scholarly journals A validated protocol for fish farm monitoring using environmental DNA

2021 ◽  
Vol 4 ◽  
Author(s):  
Xavier Pochon ◽  
Susie Wood ◽  
Javier Atalah ◽  
Lauren Fletcher ◽  
Olivier Laroche ◽  
...  
Keyword(s):  
New Zealand ◽  
Assessment Tool ◽  
Environmental Dna ◽  
Fish Farming ◽  
Cost Effective ◽  
Low Flow ◽  
Biotic Index ◽  
Fish Farms ◽  
Physico Chemical ◽  
Wide Range

Sea-based fish farms are associated with strong benthic enrichment gradients and routine monitoring is usually required by regulation. Internationally a wide range of approaches exist for measuring the degree of benthic deterioration around fish farming activities, ranging from simple visual or odour assessments to the calculation of secondary indices that combine multiple biological and/or physico-chemical metrics (e.g., AZTI Marine Biotic Index; Invertebrate Species Index; Norwegian Quality Index; Infauna Trophic Index). In New Zealand, the health of marine benthic ecosystems around coastal salmon farms is currently measured using an Enrichment State (ES) index. This index incorporates physico-chemical (redox, organic matter, sulphates, etc.) and benthic macrofaunal measurements, which requires taxonomic expertise, is time consuming and expensive. Supported by a range of private/government agencies and industry partners, we have developed and tested the robustness of bacterial, eukaryotic, and multi-trophic Metabarcoding Biotic Indices (b-MBI, e-MBI, and mt-MBI, respectively) using a molecular Eco-Group approach. The indices were calculated via automatic computer pipelines using data collected over a period of nine years from a range of high- and low-flow salmon farms (12 farms and 60 stations) from three distinct regions in New Zealand. The MBIs were compared against the established ES index. All MBIs yielded strong and highly significant relationships with the ES index. The strongest relationships (R2 > 0.9) were obtained with the b-MBI. A refinement of the b-MBI (2019-2020) was supported by highly prolific microbes throughout the ES spectrum, and in particular in the upper end of the organic enrichment scale where traditional benthic indices tend to fail. This resulted in ES values of both (molecular-based versus morphology-based) indices to follow a near one-to-one relationship, performing consistently across water flow environments and considered sub-regions. Station-averaged results were also used to compare regulated compliance outcomes between the two indices, based on the current key compliance criteria for farms within each flow regime. Of the 67 seabed monitoring stations that were subsequently classified as compliant or non‑compliant, 62 stations had identical compliance outcomes (i.e. 92% of instances). Furthermore, the b-MBI showed consistently narrower (~50%) confidence interval bands when compared to the traditional ES index. The b-MBI offers unprecedented precision for determining subtle changes along enrichment gradients, constituting a valuable asset for triggering timely management responses and improving compliance. The protocols developed in this project enable rapid, standardised, and cost-effective eDNA isolation and extraction, followed by automatic b-MBI calculation. The affordability and versatility of the b-MBI tool suggests that it could be immediately integrated into current monitoring strategies as the primary benthic assessment tool for assessing benthic impacts of salmon farms in New Zealand.

Texture effects on carbon stabilisation and storage in New Zealand soils containing predominantly 2 : 1 clays

Soil Research ◽  
2016 ◽  
Vol 54 (1) ◽  
pp. 30 ◽  
Author(s):  
Denis Curtin ◽  
Michael H. Beare ◽  
Weiwen Qiu
Keyword(s):  
New Zealand ◽  
Clay Fraction ◽  
Clay Content ◽  
Soil C ◽  
Particle Size Fractions ◽  
C Storage ◽  
Physico Chemical ◽  
Wide Range ◽  
Mass Proportion ◽  
C And N

