scholarly journals Applications of environmental DNA methods for charophyte biodiversity

2021 ◽  
Vol 4 ◽  
Author(s):  
Petra Nowak ◽  
Christina Wiebe ◽  
Rolf Karez ◽  
Hendrik Schubert
Keyword(s):  
Fish Fauna ◽  
Environmental Dna ◽  
Cost Effective ◽  
High Water ◽  
Species Group ◽  
Genetic Identification ◽  
Detection Methods ◽  
Habitats Directive ◽  
Special Importance ◽  
Anthropogenic Pressures

The use of environmental DNA (eDNA) for qualitative species inventories offers great potential as a cost-effective tool for species identification. This requires that the target species release DNA, reference information is available and detection methods exist. Environmental DNA analyses are currently used routinely to inventory fish fauna (Wang et al. 2021), molluscs (Klymus et al. 2017) or insects (Uchida et al. 2020). For other groups, such as macrophytes, there is not much information available (Scriver et al. 2015). In plants, identifying suitable eDNA markers been much more challenging, as no single DNA region has been accepted for the purposes of barcoding. Within this project, we assessed if stoneworts (Charophytes, Characeae) can be detected by using eDNA analysis and if it can be used to support macrophyte monitoring. Charophytes are macroscopic green algae which, because of their role as habitat engineers, are of special importance for aquatic ecosystems. Many charophyte species are bound to clean, nutrient-poor fresh and brackish waters (e.g. Melzer 1999) and are regarded bioindicators for water quality by national and international directives (e.g. Habitats Directive, EU Water Framework Directive). Being sensitive to anthropogenic pressures, a drastic decline in populations with increasing eutrophication has been reported (Sand-Jensen et al. 2017) . However, the diversity of Characeae is often underestimated due to difficulties in morphological determination, and the genetic identification of charophytes has been established only in the recent few years (e.g. Nowak et al. 2016). We assessed the potential utility of eDNA to document the diversity of charophyte species. eDNA from a fresh water lake (Dreetzsee, Germany, 2018) and from a brackish water site (Darß-Zingst Lagoon System, Germany, 2018) was extracted from filtered or ethanol‐precipitated water samples, and we designed and tested eDNA markers based on four regions of the chloroplast genome - atpB, rbcL, psbC, and matK. Of the four regions, matK and rbcL were most likely to amplify DNA from charophyte species. Both sites exhibit a diverse charophyte flora, which we successfully could identify to species/group level by eDNA analysis. In a current study, the developed eDNA markers are used to scrutinize the charophyte population of the Schlei estuary (Germany, Schleswig-Holstein). Since conventional monitoring can only be carried out once a year at a few sites, Characeae have not been observed in recent years, or only very sporadically. As it is not possible to survey the entire Schlei, especially due to high water turbidity, the eDNA methodology is tested to assess the presence of Characeae species.

scholarly journals Fast processing of environmental DNA metabarcoding sequence data using convolutional neural networks

2021 ◽  
Author(s):  
Benjamin Flück ◽  
Laëtitia Mathon ◽  
Stéphanie Manel ◽  
Alice Valentini ◽  
Tony Dejean ◽  
...  
Keyword(s):  
Neural Networks ◽  
Convolutional Neural Networks ◽  
Environmental Changes ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Fish Fauna ◽  
Environmental Dna ◽  
Small Region ◽  
Anthropogenic Pressures ◽  
Speed And Accuracy

The intensification of anthropogenic pressures have increased consequences on biodiversity and ultimately on the functioning of ecosystems. To monitor and better understand biodiversity responses to environmental changes using standardized and reproducible methods, novel high-throughput DNA sequencing is becoming a major tool. Indeed, organisms shed DNA traces in their environment and this "environmental DNA" (eDNA) can be collected and sequenced using eDNA metabarcoding. The processing of large volumes of eDNA metabarcoding data remains challenging, especially its transformation to relevant taxonomic lists that can be interpreted by experts. Speed and accuracy are two major bottlenecks in this critical step. Here, we investigate whether convolutional neural networks (CNN) can optimize the processing of short eDNA sequences. We tested whether the speed and accuracy of a CNN are comparable to that of the frequently used OBITools bioinformatic pipeline. We applied the methodology on a massive eDNA dataset collected in Tropical South America (French Guiana), where freshwater fishes were targeted using a small region (60pb) of the 12S ribosomal RNA mitochondrial gene. We found that the taxonomic assignments from the CNN were comparable to those of OBITools, with high correlation levels and a similar match to the regional fish fauna. The CNN allowed the processing of raw fastq files at a rate of approximately 1 million sequences per minute which was ~150 times faster than with OBITools. Once trained, the application of CNN to new eDNA metabarcoding data can be automated, which promises fast and easy deployment on the cloud for future eDNA analyses.

