Freshwater diatom biomonitoring through benthic kick-net metabarcoding

AbstractBiomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, periphyton scraping, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional microhabitat periphyton scraping and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton scraping and kick-net methodologies, but there was significant difference between diatom communities depending on site quality (P = 0.029). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms and macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes.

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Freshwater diatom biomonitoring through benthic kick-net metabarcoding

PLoS ONE ◽

10.1371/journal.pone.0242143 ◽

2020 ◽

Vol 15 (11) ◽

pp. e0242143

Author(s):

Victoria Carley Maitland ◽

Chloe Victoria Robinson ◽

Teresita M. Porter ◽

Mehrdad Hajibabaei

Keyword(s):

High Throughput Sequencing ◽

Management Strategies ◽

Bulk Sample ◽

Significant Difference ◽

Dna Metabarcoding ◽

Water Quality Status ◽

Taxonomic Groups ◽

Bulk Tissue ◽

Sampling Event ◽

Freshwater Diatom

Biomonitoring is an essential tool for assessing ecological conditions and informing management strategies. The application of DNA metabarcoding and high throughput sequencing has improved data quantity and resolution for biomonitoring of taxa such as macroinvertebrates, yet, there remains the need to optimise these methods for other taxonomic groups. Diatoms have a longstanding history in freshwater biomonitoring as bioindicators of water quality status. However, multi-substrate periphyton collection, a common diatom sampling practice, is time-consuming and thus costly in terms of labour. This study examined whether the benthic kick-net technique used for macroinvertebrate biomonitoring could be applied to bulk-sample diatoms for metabarcoding. To test this approach, we collected samples using both conventional multi-substrate microhabitat periphyton collections and bulk-tissue kick-net methodologies in parallel from replicated sites with different habitat status (good/fair). We found there was no significant difference in community assemblages between conventional periphyton collection and kick-net methodologies or site status, but there was significant difference between diatom communities depending on site (P = 0.042). These results show the diatom taxonomic coverage achieved through DNA metabarcoding of kick-net is suitable for ecological biomonitoring applications. The shift to a more robust sampling approach and capturing diatoms as well as macroinvertebrates in a single sampling event has the potential to significantly improve efficiency of biomonitoring programmes that currently only use the kick-net technique to sample macroinvertebrates.

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Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

Frontiers in Ecology and Evolution ◽

10.3389/fevo.2020.581835 ◽

2020 ◽

Vol 8 ◽

Cited By ~ 1

Author(s):

Zacchaeus G. Compson ◽

Beverly McClenaghan ◽

Gregory A. C. Singer ◽

Nicole A. Fahner ◽

Mehrdad Hajibabaei

Keyword(s):

High Throughput Sequencing ◽

Spatial Scales ◽

Individual Species ◽

Biodiversity Assessment ◽

Occupancy Models ◽

Widespread Adoption ◽

Sampling Protocols ◽

Dna Metabarcoding ◽

Global Biodiversity ◽

Taxonomic Groups

Global biodiversity loss is unprecedented, and threats to existing biodiversity are growing. Given pervasive global change, a major challenge facing resource managers is a lack of scalable tools to rapidly and consistently measure Earth's biodiversity. Environmental genomic tools provide some hope in the face of this crisis, and DNA metabarcoding, in particular, is a powerful approach for biodiversity assessment at large spatial scales. However, metabarcoding studies are variable in their taxonomic, temporal, or spatial scope, investigating individual species, specific taxonomic groups, or targeted communities at local or regional scales. With the advent of modern, ultra-high throughput sequencing platforms, conducting deep sequencing metabarcoding surveys with multiple DNA markers will enhance the breadth of biodiversity coverage, enabling comprehensive, rapid bioassessment of all the organisms in a sample. Here, we report on a systematic literature review of 1,563 articles published about DNA metabarcoding and summarize how this approach is rapidly revolutionizing global bioassessment efforts. Specifically, we quantify the stakeholders using DNA metabarcoding, the dominant applications of this technology, and the taxonomic groups assessed in these studies. We show that while DNA metabarcoding has reached global coverage, few studies deliver on its promise of near-comprehensive biodiversity assessment. We then outline how DNA metabarcoding can help us move toward real-time, global bioassessment, illustrating how different stakeholders could benefit from DNA metabarcoding. Next, we address barriers to widespread adoption of DNA metabarcoding, highlighting the need for standardized sampling protocols, experts and computational resources to handle the deluge of genomic data, and standardized, open-source bioinformatic pipelines. Finally, we explore how technological and scientific advances will realize the promise of total biodiversity assessment in a sample—from microbes to mammals—and unlock the rich information genomics exposes, opening new possibilities for merging whole-system DNA metabarcoding with (1) abundance and biomass quantification, (2) advanced modeling, such as species occupancy models, to improve species detection, (3) population genetics, (4) phylogenetics, and (5) food web and functional gene analysis. While many challenges need to be addressed to facilitate widespread adoption of environmental genomic approaches, concurrent scientific and technological advances will usher in methods to supplement existing bioassessment tools reliant on morphological and abiotic data. This expanded toolbox will help ensure that the best tool is used for the job and enable exciting integrative techniques that capitalize on multiple tools. Collectively, these new approaches will aid in addressing the global biodiversity crisis we now face.