Developing strategies to sequester carbon (C) in soils requires an understanding of the key factors that influence C stabilisation. Although fine mineral particles, especially clay, play a key role in stabilising soil organic matter (SOM), the relationship between SOM and texture is often not strong. We examined the role of the fine mineral fraction in C storage in sedimentary soils in New Zealand. Soils, representing two soil Orders (Brown and Recent) and different land use histories (total of 58 soils; 0–15 cm depth) were sampled. The concentration of C (and N) in four particle size fractions (<5, 5–20, 20–50, >50 µm) was determined (soils fractionated after dispersion by sonication). The soils had a wide range of textures and SOM; the mass proportion of clay (<5 µm) ranged from 10 to 60 g 100 g–1 and soil C from 16 to 45 g kg–1. Across both soil Orders and all land uses (dairy, sheep or beef, arable and vegetable cropping), the majority of soil C (57 to 66%) was stored in the clay fraction. However, there was no correlation (R2 = 0.02; P > 0.05) between the C concentration in whole soil and clay content. The concentration of C in the clay fraction, which varied over a wide range (35 to 135 g kg–1 clay), decreased as the mass proportion of clay increased. A similar trend in C concentration was observed for the fine (5–20 µm) silt fraction. Because of this inverse relationship between the mass of the fine fractions and their C concentration, there was little change in amount of stable C (defined as C in the <20 µm fraction) as the mass proportion of fine (<20 µm) particles increased. Differences in pyrophosphate extractable aluminium explained part of the variability in C concentration in the fine fractions; however, we were unable to identify any specific physico-chemical factor that would account for the relatively low C concentrations observed in the <5 and 5–20 µm fractions of fine-textured soils. We concluded that such soils may be under-saturated and potential may exist to store additional stable C.

scholarly journals Assessment of physico-chemical parameters of rainbow trout farms for the evaluation of potential threat to natural streams in Nepal

2017 ◽  
Vol 6 (2) ◽  
pp. 43-55
Author(s):  
Payaswini Ghimire ◽  
Archana Niraula ◽  
Anuradha Rai ◽  
Aastha Pandey ◽  
Smriti Gurung ◽  
...  
Keyword(s):  
Environmental Protection Agency ◽  
Major Ions ◽  
Fish Farming ◽  
Small Scale ◽  
Chemical Parameters ◽  
Fish Farms ◽  
Potential Threat ◽  
Physico Chemical ◽  
Natural Streams ◽  
Trout Farms

 Three trout farms from Nepal were studied to investigate the changes in physico-chemical parameters and their potential threat to natural water bodies receiving the effluents. Reference and impact sites were determined in each farm so as to find out the level of impacts due to farming activities. Some of the parameters such as dissolved oxygen, turbidity, conductivity, and total dissolve solids were significantly changed in the impacted zones compared to reference sites. Similarly, concentrations of some major ions such as calcium and sodium were increased in the impacted zones. On the other hand, some of the parameters such as pH and potassium did not change in the impacted zone although their concentrations were different among farms studied. Nevertheless, the overall changes in the physico-chemical parameters did not pose health risk to the aquatic ecosystems receiving effluents from these fish farms as the concentrations were below the prescribed levels by Environmental Protection Agency (EPA) as well as Nepal Environment Statistics. This is an indication that, although fish farming activities are degrading water qualities, there is no threat to the water quality receiving the effluents yet probably due to small scale farming. The increase in number of fish farms in the same area, however might pose risk to the ecological health in the region which warrants regular monitoring.  INTERNATIONAL JOURNAL OF ENVIRONMENTVolume-6, Issue-2, Mar-May 2017, Page: 43-55

Burnt to a crisp? Understanding drivers of burnout amongst New Zealand workers

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Jarrod Haar
Keyword(s):  
New Zealand ◽  
Organizational Support ◽  
Odds Ratio ◽  
Assessment Tool ◽  
Content Type ◽  
Large Size ◽  
Wide Range ◽  
Confirmatory Factor ◽  
Long Work Hours ◽  
Risk Rate

