scholarly journals Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

2018 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Yo Miyake ◽  
Maribet Gamboa ◽  
Kozo Watanabe
Keyword(s):  
Community Composition ◽  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Morphological Data ◽  
Morphological Identification ◽  
Biodiversity Assessment ◽  
Stream Macroinvertebrate ◽  
The Relationship ◽  
Diversity Metrics

AbstractConventional morphology-based identification is commonly used for routine assessment of freshwater ecosystems. However, cost and time efficient techniques such as high-throughput sequencing (HTS) based approaches may resolve the constraints encountered in conducting morphology-based surveys. Here, we characterized stream macroinvertebrate species diversity and community composition via metabarcoding and morphological analysis from environmental samples collected from the Shigenobu River Basin in Ehime Prefecture, Japan. We compared diversity metrics and assessed both approaches’ ability to evaluate the relationship between macroinvertebrate community and environmental variables. In total, we morphologically identified 45 taxa (3 families, six subfamilies, 31 genera, and five species) from 8,276 collected individuals from ten study sites. We detected 44 species by metabarcoding, with 35 species collapsed into 11 groups matching the morphologically identified taxa. A significant positive correlation between logged depth (number of HTS reads) and abundance of morphological taxa was observed, which implied that quantitative data can be used for subsequent analyses. Relatively higher estimates of alpha diversity were calculated from the metabarcoding data in comparison to morphology-based data. However, beta diversity estimates between metabarcoding and morphology data based on both incidence and abundance-based matrices were correlated proving that community differences between sampling sites were preserved in the molecular data. Also, both models were significant, but metabarcoding data (93%) explained a relatively higher percentage of variation in the relationship between community composition and the environmental variables than morphological data (91%). Overall, we present both the feasibility and limitations of HTS-driven estimations of taxonomic richness, community composition, and diversity metrics, and that metabarcoding was proven comparable and more sensitive against morphology-based analysis for stream macroinvertebrate biodiversity assessment and environmental monitoring.

scholarly journals Comparison of DNA metabarcoding and morphological identification for stream macroinvertebrate biodiversity assessment and monitoring

2019 ◽  
Vol 101 ◽  
pp. 963-972 ◽  
Author(s):  
Joeselle M. Serrana ◽  
Yo Miyake ◽  
Maribet Gamboa ◽  
Kozo Watanabe
Keyword(s):  
Morphological Identification ◽  
Biodiversity Assessment ◽  
Dna Metabarcoding ◽  
Assessment And Monitoring ◽  
Stream Macroinvertebrate

scholarly journals Rapid quantitative assessment of fish larvae community composition using metabarcoding

2020 ◽  
Author(s):  
Frances C. Ratcliffe ◽  
Tamsyn M. Uren Webster ◽  
Deiene Rodriguez-Barreto ◽  
Richard O’Rorke ◽  
Carlos Garcia de Leaniz ◽  
...  
Keyword(s):  
Community Composition ◽  
Early Life ◽  
High Throughput Sequencing ◽  
Fish Larvae ◽  
Morphological Identification ◽  
Taxon Richness ◽  
Life Stages ◽  
Early Life Stages ◽  
Abundance Estimates ◽  
Family Level

AbstractClimate change stressors greatly impact the early life-stages of many organisms but their cryptic morphology often renders them difficult to monitor using morphological identification. High-throughput sequencing of DNA amplicons (metabarcoding) is potentially a rapid and cost-effective method to monitor early life-stages for management and environmental impact assessment purposes. Yet, there is conflicting information about the quantitative capability of metabarcoding. We compared metabarcoding with traditional morphological identification to evaluate taxonomic precision and reliability of abundance estimates, using 332 fish larvae from multinet hauls (0-50m depth) collected at 14 offshore sampling sites in the Irish and Celtic seas. To improve relative abundance estimates, the amount of tissue for each specimen was standardised and mitochondrial primers with conserved binding sites were used. Family level correction factors for amplification bias and back-calculations were applied to estimate numbers of individuals of a given taxon in a sample. Estimates from metabarcoding reads and morphological assessment were positively correlated for relative family abundances as well as taxon richness (Rs=0.81, P=0.007) and diversity (Rs=0.88, P=0.003). After applying family level correction, back-estimates of the number of individuals per family within a sample were accurate to ± 2 individuals. Spatial patterns of community composition did not differ significantly between metabarcoding and morphological assessments.Our results show that DNA metabarcoding of bulk tissue samples can be used to monitor changes in fish larvae abundance and community composition. This represents a feasible, efficient and faster alternative to morphological identification that can be applied to terrestrial and aquatic habitats.