scholarly journals The Life “SeResto” project: A new strategic approach to meet HD and WFD objectives by SEagrass RESTOration

2015 ◽  
Author(s):  
Alessandro Buosi ◽  
Chiara Facca ◽  
Emanuele Ponis ◽  
Andrea Bonometto ◽  
Rossella Boscolo ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
Great Part ◽  
Ecological Status ◽  
Fish Fauna ◽  
Weather Conditions ◽  
High Water ◽  
Venice Lagoon ◽  
Fish Farms ◽  
Anthropogenic Pressures ◽  
Aquatic Angiosperms

Pristine conditions in transitional water ecosystems are characterized by the dominance of aquatic angiosperms. Aquatic plants consolidate bottoms, prevent erosion, support benthic and fish communities as nursery and food areas, and favour the bird presence. Hence, they may contribute to the achievement of a good ecological status as required by the WFD (2000/60/EC). Their reduction or disappearance is a symptom of environmental deterioration. Over the past few decades, the aquatic angiosperms have shown a significant decrease on a worldwide scale and in some areas of Venice Lagoon (Adriatic Sea), particularly in the central and Northern basins, as a consequence of anthropogenic activities. At present, most of the anthropogenic pressures which caused their decline or disappearance in Venice Lagoon have significantly decreased creating the ecological conditions for a new colonization. In this context, the project SeResto (LIFE12 NAT/IT/000331), funded by the European Commission, aims at restoring the angiosperm meadows in the Northern basin of Venice Lagoon where the natural seed spreading is hampered by the presence of island, tidal marsh barriers and long residence times. The project has two main strengths: i) the widespread transplantations of small angiosperm sods and manual dispersion of rhizomes and seeds and based on a low costs and low impact on donor sites approach, ii) the participation of fishermen and hunters daily living the lagoon for recreational purposes. Thirty-five sites have been selected and in each one 9 sod-bearing plants (diameter: 30 cm), supplied by fish farms where angiosperm meadows are almost natural, have been transplanted. In addition, the plant spreading is enhanced by the dissemination of hundreds of rhizomes, 1500 at minimum in each area during the project period (52 months). In 8 sites, out of the 35, biological and chemico-physical conditions are being monitored monthly during the first and last year and quarterly in the intermediate period. Ecological indices, based on the study of macrophytes, macrobenthic fauna and fish fauna (Biological Quality Elements), as required by the WFD 2000/60/EC, will allow to assess changes in the Ecological Status of the study sites. Preliminary results are encouraging in great part of the selected areas although some difficulties have been recorded in areas with high water turbidity and the presence of thionitrophilous macroalgae, especially Ulvaceae, favoured by the unexpected weather conditions of summer 2014. Information on the restoration effectiveness and the relationship between the angiosperm presence/growth and the environmental conditions can be employed for interventions in other lagoon areas and can be exported in other similar transitional environments.

scholarly journals The Life “SeResto” project: A new strategic approach to meet HD and WFD objectives by SEagrass RESTOration

2015 ◽  
Author(s):  
Alessandro Buosi ◽  
Chiara Facca ◽  
Emanuele Ponis ◽  
Andrea Bonometto ◽  
Rossella Boscolo ◽  
...  
Keyword(s):  
Anthropogenic Activities ◽  
Great Part ◽  
Ecological Status ◽  
Fish Fauna ◽  
Weather Conditions ◽  
High Water ◽  
Venice Lagoon ◽  
Fish Farms ◽  
Anthropogenic Pressures ◽  
Aquatic Angiosperms