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Evaluation of Nurse Crops for Weed Control and Plant Establishment in Prairie Restoration

HortScience ◽

10.21273/hortsci.33.3.485b ◽

1998 ◽

Vol 33 (3) ◽

pp. 485b-485

Author(s):

Lisa M. Barry ◽

Michael N. Dana

Keyword(s):

Plant Biomass ◽

Spring Barley ◽

Dry Weight ◽

Site Quality ◽

Prairie Restoration ◽

Plant Establishment ◽

Significant Difference ◽

Nurse Crops ◽

Partridge Pea ◽

Prairie Plant

Nurse crops are often recommended in prairie restoration planting. This work investigated several alternative nurse crops to determine their utility in prairie planting. Nurse crops were composed of increasing densities (900, 1800, or 2700 seeds/m2) of partridge pea, spring oats, spring barley, Canada wild rye, or equal mixtures of partridge pea and one of the grasses. The experimental design was a randomized complete-block set in two sites with three blocks per site and 48 treatments per block. Each 3 × 3-m plot contained 1 m2 planted in Dec. 1995 or Mar. 1996 with an equal mix of seven prairie species. The nurse crops were sown over each nine square meter area in April 1996. Plots lacking nurse crops served as controls. Evaluated data consisted of weed pressure rankings and weed and prairie plant dry weight. Nurse crop treatments had a significant effect on weed pressure in both sites. Barley (1800 and 2700 seeds/m2) as well as partridge pea + barley (2700 seeds/m2) were most effective at reducing weed pressure. When weed and prairie plant biomass values were compared, a significant difference was observed for site quality and planting season. Prairie plant establishment was significantly greater in the poorly drained, less-fertile site and spring-sown plots in both sites had significantly higher prairie biomass values. Overall, after two seasons, there was no advantage in using nurse crops over the control. Among nurse crop treatments, oats were most effective in reducing weed competition and enhancing prairie plant growth.

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An evaluation of a shoulder rehabilitation class in a UK hospital following evidence-based modifications

Physiotherapy Practice and Research ◽

10.3233/ppr-200408 ◽

2021 ◽

pp. 1-8

Author(s):

Emily Kell ◽

John A. Hammond ◽

Sophie Andrews ◽

Christina Germeni ◽

Helen Hingston ◽

...

Keyword(s):