PurposeJob burnout is a popular topic for researchers and a pressing issue for employees and employers. However, the most popular measure has become widely critiqued, and a new construct – the Burnout Assessment Tool (BAT) – has been offered as a better way to assess burnout.Design/methodology/approachThe study uses data from 1,022 employees across a wide range of occupations, sectors and industries. Confirmatory factor analysis (CFA) and odds ratio calculations are explored.FindingsThe present psychometric properties of the BAT construct are supported. Overall, 11.1% of employees met the high burnt-out risk threshold. Determinants of burnt-out risk were explored, with significant findings from high perceptions of organizational support, large firm-size, young age and long work hours found. No gender differences. The odds ratio provides greater insights into the risks associated with factors, especially working 55+ hours/week, which resulted in 580% higher risk of burnt-out risk.Research limitations/implicationsThe findings highlight the danger of burnt-out risk and provide a useful benchmark for those exploring the burnt-out risk rate.Originality/valueThe BAT has not been tested in New Zealand across a sample of employees. Given the large size and breadth of employees, this provides useful generalizability to the BAT-NZ. The determinants tested here are all unique to the literature and provide new insights.

scholarly journals Airborne environmental DNA for terrestrial vertebrate community monitoring

2021 ◽  
Author(s):  
Christina Lynggaard ◽  
Mads Frost Bertelsen ◽  
Casper V. Jensen ◽  
Matthew S. Johnson ◽  
Tobias Guldberg Froslev ◽  
...  
Keyword(s):  
Large Scale ◽  
Environmental Dna ◽  
Cost Effective ◽  
Monitoring Methods ◽  
Natural Ecosystems ◽  
Terrestrial Vertebrate ◽  
Detection Failure ◽  
Routine Monitoring ◽  
Community Monitoring ◽  
Wide Range

Assessing and studying the distribution, ecology, diversity and movements of species is key in understanding environmental and anthropogenic effects on natural ecosystems. Although environmental DNA is rapidly becoming the tool of choice to assess biodiversity there are few eDNA sample types that effectively capture terrestrial vertebrate diversity and those that do can be laborious to collect, require special permits and contain PCR inhibitory substances, which can lead to detection failure. Thus there is an urgent need for novel environmental DNA approaches for efficient and cost-effective large-scale routine monitoring of terrestrial vertebrate diversity. Here we show that DNA metabarcoding of airborne environmental DNA filtered from air can be used to detect a wide range of local vertebrate taxa. We filtered air at three localities in Copenhagen Zoo, detecting mammal, bird, amphibian and reptile species present in the zoo or its immediate surroundings. Our study demonstrates that airDNA has the capacity to complement and extend existing terrestrial vertebrate monitoring methods and could form the cornerstone of programs to assess and monitor terrestrial communities, for example in future global next generation biomonitoring frameworks.

scholarly journals Using in-situ environmental DNA sampling to detect the invasive New Zealand Mud Snail (Potamopyrgus antipodarum) in freshwaters

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11835
Author(s):  
Jake J. Ponce ◽  
Ivan Arismendi ◽  
Austen Thomas
Keyword(s):  
Invasive Species ◽  
New Zealand ◽  
Environmental Dna ◽  
Cost Effective ◽  
Potamopyrgus Antipodarum ◽  
Real Time Quantitative Pcr ◽  
Mud Snail ◽  
Rapid Responses ◽  
Detection Approach ◽  
New Zealand Mud Snail

Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.

scholarly journals Microbiological and physical-chemical characteristics of the water used to Tambaqui Colossoma macropomum species, in Maranhão State

2017 ◽  
Vol 18 (3) ◽  
pp. 430-438
Author(s):  
Maria Cecília de Sousa CUNHA ◽  
Ana Cristina Vieira COSTA ◽  
Márcia Araújo Vander BOOR ◽  
Francisca Neide COSTA
Keyword(s):  
Dissolved Oxygen ◽  
Heterotrophic Bacteria ◽  
Fish Farming ◽  
Climatic Conditions ◽  
Physical Parameters ◽  
Chemical Characteristics ◽  
Fish Farms ◽  
Colossoma Macropomum ◽  
Physical Chemical ◽  
Physico Chemical