Pristine conditions in transitional water ecosystems are characterized by the dominance of aquatic angiosperms. Aquatic plants consolidate bottoms, prevent erosion, support benthic and fish communities as nursery and food areas, and favour the bird presence. Hence, they may contribute to the achievement of a good ecological status as required by the WFD (2000/60/EC). Their reduction or disappearance is a symptom of environmental deterioration. Over the past few decades, the aquatic angiosperms have shown a significant decrease on a worldwide scale and in some areas of Venice Lagoon (Adriatic Sea), particularly in the central and Northern basins, as a consequence of anthropogenic activities. At present, most of the anthropogenic pressures which caused their decline or disappearance in Venice Lagoon have significantly decreased creating the ecological conditions for a new colonization. In this context, the project SeResto (LIFE12 NAT/IT/000331), funded by the European Commission, aims at restoring the angiosperm meadows in the Northern basin of Venice Lagoon where the natural seed spreading is hampered by the presence of island, tidal marsh barriers and long residence times. The project has two main strengths: i) the widespread transplantations of small angiosperm sods and manual dispersion of rhizomes and seeds and based on a low costs and low impact on donor sites approach, ii) the participation of fishermen and hunters daily living the lagoon for recreational purposes. Thirty-five sites have been selected and in each one 9 sod-bearing plants (diameter: 30 cm), supplied by fish farms where angiosperm meadows are almost natural, have been transplanted. In addition, the plant spreading is enhanced by the dissemination of hundreds of rhizomes, 1500 at minimum in each area during the project period (52 months). In 8 sites, out of the 35, biological and chemico-physical conditions are being monitored monthly during the first and last year and quarterly in the intermediate period. Ecological indices, based on the study of macrophytes, macrobenthic fauna and fish fauna (Biological Quality Elements), as required by the WFD 2000/60/EC, will allow to assess changes in the Ecological Status of the study sites. Preliminary results are encouraging in great part of the selected areas although some difficulties have been recorded in areas with high water turbidity and the presence of thionitrophilous macroalgae, especially Ulvaceae, favoured by the unexpected weather conditions of summer 2014. Information on the restoration effectiveness and the relationship between the angiosperm presence/growth and the environmental conditions can be employed for interventions in other lagoon areas and can be exported in other similar transitional environments.

scholarly journals Food Allergen Detection Methods: A Coordinated Approach

2004 ◽  
Vol 87 (6) ◽  
pp. 1383-1390 ◽  
Author(s):  
Philip R Goodwin
Keyword(s):  
Hazard Analysis ◽  
Adult Population ◽  
Control Point ◽  
Cost Effective ◽  
Test Methods ◽  
Detection Methods ◽  
Critical Control Point ◽  
Life Threatening ◽  
Monitoring And Surveillance ◽  
Analytical Approaches

Abstract The levels (1–2%) and increasing severity of allergic responses to food in the adult population are well documented, as is the phenomenon of even higher (3–8%) and apparently increasing incidence in children, albeit that susceptibility decreases with age. Problematic foods include peanut, milk, eggs, tree nuts, and sesame, but the list is growing as awareness continues to rise. The amounts of such foods that can cause allergic reactions is difficult to gauge; however, the general consensus is that ingestion of low parts per million is sufficient to cause severe reactions in badly affected individuals. Symptoms can rapidly—within minutes—progress from minor discomfort to severe, even life-threatening anaphylactic shock in those worst affected. Given the combination of high incidence of atopy, potential severity of response, and apparently widespread instances of “hidden” allergens in the food supply, it is not surprising that this issue is increasingly subject to legislative and regulatory scrutiny. In order to assist in the control of allergen levels in foods to acceptable levels, analysts require a combination of test methods, each designed to produce accurate, timely, and cost-effective analytical information. Such information contributes significantly to Hazard Analysis Critical Control Point programs to determine food manufacturers’ risk and improves the accuracy of monitoring and surveillance by food industry, commercial, and enforcement laboratories. Analysis thereby facilitates improvements in compliance with labeling laws with concomitant reductions in risks to atopic consumers. This article describes a combination of analytical approaches to fulfill the various needs of these 3 analytical communities.

scholarly journals The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Michael J. Allison ◽  
Jessica M. Round ◽  
Lauren C. Bergman ◽  
Ali Mirabzadeh ◽  
Heather Allen ◽  
...  
Keyword(s):  
Silica Gel ◽  
Storage Temperature ◽  
Environmental Dna ◽  
Cost Effective ◽  
Storage Conditions ◽  
Systematic Evaluation ◽  
Silica Bead ◽  
Gel Beads ◽  
Polymerase Chain

Abstract Objective Silica gel beads have promise as a non-toxic, cost-effective, portable method for storing environmental DNA (eDNA) immobilized on filter membranes. Consequently, many ecological surveys are turning to silica bead filter desiccation rather than ethanol preservation. However, no systematic evaluation of silica bead storage conditions or duration past 1 week has been published. The present study evaluates the quality of filter-immobilized eDNA desiccated with silica gel under different storage conditions for over a year using targeted quantitative real-time polymerase chain reaction (qPCR)-based assays. Results While the detection of relatively abundant eDNA target was stable over 15 months from either ethanol- or silica gel-preserved filters at − 20 and 4 °C, silica gel out-performed ethanol preservation at 23 °C by preventing a progressive decrease in eDNA sample quality. Silica gel filter desiccation preserved low abundance eDNA equally well up to 1 month regardless of storage temperature (18, 4, or − 20 °C). However only storage at − 20 °C prevented a noticeable decrease in detectability at 5 and 12 months. The results indicate that brief storage of eDNA filters with silica gel beads up to 1 month can be successfully accomplished at a range of temperatures. However, longer-term storage should be at − 20 °C to maximize sample integrity.