Patient Satisfaction ◽

Shoulder Pain ◽

Management Strategies ◽

Cost Effective ◽

Rehabilitation Programme ◽

Patient Specific ◽

Satisfaction Survey ◽

Evidence Based ◽

Patient Satisfaction Survey ◽

Significant Difference

OBJECTIVES: Shoulder pain is a common musculoskeletal disorder, which carries a high cost to healthcare systems. Exercise is a common conservative management strategy for a range of shoulder conditions and can reduce shoulder pain and improve function. Exercise classes that integrate education and self-management strategies have been shown to be cost-effective, offer psycho-social benefits and promote self-efficacy. This study aimed to examine the effectiveness of an 8-week educational and exercise-based shoulder rehabilitation programme following the introduction of evidence-based modifications. METHODS: A retrospective evaluation of a shoulder rehabilitation programme at X Trust was conducted, comparing existing anonymised Shoulder Pain and Disability Index (SPADI) and Patient-Specific Functional Scale (PSFS) scores from two cohorts of class participants from 2017-18 and 2018-19 that were previously collected by the physiotherapy team. Data from the two cohorts were analysed separately, and in comparison, to assess class efficacy. Descriptive data were also analysed from a patient satisfaction survey from the 2018-19 cohort. RESULTS: A total of 47 patients completed the 8-week shoulder rehabilitation programme during the period of data collection (2018-2019). The 2018-19 cohort showed significant improvements in SPADI (p 0.001) and PSFS scores (p 0.001). No significant difference was found between the improvements seen in the 2017-18 cohort and the 2018-19 cohort. 96% of the 31 respondents who completed the patient satisfaction survey felt the class helped to achieve their goals. CONCLUSION: A group-based shoulder rehabilitation class, which included loaded exercises and patient education, led to improvements in pain, disability and function for patients with rotator cuff related shoulder pain (RCRSP) in this outpatient setting, but anticipated additional benefits based on evidence were not observed.

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Total Organic Carbon Assessment in Soils Cultivated with Agave tequilana Weber in Jalisco, Mexico

Sustainability ◽

10.3390/su13010208 ◽

2020 ◽

Vol 13 (1) ◽

pp. 208

Author(s):

Celia De La Mora-Orozco ◽

José G. Flores-Garnica ◽

Lucia M. Vega-Ramírez ◽

Irma J. González-Acuña ◽

Juan Nápoles-Armenta ◽

...

Keyword(s):

Organic Carbon ◽

Total Organic Carbon ◽

Management Practices ◽

Water Saturation ◽

Management Strategies ◽

Information Criterion ◽

Agave Tequilana ◽

Tukey Test ◽

Significant Difference ◽

Agriculture Management

The Agave tequilana Weber is an important commercial crop in the State of Jalisco, Mexico. However, the agave cultivation generates significant soil loss. For that reason, knowledge about the implementation of the agriculture management practices, such as manure application and the combination of inorganic fertilizers and manure, are relevant. The objective of this research was to determine the effect of agricultural management practices on the total organic carbon (TOC) in the soil in three study locations: Arandas, Tepatitlán, and Acatic in the Altos Sur region of Jalisco. A random sampling was carried out in each study location, 12 samples were obtained for each location at 0–30 cm deep, and a total of 36 samples were analyzed. The evaluated parameters were the potential hydrogen (pH), electrical conductivity (EC), bulk density (BD), soil-water saturation (SWS), total nitrogen (TN), and total organic carbon (TOC). Basic statistics and correlations between parameters were generated. In addition, to estimate TOC from a multivariate analysis, models were developed based on the lowest Akaike information criterion (AIC) and of the classification and regression trees (CART). ANOVA and Tukey test were determined. Results demonstrated a significant difference in the TOC percentages between the study locations. The Tukey test showed that there is no difference in TOC content between the Tepatitlán and Arandas sites, but there is a difference between these two sites and the Acatic. The latter resulted with the lowest values of TOC. Long-term studies are recommended to develop crop management strategies.

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Periphyton diversity in two different Antarctic lakes assessed using metabarcoding

Antarctic Science ◽

10.1017/s0954102021000316 ◽

2021 ◽

pp. 1-9

Author(s):

Paulo E.A.S. Câmara ◽

Láuren M.D. De Souza ◽

Otávio Henrique Bezerra Pinto ◽

Peter Convey ◽

Eduardo T. Amorim ◽

...