SUMMARY Brazil has favorable hydrographic and climatic conditions for the development of fish farming. The success of this activity depends on the quality of the water, since it directly influences its productivity. Therefore, in order to verify the microbiological and physico - chemical characteristics of the water in the creation of the tambaqui (Colossoma macropomum) species in fish farming in São Bento, a municipality located in the. State, 16 water samples from six fish farms were evaluated for the physical parameters (Temperature, transparency, dissolved oxygen, pH, turbidity, color, alkalinity, hardness, nitrate and nitrite) and microbiological (coliforms and heterotrophic mesophilic bacteria). According to the findings, all samples were contaminated by total and thermotolerant coliforms, 13 (77.15%) were outside the standards recommended by the legislation. As for the mesophilic aerobic heterotrophic bacteria, the mean counts ranged from 30.6 x 102 to 4.7 x 104 CFU / mL. As for the physical-chemical parameters, it was verified that the temperature ranged from 27.4°C to 30°C; PH 5.0 to 8.2; Transparency ranged from 0 to 46 cm; Turbidity from 12 to 1,251 NTU, the color from 0 to 666.50 UH; Dissolved oxygen from 7.1 to 14.7 mg / L; Alkalinity of 17.5 to 412 mg / L; Hardness from 14.6 to 1027.8 mg / L; Nitrate from 1 to 160 mg / L and nitrite from 0.01 to 0.45 mg / L. The findings show that the water of fish farms has inadequate microbiological and physico-chemical characteristics for fish farming.

scholarly journals Towards a simple way to collect eDNA using a 3D-printed passive sampler

2021 ◽  
Vol 4 ◽  
Author(s):  
Héloïse Verdier ◽  
Lara Konecny ◽  
Christophe Marquette ◽  
Tristan Lefebure
Keyword(s):  
Field Experiments ◽  
High Efficiency ◽  
Environmental Dna ◽  
Aquatic Biodiversity ◽  
Non Invasive ◽  
Physico Chemical ◽  
Wide Range ◽  
3D Printed ◽  
Promising Solution ◽  
High Binding Affinity

Environmental DNA has emerged as a revolutionary approach to monitor aquatic biodiversity. The study of the DNA released by macro-organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Despite its many advantages, methodological challenges limit the widespread use of eDNA. Among them, eDNA sampling represents one of the most challenging step. Often based on the filtration of a large volume of water, this process can be long and tedious, requiring human intervention and special care, and which is not applicable to a wide range of habitats. As an alternative to filtration, passive eDNA sampling using natural substrates appears to be a promising solution. This approach uses the natural properties of some minerals (eg. silica), organisms (eg. sponges) or even communities (e.g. biofilms) to collect and preserved eDNA. Yet, such approaches are difficult to standardize and may not be applicable in many habitats. To circumvent that problem, we have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape of the samplers has been designed to facilitate their handling in laboratory and field experiments. Here we describe and test the ability of HAp samplers to recover freshwater eDNA. We show that HAp samplers recover DNA with high efficiency and are effective even on small amounts of waterlouse eDNA. However, the eDNA recovery is also highly variable across experiments. We show that by understanding the physico-chemical interactions between DNA and the HAp sampler surface, we could improve the replicability of the process and provide a robust alternative to filtration.

Bacterial consortia for crude oil spill remediation

1996 ◽  
Vol 34 (10) ◽  
pp. 187-193 ◽  
Author(s):  
Suneel Chhatre ◽  
Hemant Purohit ◽  
Rishi Shanker ◽  
Purushottam Khanna
Keyword(s):  
Crude Oil ◽  
Oil Spills ◽  
Cost Effective ◽  
Bacterial Consortium ◽  
Alternative Technologies ◽  
Bacterial Consortia ◽  
Physico Chemical ◽  
Wide Range ◽  
Environmentally Sound ◽  
Sound Technology