scholarly journals Study on microcrystalline cellulose/chitosan blend foam gel material

2020 ◽  
Vol 27 (1) ◽  
pp. 424-432
Author(s):  
Hongkai Zhao ◽  
Kehan Zhang ◽  
Shoupeng Rui ◽  
Peipei Zhao
Keyword(s):  
Microcrystalline Cellulose ◽  
Raw Materials ◽  
Pore Space ◽  
Sodium Dodecyl ◽  
Cost Effective ◽  
High Water ◽  
Aldehyde Group ◽  
Sem Analysis ◽  
Present Contribution ◽  
Bet Analysis

AbstractIn the present contribution, an environmental-friendly and cost-effective adsorbent was reported for soil treatment and desertification control. A novel foam gel material was synthesized here by the physical foaming in the absence of catalyst. By adopting modified microcrystalline cellulose and chitosan as raw materials and sodium dodecyl sulfonate (SDS) as foaming agent, a microcrystalline cellulose/chitosan blend foam gel was synthesized. It is expected to replace polymers derived from petroleum for agricultural applications. In addition, a systematical study was conducted on the adsorbability, water holding capacity and re-expansion performance of foam gel in deionized water and brine under different SDS concentrations (2%–5%) as well as adsorption time. To be specific, the adsorption capacity of foam gel was up to 105g/g in distilled water and 54g/g in brine, indicating a high water absorption performance. As revealed from the results of Fourier transform infrared spectroscopy (FTIR) analysis, both the amino group of chitosan and the aldehyde group modified by cellulose were involved. According to the results of Scanning electron microscope (SEM) analysis, the foam gel was found to exhibit an interconnected pore network with uniform pore space. As suggested by Bet analysis, the macroporous structure was formed in the sample, and the pore size ranged from 0 to 170nm. The mentioned findings demonstrated that the foam gel material of this study refers to a potential environmental absorbent to improve soil and desert environments. It can act as a powerful alternative to conventional petroleum derived polymers.

scholarly journals Monitoring Skeletal Anomalies in Big-Scale Sand Smelt, Atherina boyeri, as a Potential Complementary Tool for Early Detection of Effects of Anthropic Pressure in Coastal Lagoons

Water ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 159
Author(s):  
Chiara Leone ◽  
Francesca De Luca ◽  
Eleonora Ciccotti ◽  
Arianna Martini ◽  
Clara Boglione
Keyword(s):  
Early Detection ◽  
Habitat Degradation ◽  
Anthropogenic Impacts ◽  
Coastal Lagoons ◽  
Ecological Status ◽  
Detection Methods ◽  
Anthropogenic Pressures ◽  
Morphological Examination ◽  
Skeletal Anomalies

Mediterranean coastal lagoons are increasingly affected by several threats, all concurrently leading to habitat degradation and loss. Methods based on fish for the assessment of the ecological status are under implementation for the Water Framework Directive requirements, to assess the overall quality of coastal lagoons. Complementary tools based on the use of single fish species as biological indicators could be useful as early detection methods of anthropogenic impacts. The analysis of skeletal anomalies in the big-scale sand smelt, Atherina boyeri, from nine Mediterranean coastal lagoons in Italy was carried out. Along with the morphological examination of fish, the environmental status of the nine lagoons was evaluated using a method based on expert judgement, by selecting and quantifying several environmental descriptors of direct and indirect human pressures acting on lagoon ecosystems. The average individual anomaly load and the frequency of individuals with severe anomalies allow to discriminate big-scale sand smelt samples on the basis of the site and of its quality status. Furthermore, a relationship between skeletal anomalies and the environmental quality of specific lagoons, driven by the anthropogenic pressures acting on them, was found. These findings support the potentiality of skeletal anomalies monitoring in big-scale sand smelt as a tool for early detection of anthropogenic impacts in coastal lagoons of the Mediterranean region.