Keyword(s):

Dna Sequences ◽

High Throughput Sequencing ◽

Shannon Index ◽

South Shetland Islands ◽

King George Island ◽

Deception Island ◽

Maritime Antarctic ◽

Shetland Islands ◽

Antarctic Lakes ◽

Significant Difference

Abstract Antarctic lakes have generally simple periphyton communities when compared with those of lower latitudes. To date, assessment of microbial diversity in Antarctica has relied heavily on traditional direct observation and cultivation methods. In this study, sterilized cotton baits were left submerged for two years in two lakes on King George Island and Deception Island, South Shetland Islands (Maritime Antarctic), followed by assessment of diversity by metabarcoding using high-throughput sequencing. DNA sequences of 44 taxa belonging to four kingdoms and seven phyla were found. Thirty-six taxa were detected in Hennequin Lake on King George Island and 20 taxa were detected in Soto Lake on Deception Island. However, no significant difference in species composition was detected between the two assemblages (Shannon index). Our data suggest that metabarcoding provides a suitable method for the assessment of periphyton biodiversity in oligotrophic Antarctic lakes.

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Effect of heat stress on milk production and its composition of Holstein Friesian crossbred dairy cows

Asian Journal of Medical and Biological Research ◽

10.3329/ajmbr.v2i2.29060 ◽

2016 ◽

Vol 2 (2) ◽

pp. 190-195 ◽

Cited By ~ 1

Author(s):

Mahmud Al Reyad ◽

Md Abid Hasan Sarker ◽

Md Elias Uddin ◽

Raihan Habib ◽

Md Harun Ur Rashid

Keyword(s):

Heat Stress ◽

Dairy Cows ◽

Milk Yield ◽

Management Practices ◽

Management Strategies ◽

Dairy Farm ◽

Milk Composition ◽

Mustard Oil ◽

Holstein Friesian ◽

Significant Difference

The aim of this research was to observe the effect of heat stress on milk yield and milk compositions of Holstein Friesian crossbred (HF) dairy cows. To fulfill the objectives, a total of 9 Holstein Friesian crossbred cows were selected for this study. Green grasses (German, Para) were supplied adlibitum and concentrate feeds (mixture of wheat bran, rice polish, mustard oil cake, di-calcium phosphate and salt) were supplied at the rate of 2.0 kg/day/cow. Management practices for all the cows were similar following the BAU Dairy farm practices. Data were collected on milk yield (l/h/d), relative humidity (%) and barn temperature (0C). The obtained temperature humidity index (THI) of July, August, September and October were 84.95, 81.99, 81.40 and 79.57, respectively. The highest THI was found in July which indicated higher heat stress during this month. A significant difference (p<0.05) in milk yield of cows was found among different months of July to October. The highest milk yield (6.10±0.50 l/h/d) was found in October among observed months. The compositions of milk such as total solids (TS), solids-not-fat (SNF), fat, protein, lactose, and ash also differed significantly (p<0.01). The highest values (%) of TS, SNF, fat, protein, lactose and ash content of milk were found in October as 12.63, 8.80, 3.83, 3.69, 4.39 and 0.72, respectively and lowest values (%) were in July as 12.20, 8.50, 3.71, 3.50, 4.30 and 0.69, respectively due to the high THI value. From these results, it is concluded that heat stress has strong effect on milk yield and milk composition of HF cows in Bangladesh. Management strategies are needed to minimize heat stress and attain optimal dairy animal performance.Asian J. Med. Biol. Res. June 2016, 2(2): 190-195

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Assessing pollution of aquatic environments with diatoms’ DNA metabarcoding: experience and developments from France water framework directive networks

Metabarcoding and Metagenomics ◽

10.3897/mbmg.3.39646 ◽

2019 ◽

Vol 3 ◽

Cited By ~ 3

Author(s):

Vasselon Valentin ◽

Rimet Frédéric ◽

Domaizon Isabelle ◽

Monnier Olivier ◽

Reyjol Yorick ◽

...

Keyword(s):