scholarly journals Distribution patterns of dinoflagellate communities along the Songhua River

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6733 ◽  
Author(s):  
Yangchun Gao ◽  
Yiyong Chen ◽  
Wei Xiong ◽  
Shiguo Li ◽  
Aibin Zhan
Keyword(s):  
Environmental Factors ◽  
Geographical Distribution ◽  
High Throughput ◽  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Distribution Patterns ◽  
Freshwater Ecosystems ◽  
Songhua River ◽  
Significant Difference ◽  
The Songhua River

Background Dinoflagellates have the potential to pose severe ecological and economic damages to aquatic ecosystems. It is therefore largely needed to understand the causes and consequences of distribution patterns of dinoflagellate communities in order to manage potential environmental problems. However, a majority of studies have focused on marine ecosystems, while the geographical distribution patterns of dinoflagellate communities and associated determinants in freshwater ecosystems remain unexplored, particularly in running water ecosystems such as rivers and streams. Methods Here we utilized multiple linear regression analysis and combined information on species composition recovered by high-throughput sequencing and spatial and environmental variables to analyze the distribution patterns of dinoflagellate communities along the Songhua River. Results After high-throughput sequencing, a total of 490 operational taxonomic units (OTUs) were assigned to dinoflagellates, covering seven orders, 13 families and 22 genera. Although the sample sites were grouped into three distinctive clusters with significant difference (p < 0.05) in environmental variables, OTUs-based dinoflagellate communities among the three clusters showed no significant difference (p > 0.05). Among all 24 environmental factors, two environmental variables, including NO3-N and total dissolved solids (TDS), were selected as the significantly influential factors (p < 0.05) on the distribution patterns of dinoflagellate communities based on forward selection. The redundancy analysis (RDA) model showed that only a small proportion of community variation (6.1%) could be explained by both environmental (NO3-N and TDS) and dispersal predictors (watercourse distance) along the River. Variance partitioning revealed a larger contribution of local environmental factors (5.85%) than dispersal (0.50%) to the total variation of dinoflagellate communities. Discussion Our findings indicated that in addition to the two quantifiable processes in this study (species sorting and dispersal), more unquantifiable stochastic processes such as temporal extinction and colonization events due to rainfall may be responsible for the observed geographical distribution of the dinoflagellate community along the Songhua River. Results obtained in this study suggested that deeper investigations covering different seasons are needed to understand the causes and consequences of geographical distribution patterns of dinoflagellate biodiversity in river ecosystems.

scholarly journals Testing the relationship between testate amoeba community composition and environmental variables in a coastal tropical peatland

2018 ◽  
Vol 91 ◽  
pp. 636-644 ◽  
Author(s):  
Graeme T. Swindles ◽  
Andy J. Baird ◽  
Elliot Kilbride ◽  
Rob Low ◽  
Omar Lopez
Keyword(s):  
Community Composition ◽  
Environmental Variables ◽  
Testate Amoeba ◽  
Tropical Peatland ◽  
The Relationship

scholarly journals High-throughput Sequencing Analysis of the Rhizosphere Arbuscular Mycorrhizal Fungi (AMF) Community Composition Associated with Ferula Sinkiangensis

2020 ◽  
Author(s):  
Yunfeng Luo ◽  
Yaling He ◽  
Guifang Li ◽  
Xinhua Lv ◽  
Zhongke Wang ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Community Composition ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Slope Position ◽  
Sequencing Analysis ◽  
Soil Physicochemical Properties ◽  
Ferula Sinkiangensis ◽  
The Relationship