Oil spills generate enourmous public concern and highlight the need for cost effective and environmentally acceptable mitigation technologies. Physico-chemical methods are not completely effective after a spill. Hence, there is a need for improved and alternative technologies. Bioremediation is the most environmentally sound technology for clean up. This report intends to determine the potential of a bacterial consortium for degradation of Gulf and Bombay High crude oil. A number of bacteria were isolated from an acclimated semicontinuous reactor fed with crude oil. A four membered consortium was designed that could degrade 70% of the crude oil. A member of consortium produced a biosurfactant, rhamnolipid, that emulsified crude oil efficiently for effective degradation by the other members of consortium. The wide range of hydrocarbonoclastic capabilities of the selected members of bacterial consortium leads to the degradation of both aromatic and aliphatic fractions of crude oil in 72 hours.

scholarly journals A Substrate-Independent Benthic Sampler (SIBS) for Hard and Mixed-Bottom Marine Habitats: A Proof-of-Concept Study

2021 ◽  
Vol 8 ◽  
Author(s):  
Nigel Keeley ◽  
Olivier Laroche ◽  
Murray Birch ◽  
Xavier Pochon
Keyword(s):  
Environmental Dna ◽  
Biotic Index ◽  
Rrna Gene ◽  
Substrate Type ◽  
Fish Farms ◽  
Marine Habitats ◽  
Inorganic Matter ◽  
Sea Cage ◽  
Substrate Independent ◽  
The Impact

Sea cage fish farms are increasingly situated over hard and mixed substrate habitats for production and waste-dispersion reasons; yet in many cases, these installations are not being effectively managed with respect to benthic impacts due to the lack of a practical sampling method. This study presents the first set of results from a newly developed Substrate Independent Benthic Sampler (SIBS) device that captures the unconsolidated organic and inorganic matter that overlies almost all substrates. The contents of the samples were analyzed using extracted environmental DNA (eDNA) followed by metabarcoding of the bacterial 16S rRNA gene. SIBS microbial assemblages reliably changed with proximity to farm and concurred with visual assessments of impact. Moreover, the approach appeared to be very sensitive with respect to the enrichment gradient, being able to discern influences at distances of 500–1500 m from the impact source. Other spatial differences, due to region and farm, were small in comparison, and the effect of the underlying substrate type was minor. The samples contained sufficient previously described bacterial bioindicator taxa from enriched sediments, such that a meaningful biotic index could be calculated, thereby placing them on a well-established benthic enrichment spectrum with established environmental thresholds. SIBS-derived bacterial data provide a powerful new approach for mapping spatial boundaries of farm effects irrespective of substrate type and topography. More importantly, the tool should also permit quantitative assessment of benthic enrichment levels irrespective of substrate type from depths of at least 100 m. It therefore has the potential to solve the hard-bottom problem that has until now prohibited effective environmental monitoring at mixed and hard-bottom locations.

scholarly journals Passive sampling of environmental DNA in aquatic environments using 3D-printed hydroxyapatite samplers

2021 ◽  
Author(s):  
Heloise Verdier ◽  
Lara Konecny-Dupre ◽  
Christophe Marquette ◽  
Helen Reveron ◽  
Solene Tadier ◽  
...  
Keyword(s):  
Aquatic Organisms ◽  
Environmental Dna ◽  
Aquatic Environments ◽  
Non Invasive ◽  
Turbid Waters ◽  
Physico Chemical ◽  
Wide Range ◽  
Artificial Dna ◽  
3D Printed ◽  
High Binding Affinity

1. The study of environmental DNA released by aquatic organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Common eDNA sampling methods such as filtration and precipitation are time consuming, require human intervention and are not applicable to a wide range of habitats such as turbid waters and poorly-accessible environments. To circumvent these limitations, we propose to use the binding properties of minerals to create a passive eDNA sampler. 2. We have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape and the geometry of the samplers have been designed to facilitate their handling in laboratory and field. Here we describe and test the ability of HAp samplers to recover artificial DNA and eDNA. 3. We show that HAp samplers efficiently recover DNA and are effective even on small amounts of eDNA (<1 ng). However, we also observed large variations in the amount of DNA recovered even under controlled conditions. 4. By better understanding the physico-chemical interactions between DNA and the HAp sampler surface, one could improve the repeatability of the sampling process and provide an easy-to-use eDNA sampling tool for aquatic environments.

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