Water Framework Directive ◽

High Throughput Sequencing ◽

Ecological Status ◽

Aquatic Environments ◽

Morphological Identification ◽

The Past ◽

Sequencing Technologies ◽

Dna Metabarcoding ◽

Morphological Approach ◽

Status Assessment

Ecological status assessment of watercourses is based on the calculation of quality indices using pollution sensitivity of targeted biological groups, including diatoms. The determination and quantification of diatom species is generally based on microscopic morphological identification, which requires expertise and is time-consuming and costly. In Europe, this morphological approach is legally imposed by standards and regulatory decrees by the Water Framework Directive (WFD). Over the past decade, a DNA-based molecular biology approach has newly been developed to identify species based on genetic criteria rather than morphological ones (i.e. DNA metabarcoding). In combination with high throughput sequencing technologies, metabarcoding makes it possible both to identify all species present in an environmental sample and to process several hundred samples in parallel. This article presents the results of two recent studies carried out on the WFD networks of rivers of Mayotte (2013–2018) and metropolitan France (2016–2018). These studies aimed at testing the potential application of metabarcoding for biomonitoring in the context of the WFD. We discuss the various methodological developments and optimisations that have been made to make the taxonomic inventories of diatoms produced by metabarcoding more reliable, particularly in terms of species quantification. We present the results of the application of this DNA approach on more than 500 river sites, comparing them with those obtained using the standardised morphological method. Finally, we discuss the potential of metabarcoding for routine application, its limits of application and propose some recommendations for future implementation in WFD.

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The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes

ARPHA Conference Abstracts ◽

10.3897/aca.4.e65309 ◽

2021 ◽

Vol 4 ◽

Author(s):

Sara Atienza Casas ◽

Markus Majaneva ◽

Thomas Jensen ◽

Marie Davey ◽

Frode Fossøy ◽

...

Keyword(s):

High Throughput Sequencing ◽

Ecological Status ◽

Ecological Condition ◽

Molecular Techniques ◽

Taxonomic Resolution ◽

Potential Cost ◽

Running Water ◽

National Monitoring ◽

Monitoring Programs ◽

Dna Metabarcoding

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles. In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway. The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be: - Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes. - Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD. - Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level. - Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD. - Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.

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Comparison of Oral Hygiene Status and Relative Abundance of Periodontal Pathogens Between Individuals With and Without Intellectual Disabilities: a Cross-Sectional Study

10.21203/rs.3.rs-49931/v1 ◽

2020 ◽

Author(s):

Yuki Oda ◽

Chiaki Furutani ◽

Reo Kawano ◽

Jumpei Murakami ◽

Yuika Mizota ◽

...

Keyword(s):

Periodontal Disease ◽

Relative Abundance ◽

Outpatient Clinic ◽

High Throughput Sequencing ◽

Analysis Of Covariance ◽

University Hospital ◽

Permanent Teeth ◽

Control Group ◽

Periodontal Pathogens ◽

Significant Difference

Abstract Background: Studies have reported a high prevalence of periodontal disease in individuals with intellectual disability (ID). The aim of this study was to compare the relative abundance of periodontal pathogens (red, orange, yellow, purple, and green complexes) between individuals with ID and healthy controls.Methods: Of the 31 subjects enrolled in this study, 16 with severe ID were selected from the outpatient clinic of the Special Care Dentistry of Hiroshima University Hospital, and 14 healthy subjects were selected from the outpatient clinic of another department at the same hospital. Dental plaque was sampled after oral examination. Decayed, missing, and filled permanent teeth (DMFT) counts were obtained and periodontal measurements were taken using the papillary-marginal-attached (PMA) index, plaque index (PI), gingival index (GI), and probing depth (PD). Gene sequencing (16S rRNA) was performed for each sample using next-generation high-throughput sequencing methods. The relative abundance of the periodontal pathogens and the clinical parameters were compared. An unpaired t-test was used to compare the oral health status in both groups and analysis of covariance was performed to compare the relative abundance of each pathogen.Results: No statistically significant difference in DMFT was observed between the two groups. However, significant differences in the median PMA index, PI, and GI were noted between the groups (P < 0.0001). In addition, the mean PD in the ID group was significantly higher than that in the control group (P < 0.0001). The relative abundances of Tannerella spp. and Treponema spp. were significantly higher in the ID group when compared to the control group at the genus level (P = 0.0383 and 0.0432, respectively); alternatively, the relative abundance of Porphyromonas spp. was significantly lower in the ID group (P < 0.0001).Conclusions: The PMA index, PI, GI, and PD were significantly lower in the ID group than in the control group. On the other hand, no significant difference in DMFT was observed between the two groups. Furthermore, our findings indicate that Tannerella forsythia might be more closely associated with periodontal disease than Porphyromonas gingivalis in individuals with ID.

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