Abstract Background: Ferula sinkiangensis is an important and increasingly endangered medicinal plant. Arbuscular mycorrhiza fungi (AMF) are microbes that live in the soil and can enhance nutrient uptake, stress resistance, and pathogen defens in host plants. The composition of AMF communities associated with Ferula sinkiangensis and the relationship between these fungi and other pertinent abiotic factors, however, remains uncertain. Herein, we collected samples of rhizosphere and surrounding soil at a range of depths (0-20, 20-40, and 40-60 cm) and a range of slop positions (bottom, middle, top). These samples were then subjected to analyses of soil physicochemical properties and high-throughput sequencing (Illumina MiSeq), enabling us to examine AMF community composition and diversity, as well as the relationship between these parameters and other abiotic factors. Results: Through this analysis, we determined that Glomus and Diversispora were enriched in all samples. AMF diversity and richness varied significantly as a function of slope position, with this variation primarily being tied to differences in Glomus and Diversispora abundance. In contrast, no significant relationship between soil depth and overall AMF composition was noted, although some AMF were found to be sensitive to depth. Many factors were found to significantly affect AMF community composition, including organic matter (OM), TN (total nitrogen), TK (total potassium), AN (ammonium nitrogen), NN (nitrate nitrogen), AK (available potassium), TDS (total soluble salt), pH, SM (soil water content), and AE (slope position). We further found that Shannon diversity index values in these communities were positively correlated with TP (total phosphorus), NN, and pH values (p<0.05), while TP, TDS, and pH were positively correlated with Chao1 values (p<0.05). Conclusion: In summary, these findings reveal that Glomus and Diversispora are key AMF genera found within the rhizosphere soil of Ferula sinkiangensis. These fungi are closely associated with specific environmental and soil physicochemical properties. And The physical and chemical properties of soil were significantly different (p<0.05) because of slope position. Together, our results provide a novel understanding of the relationship between AMF species and Ferula sinkiangensis, providing a theoretical basis for further studies of their development.

scholarly journals Effects of anthropogenic pressures on diatom communities using morphological and molecular approaches

2021 ◽  
Vol 4 ◽  
Author(s):  
Marco Teixeira ◽  
Salomé Almeida ◽  
Maria Feio ◽  
Andreia Mortágua ◽  
Manuela Sales
Keyword(s):  
Environmental Variables ◽  
High Throughput Sequencing ◽  
Dna Barcode ◽  
Ecological Indicator ◽  
Morphological Identification ◽  
Anthropogenic Pressure ◽  
Reference Library ◽  
Promising Alternative ◽  
The North ◽  
Diatom Communities

The relevance of molecular composition of diatom assemblages to detect river impairment caused by different intensive land uses (industrial, agricultural, and urbanization) was tested in this study with data from two rivers (Ferreira and Sousa rivers) and 21 sampling sites located in the north of Portugal. The Water Framework Directive (WFD) gives the legal basis for the use of this ecological indicator for water quality assessment (Vasselon et al. 2017 ). However, the morphological identification and count of diatoms using the light microscope requires a high level of expertise, is time-consuming and costly (Valentin et al. 2019). DNA metabarcoding combined with high-throughput sequencing techniques (HTS), offers a promising alternative to classic methodologies, reducing time and costs (Mortágua et al. 2019 ). Thus, here we compared the response of the two approaches in terms of ecological assessments (IPS Ecological Quality Ratios) to the different types of pressures felt in the 21 sites. Diatoms were sampled at 21 sites located in the North of Portugal in autumn of 2019 (Fig. 1). Samples were submitted in parallel to the molecular and morphological analyses. The eDNA was extracted, PCR amplified (312 bp rbcL DNA barcode), and finally sequenced (Illumina MiSeq). The Mothur software was used to obtain the Operational Taxonomic Units (OTUs), which were then taxonomically assigned to the species through the R-Syst::diatom version 7.1 (Rimet et al. 2018) reference library. EQR values indicated a good correlation between morphological and molecular methods (Fig. 2). PCA analysis (Fig. 3 ) revealed that in urban, agricultural, and industrial areas there is a greater concentration of nutrients (phosphorus and nitrogen), organic matter, and heavy metals due to the discharge of urban/industrial effluents, while in places considered natural (without any type of anthropogenic pressure) we find low levels of these pollutants and high concentrations of dissolved oxygen (DO). The BEST (BIO-ENV) analysis (Tables 1, 2) shows in the case of the morphological approach, the combination of 4 environmental variables (NO₃⁻, Li, K, and Cu) is highly correlated with the biological patterns, and in the molecular approach the combination of only 2 of the environmental variables (Li and K), explains the distribution of diatom communities composition and has a slightly higher correlation. The morphological methodology seems to demonstrate a better response to urban pressures, mainly to effluent discharges, while the molecular one demonstrates a more diffuse response with special emphasis on good correlation with variables such as zinc and nitrate, which may also be related to effluent discharges and use of fertilizers in agriculture. However, it is necessary to improve the reference library so that there is a better response of the molecular methodology to the existing pressures.

