these ecosystems should therefore be an ongoing priority.

Fipronil and Fipronil Sulfone Distribution in Chicken Feathers and Eggs after Oral and Dermal Exposure.

This work aimed to investigate the bio-distribution and the persistence of fipronil and its primary metabolite fipronil sulfone after oral and dermal administration by simulating natural farming conditions. Fipronil and fipronil sulfone detection and quantification were performed in different poultry matrices using an LC-MS/MS method coupled with modified QuEChERS extraction. After oral administration, fipronil was detected in feathers at each sampling time, in eggs for 28 days, and in the internal organs at the end of the experiment. After dermal administration, high levels of fipronil were detected in feathers, accounting for 195.85 ± 8.54 mg/kg, which were reduced by a third after 60 days. No traces of fipronil were detected in the eggs or internal organs. In addition, fipronil sulfone showed remarkable residues in all samples in trial 2. The data obtained confirmed that inappropriate use of unauthorized pesticides can lead to severe contamination of entire poultry farms. The contemporary presence of fipronil sulfone in feathers and eggs associated with the lack of fipronil in eggs suggests recent dermal contamination or past oral contamination. Moreover, simultaneous analysis of hens’ feathers and eggs could represent a new method to improve large-scale monitoring programs and animal welfare, limiting their slaughter.

Optimizing SARS-CoV-2 Surveillance in the United States: Insights From the National Football League Occupational Health Program.

Evidence to understand effective strategies for surveillance and early detection of SARS-CoV-2 is limited. To describe the results of a rigorous, large-scale COVID-19 testing and monitoring program. The U.S. National Football League (NFL) and the NFL Players Association (NFLPA) instituted a large-scale COVID-19 monitoring program involving daily testing using 2 reverse transcription polymerase chain reaction (RT-PCR) platforms (Roche cobas and Thermo Fisher QuantStudio), a transcription-mediated amplification platform (Hologic Panther), and an antigen point-of-care (aPOC) test (Quidel Sofia). 32 NFL clubs in 24 states during the 2020 NFL season. NFL players and staff. SARS-CoV-2 test results were described in the context of medically adjudicated status. Cycle threshold (Ct) values are reported when available. A total of 632370 tests administered across 11668 persons identified 270 (2.4%) COVID-19 cases from 1 August to 14 November 2020. Positive predictive values ranged from 73.0% to 82.0% across the RT-PCR platforms. High Ct values (33 to 37) often indicated early infection. For the first positive result, the median Ct value was 32.77 (interquartile range, 30.02 to 34.72) and 22% of Ct values were above 35. Among adjudicated COVID-19 cases tested with aPOC, 42.3% had a negative result. Positive concordance between aPOC test result and adjudicated case status increased as viral load increased. Platforms varied by laboratory, and test variability may reflect procedural differences. Routine RT-PCR testing allowed early detection of infection. Cycle threshold values provided a useful guidepost for understanding results, with high values often indicating early infection. Antigen POC testing was unable to reliably rule out COVID-19 early in infection. The NFL and the NFLPA.

Integrating Diel Vertical Migrations of Bioluminescent Deep Scattering Layers Into Monitoring Programs

The deep sea (i.e., &amp;gt;200 m depth) is a highly dynamic environment where benthic ecosystems are functionally and ecologically connected with the overlying water column and the surface. In the aphotic deep sea, organisms rely on external signals to synchronize their biological clocks. Apart from responding to cyclic hydrodynamic patterns and periodic fluctuations of variables such as temperature, salinity, phytopigments, and oxygen concentration, the arrival of migrators at depth on a 24-h basis (described as Diel Vertical Migrations; DVMs), and from well-lit surface and shallower waters, could represent a major response to a solar-based synchronization between the photic and aphotic realms. In addition to triggering the rhythmic behavioral responses of benthic species, DVMs supply food to deep seafloor communities through the active downward transport of carbon and nutrients. Bioluminescent species of the migrating deep scattering layers play a not yet quantified (but likely important) role in the benthopelagic coupling, raising the need to integrate the efficient detection and quantification of bioluminescence into large-scale monitoring programs. Here, we provide evidence in support of the benefits for quantifying and continuously monitoring bioluminescence in the deep sea. In particular, we recommend the integration of bioluminescence studies into long-term monitoring programs facilitated by deep-sea neutrino telescopes, which offer photon counting capability. Their Photo-Multiplier Tubes and other advanced optical sensors installed in neutrino telescope infrastructures can boost the study of bioluminescent DVMs in concert with acoustic backscatter and video imagery from ultra-low-light cameras. Such integration will enhance our ability to monitor proxies for the mass and energy transfer from the upper ocean into the deep-sea Benthic Boundary Layer (BBL), a key feature of the ocean biological pump and crucial for monitoring the effects of climate-change. In addition, it will allow for investigating the role of deep scattering DVMs in the behavioral responses, abundance and structure of deep-sea benthic communities. The proposed approach may represent a new frontier for the study and discovery of new, taxon-specific bioluminescence capabilities. It will thus help to expand our knowledge of poorly described deep-sea biodiversity inventories and further elucidate the connectivity between pelagic and benthic compartments in the deep-sea.