Mature Field Economic Rejuvenation with Infill and Re-Entry Multilateral Well Creation Techniques

2021 ◽  
Author(s):  
Benjamin Butler ◽  
Justin Roberts ◽  
Matthew Kelsey ◽  
Steffen Van Der Veen
Keyword(s):  
Case Studies ◽  
Field Performance ◽  
Cost Effective ◽  
High Water ◽  
Additional Time ◽  
Flow Management ◽  
Performance Improvements ◽  
Mature Field ◽  
Water Cut ◽  
Time Required

Abstract Multilateral wells have been proven over decades and have developed into a reliable and cost effective approach to mature field rejuvenation and extended commercial viability. This paper will discuss case studies demonstrating a number of techniques used to create infill multilateral wells in existing fields with a high level of reliability and repeatability. Techniques reviewed will cover cutting and pulling production casing to drill and case a new mainbore versus sidetracking and adding laterals to an existing mainbore. Discussion will also cover completion designs that tie new laterals into existing production casing providing significantly greater reservoir contact. Temporary isolation of high water-cut laterals brought into production later in the well's life through bespoke completion designs will also be discussed. Case studies will include discussion of workover operations, isolation methods, and lateral creation systems. Where available, resulting field performance improvements will also be discussed. In Norway, slot recoveries are commonly performed by cutting and pulling the 10-3/4" casing, redrilling a new mainbore, and running new casing. This enables junction placement closer to unswept zones and easier lateral drilling to targets. It does have drawbacks, however, related to the additional time required to pull the subsea xmas tree and challenges associated with pulling casing. In 2019, Norway successfully completed a 10-3/4" retrofit installation, whereas a sidetrack was made from the 10-3/4" and an 8-5/8" expandable liner was run down into the reservoir pay zone where two new laterals were created. The 8-5/8" liner saved time otherwise spent having to drill the section down to the payzone from the laterals. These wells have a TAML Level 5 isolated junction, Autonomous Inflow Control Devices (AICDs) in each lateral, and an intelligent completion interface across the junction, enabling active flow management and monitoring of both branches. In Asia, infill laterals were added to existing wellbores by sidetracking 9-5/8" casing and tying production back to the original mainbore. These dual laterals were completed with intelligent completions to enable lateral flow management and monitoring of both laterals. In Australia, dual laterals were created in a similar fashion; laterals are added to existing wells; however, a novel approach was used to manage water from existing lower mainbore laterals whereby they are shut in at completion and opened later when the new lateral is watered out. The older lateral now produces at lower water cut given the time allowed for water coning in the lateral to relax. Using this practice, production is alternated back and forth between the two laterals. In the Middle East, an older well has been converted from TAML Level 4 to Level 5 in order to prevent detected gas migrating into the mainbore at the junction. This conversion of a cemented junction well has enabled production to resume on this well. The well was converted to incorporate an intelligent completion to enable flow control of each lateral. This paper intends to provide insights into the various mature field re-entry methods for multilateral well construction, and a review of the current technology capabilities and well designs through the review of multiple case histories.

scholarly journals Ultralow-temperature-driven water-based sorption refrigeration enabled by low-cost zeolite-like porous aluminophosphate

2022 ◽  
Vol 13 (1) ◽  
Author(s):  
Zhangli Liu ◽  
Jiaxing Xu ◽  
Min Xu ◽  
Caifeng Huang ◽  
Ruzhu Wang ◽  
...  
Keyword(s):  
Low Temperature ◽  
Water Sorption ◽  
High Performance ◽  
Global Climate ◽  
Low Cost ◽  
Cost Effective ◽  
High Water ◽  
Coefficient Of Performance ◽  
High Efficient ◽  
Water Based

AbstractThermally driven water-based sorption refrigeration is considered a promising strategy to realize near-zero-carbon cooling applications by addressing the urgent global climate challenge caused by conventional chlorofluorocarbon (CFC) refrigerants. However, developing cost-effective and high-performance water-sorption porous materials driven by low-temperature thermal energy is still a significant challenge. Here, we propose a zeolite-like aluminophosphate with SFO topology (EMM-8) for water-sorption-driven refrigeration. The EMM-8 is characterized by 12-membered ring channels with large accessible pore volume and exhibits high water uptake of 0.28 g·g−1 at P/P0 = 0.2, low-temperature regeneration of 65 °C, fast adsorption kinetics, remarkable hydrothermal stability, and scalable fabrication. Importantly, the water-sorption-based chiller with EMM-8 shows the potential of achieving a record coefficient of performance (COP) of 0.85 at an ultralow-driven temperature of 63 °C. The working performance makes EMM-8 a practical alternative to realize high-efficient ultra-low-temperature-driven refrigeration.

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