scholarly journals DNA metabarcoding and morphological methods show complementary patterns in the metacommunity organization of lentic epiphytic diatoms

2021 ◽  
Vol 4 ◽  
Author(s):  
Alejandro Nistal ◽  
Pedro Garcia ◽  
Jorge Garcia ◽  
María Borrego ◽  
Saúl Blanco ◽  
...  
Keyword(s):  
Community Composition ◽  
High Throughput Sequencing ◽  
Freshwater Ecosystems ◽  
Reference Database ◽  
Compositional Variation ◽  
Diatom Community ◽  
Morphological Method ◽  
Dna Metabarcoding ◽  
Geographical Distances ◽  
Diatom Community Composition

Diatoms are important organisms in freshwater ecosystems due to their position as primary producers and therefore, analyzing their communities provides relevant information on ecosystem functioning. Diatoms have historically been identified based on morphological traits, which is time-consuming and requires well-trained specialists. Nevertheless, DNA barcoding offers an alternative approach to overcome some limitations of the morphological method. Here, we assess if both approaches are comparable methods to study patterns and mechanisms (including environmental filtering and dispersal limitation) of epiphytic diatom metacommunities using a comprehensive dataset from 22 Mediterranean ponds at different taxonomic resolutions. We used a fragment of rbcL barcode gene combined with High-Throughput Sequencing to infer diatom community composition. The overall degree of correspondence between both approaches was assessed by Procrustean rotation analysis and Procrustean randomization tests, whereas the role of local environmental variables and geographical distances was studied using a comprehensive combination of BIOENV, Mantel tests and distance-based redundancy analysis. Our results showed a relatively poor correspondence in the compositional variation of diatom metacommunity between both approaches. We speculate that the incompleteness of the reference database and the bioinformatics processing are the biases most likely affecting the molecular approach, whereas the limited counting effort and the presence of cryptic species are presumably the major biases related with the morphological method. On the other hand, variation in diatom community composition detected with both approaches was strongly related to the environmental template, which may be related with the narrow ecological niche and the strong preferences for particular substrata of some diatom species. Nevertheless, we found no significant relationship between compositional variation and geographical distances at regional extent. Overall, our work highlights the importance of DNA metabarcoding to address empirical research questions of community ecology in freshwaters, especially once the reference databases include most genotypes of occurring taxa and bioinformatics biases are overcome.

scholarly journals New trends in bioassessment of aquatic ecosystems: from organisms to DNA-based metrics

2021 ◽  
Vol 4 ◽  
Author(s):  
Jan Pawlowski ◽  
Maria Kahlert
Keyword(s):  
Machine Learning ◽  
Aquatic Ecosystems ◽  
Freshwater Ecosystems ◽  
Environmental Indicators ◽  
Morphological Data ◽  
Future Application ◽  
Morphological Identification ◽  
Biotic Indices ◽  
Biological Quality ◽  
Reference Databases