Assessing the Distribution of Exotic Egg Parasitoids of Halyomorpha halys in Europe with a Large-Scale Monitoring Program.

Simple SummaryThe management of invasive alien species is a very challenging task. For the brown marmorated stink bug (Halyomorpha halys), classical biological control has been identified as the most suitable method to sustainably reduce its populations in the long-term. Among its natural enemies, two species were identified as the most promising candidates for biocontrol, Trissolcus japonicus and Trissolcus mitsukurii. Populations of these two species have recently been detected in Europe and to assess their distribution, a large-scale study was performed. Combining several monitoring methods, in four months (May–September 2019), a wide area covering northern Italy and parts of Switzerland was surveyed. The results showed that both species have spread into all types of habitats where H. halys is present and the parasitization of native species was rarely observed. Among native species, Anastatus bifasciatus was the predominant parasitoid of H. halys. This study supported the development of the first release program of Tr. japonicus in Europe.The brown marmorated stink bug Halyomorpha halys is an invasive agricultural pest with a worldwide distribution. Classical biological control has been identified as the most promising method to reduce the populations of H. halys. Adventive populations of two candidates for releases, Trissolcus japonicus and Trissolcus mitsukurii, have recently been detected in Europe. To assess their distribution and abundance, a large-scale survey was performed. From May to September 2019, a wide area covering northern Italy and parts of Switzerland was surveyed, highlighting the expanding distribution of both Tr. japonicus and Tr. mitsukurii. Within four years after their first detection in Europe, both species have rapidly spread into all types of habitats where H. halys is present, showing a wide distribution and continuous expansion. Both exotic Trissolcus showed high levels of parasitism rate towards H. halys, while parasitization of non-target species was a rare event. The generalist Anastatus bifasciatus was the predominant native parasitoid of H. halys, while the emergence of native scelionids from H. halys eggs was rarely observed. The presence of the hyperparasitoid Acroclisoides sinicus was also recorded. This study provided fundamental data that supported the development of the first inoculative release program of Tr. japonicus in Europe.

Application of a Simple, Low-Cost, Low-Tech Method to Monitor Intertidal Rocky Shore Assemblages on a Broad Geographic Scale

Identifying susceptible regions where biodiversity changes occur at fast rates is essential in order to protect and ameliorate affected areas. Large-scale coastal monitoring programs that focus on long-term variability are scarce, yet the Marine Biodiversity Observation Network Pole to Pole is currently developing a regional collaboration throughout the American continent collecting biodiversity data in coastal habitats with a standardized systematic protocol. The use of photographic methods to collect assemblage data on intertidal rocky shores can be appropriate. The goal of this study was to analyze the performance of a simple, low-cost, non-destructive and low-tech photographic method on a broad geographical scale (∼ 2,000 km) of Atlantic Patagonian coastline. Concurrently, we aimed to identify indicators whose cover, presence or condition can be followed in time and used as beacons of change in biodiversity on these rocky intertidal shores. We also explored the potential relationships between assemblage structure and environmental variables, such as seascape classes. We identified and propose cover of mytilids, Corallina spp. and bare substrate as indicators of change due to their ecological relevance in intertidal assemblages and their visible and rapid response to human stressors or changes in environmental conditions. Finally, we illustrate the practicality and usefulness of remotely accessible environmental data, for instance the seascape classes approach as an integrative tool for large-scale rocky shore studies.

Establishement of a national monitoring program based on environmental DNA for amphibians and the chytrid fungus Batrachochytrium dendrobatidis

National monitoring programs provide the basis for evaluating the integrity of ecosystems, their responses to disturbances, and the success of actions taken to conserve or recover biodiversity. In this study, we successfully established a national program for the invasive chytrid fungus Batrachochytrium dendrobatidis (Bd) based on dual TaqMan assays. Amphibian diversity based on metabarcoding of the mitochondrial 12S rRNA gene was also performed. Assays were optimized for sensitive detection of target species from a wide range of amphibian ponds with variable potential of inhibitions for eDNA based detection. An amphibian mock community of 5 species was used to validate the metabarcoding approach while internal standards were used in the case of the dual TaqMan assays. First sampling of over 170 ponds in Norway resulted in Bd detection in 12 environmental samples and one swab sample taken over multiple years indicating the establishment of Bd in Norway. Five amphibian species Bufo bufo, Lissotriton vulgaris, Triturus cristatus, Rana arvalis and Rana temporaria as predicted from data in long-term citizen science reporting systems were widely detected in the collected eDNA samples. Our large scale-monitoring program indicates a low risk of a Bd outbreak and amphibian decline caused by chytridiomycosis but continued monitoring is recommended in the future. These findings indicate that eDNA is an effective method to detect invasive species, and to monitor endangered amphibian species. Still, several shortcomings (such as PCR inhibitors and sample volume) were identified that need to be addressed to improve eDNA-based monitoring at the national level.

Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics

DNA metabarcoding is an efficient tool to characterize invertebrate species composition in environmental samples. Most metabarcoding protocols for invertebrate bulk samples start with sample homogenization, followed by DNA extraction, amplification of a specific marker region and sequencing on a high-throughput sequencer. Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist. Giving the amount of research done to validate almost all laboratory steps of metabarcoding workflows it is surprising that there is no clear recommendation for the basis of almost all metabarcoding studies: the homogenization of samples itself. For homogenization, different devices are used that can be divided into two major categories: bead mills and blenders. While bead-mills accelerate small, hard particles in a closed container or tube to break down specimens into small tissue fragments, blenders work with a rapidly rotating blades that reliably slice specimens as well as other substrate of the sample. Both methods are currently used in metabarcoding studies and have downsides to consider. Bead-mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large scale studies. Blenders on the other hand offer the opportunity to be cleaned and can handle larger sample volumes in shorter time, with an increased risk of cross-contamination. We here aimed to develop a fast, robust, cheap and reliable sample homogenization protocol that overcomes the above-mentioned limitations of both methods, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six sorted Malaise trap insect samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 technical replicates of each sample and many negative controls per sample (Fig. 1) to quantify impacts of i) insufficient homogenization and ii) possible sources of cross-contamination. Our results show that homogenization is sufficient after 3 minutes of homogenization. Rinsing the blender with water is sufficient in most cases but leads to low read-numbers in some of the negative controls. These could be further reduced by rinsing the blender with self-made drain-safe sterilization solution based on bleach but far less corrosive than pure bleach. Our results suggest that rinsing 1-2 times for 20 seconds is sufficient to avoid any cross-contamination. The improvements of the protocol in terms of speed, ease of handling, overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenization after sampling in particular for large-scale and regulatory metabarcoding biodiversity assessments and monitoring programs.

Biodiversity monitoring in rocky shores: Challenges of devising a globally applicable and cost-effective protocol

Large-scale coastal monitoring programs that focus on long-term inter-annual and seasonal community variability are rare mostly because they are costly, logistically complex and require coordination by groups of dedicated scientists. The Marine Biodiversity Observation Network (MBON) is currently developing a regional collaboration throughout the American continent to collect biological data in coastal habitats using common methodologies and sharing best practices. The goal of this paper is to compare two survey methods with contrasting field time demands (i.e. in situ collected data vs. photoquadrats), identify the scales at which they may differ, and determine the convenience and suitability for their use in large-scale standardized biodiversity studies on rocky intertidal shores. Visual quadrat (VQ) data collected in the field was compared with data obtained from photographs of those same quadrats (PQ) digitally analyzed at three intertidal levels within two sites during four different times of the year. Analysis by site showed a seasonal effect in all shore levels and an effect of methods only at the low intertidal level at both sites. The PQ method is a reliable, cheap and time efficient tool for the long-term study of rocky intertidal communities. It is capable of detecting the spatial and temporal variability as the VQ method at various scales including tidal height, time of the year and site. We suggest the use of the mid intertidal level as the standardized sampling zone across latitudes on the basis of having higher diversity than the high intertidal, more sampling time than the low intertidal level, and being more affected by climate change both through changes in the air (temperature and wind) and in the ocean (warming and acidification). This study provides empirical evidence that a simple, low-cost and low-tech method may offer the required information that large-scale monitoring programs need.

Global warning: challenges, threats and opportunities for ground beetles (Coleoptera: Carabidae) in high altitude habitats

Aim of this paper is to provide the first comprehensive synthesis about ground beetle (Coleoptera: Carabidae) distribution in high altitude habitats. Specifically, the attention is focused on the species assemblages living on the most common ice-related mountain landforms (glaciers, debris-covered glaciers, glacier forelands and rock glaciers) and the challenges, threats and opportunities carabids living in these habitats have to face concerning the ongoing climate warming. The suggested role of the ice-related alpine landforms, as present climatic refugia for cold-adapted ground beetles, is discussed. Finally, the needs to develop a large-scale High-alpine Biodiversity Monitoring Program to describe how the current climate change is shaping the distribution of high altitude specialists is highlighted.