Traditionally, the biological quality of aquatic ecosystems is assessed using selected groups of organisms that can be identified morphologically. Recent advances in high-throughput genomic approaches offered new opportunities to monitor biodiversity and assess ecological status using DNA barcoding and metabarcoding. The DNA-based tools have been used in three different ways: (1) to replace morphological identification of biological quality elements in existing biotic indices, (2) to develop new molecular indices based on morphologically inconspicuous groups of potential environmental indicators, and (3) to predict biotic indices from environmental DNA datasets using machine learning methods (Pawlowski et al. 2018). The next steps need to take advantages and challenges of these different approaches into account in view of their future application in routine bioassessment.The Working Group 2 of DNAqua-Net, Biotic Indices &amp; Metrics, has worked with several task forces tackling different organism groups (fish, macroinvertebrates, diatoms, bacteria, protists, meiofauna), because challenges have been shown to be quite different dependent on the target organisms Kahlert et al. 2019. For the fish the eDNA-metabarcoding methods are well developed and give very good results in terms of species detection. The important question is to see if the semi-quantitative data retrieved from the metabarcoding (proportion in eDNA sequences) could be translated to proportions in biomass/numbers that are now used in many indices. The fish researchers are trying to fit these data in, but some correction factors might be needed to correct for differences between molecular and conventional methodsRegarding the macroinvertebrates, much discussion regarding index development was focusing on the importance of abundance measurements, and it was tested how existing indices would perform if barcoding data would be used instead of morphological data. Still discussion is ongoing on several technical issues, including the use of preservative for DNA extraction from bulk samples, the choice of primers for PCR amplification and the incompleteness of reference databases which impedes the correct assignment of eDNA sequences. Also minimum standards for routine operation are still missing.The diatom group has worked much on practical issues, starting a large initiative to compare diatom metabarcoding protocols used in routine freshwater biomonitoring for standardization (Bailet et al. 2019, Keck et al. 2018, Vasselon et al. 2017). With diatoms, all three approaches to develop molecular indices have been tested and seem promising, i.e. using existing indices with taxa names derived by matching sequences with reference databases, developing new indices based on molecular data only with traditional fixed scores, and using machine-learning techniques (Bailet et al. 2020, Vasselon et al. 2018, Tapolczai et al. 2019, Keck et al. 2018) The micro- and meiobiota group has worked towards an inclusion of microorganisms into aquatic assessment, because the microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems (Sagova-Mareckova et al. 2021). Another focus was on how sediment DNA analysis can be integrated into stated goals of routine monitoring applications. It has been an interesting journey, and we WG2 coordinators would like to thank all the people for their engagement! Keep up the good work!

scholarly journals Comparison of Fish, Macroinvertebrates and Diatom Communities in Response to Environmental Variation in the Wei River Basin, China

Water ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3422
Author(s):  
Linfei Liu ◽  
Zongxue Xu ◽  
Fan Yang ◽  
Xuwang Yin ◽  
Wei Wu ◽  
...  
Keyword(s):  
Land Use ◽  
River Basin ◽  
Environmental Variables ◽  
Agricultural Land ◽  
Aquatic Organisms ◽  
Freshwater Ecosystems ◽  
The Wei River Basin ◽  
The Relationship ◽  
Wei River Basin ◽  
Wei River

Land use changes usually lead to the deterioration of freshwater ecosystems and reduced biodiversity. Aquatic organisms are considered valuable indicators for reflecting the conditions of freshwater ecosystems. Understanding the relationship between organisms and land use type, as well as physiochemical conditions, is beneficial for the management, monitoring and restoration of aquatic ecosystems. In this study, fish, macroinvertebrates, and diatoms were investigated at 60 sampling sites in the Wei River basin from October 2012 to April 2013 to determine the relationships between the environment and aquatic organisms. The richness, abundance, Shannon diversity, evenness, Margalef diversity, and Simpson diversity were selected as biological indices for analyzing the correlation between these communities and environmental variables according to Pearson’s coefficient. Canonical correspondence analysis (CCA) was used to analyze the relationship between the biotic communities and environmental variables. The results showed that three diatom indices were weakly correlated with chemical oxygen demand (COD), qualitative Habitat Evaluation Index (QH), and dissolved oxygen (DO). Four macroinvertebrate indices were associated with total phosphorus (TP) while total nitrogen (TN), and agricultural land (AL) had a significant influence on assemblages, suggesting that macroinvertebrates could respond to nutrient levels in the Wei River basin. All land use types had a strong effect on fish indices except AL, indicating that fish would be better used as indicators of spatial changes in the aquatic ecosystem. In conclusion, fish and macroinvertebrates have the potential for use in routine monitoring programs in the Wei River basin.

scholarly journals Experimental N and P additions alter stream macroinvertebrate community composition via taxon‐level responses to shifts in detrital resource stoichiometry

2019 ◽  
Vol 33 (5) ◽  
pp. 855-867 ◽  
Author(s):  
Lee M. Demi ◽  
Jonathan P. Benstead ◽  
Amy D. Rosemond ◽  
John C. Maerz
Keyword(s):  
Community Composition ◽  
Macroinvertebrate Community ◽  
Stream Macroinvertebrate
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