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.

Frustule-related gene transcription and the influence of diatom community composition on silica precipitation in an iron-limited environment

2012 ◽  
Vol 57 (6) ◽  
pp. 1619-1633 ◽  
Author(s):  
Colleen A. Durkin ◽  
Adrian Marchetti ◽  
Sara J. Bender ◽  
Tiffany Truong ◽  
Rhonda Morales ◽  
...  
Keyword(s):  
Community Composition ◽  
Gene Transcription ◽  
Related Gene ◽  
Diatom Community ◽  
Silica Precipitation ◽  
Diatom Community Composition

scholarly journals An account of epiphytic diatoms in mediterranean wetlands: comparing morphological and molecular assessments

2021 ◽  
Vol 4 ◽  
Author(s):  
María Borrego-Ramos ◽  
Eloy Bécares ◽  
Pedro García-García ◽  
Alejandro Nistal ◽  
Saúl Blanco
Keyword(s):  
Water Quality ◽  
Dna Sequences ◽  
High Throughput Sequencing ◽  
Reference Database ◽  
Good Correspondence ◽  
Quality Class ◽  
Dna Metabarcoding ◽  
Shallow Ponds ◽  
Relative Abundances ◽  
Cryptic Taxa

Benthic diatoms are well known bioindicators of water quality, used in many aquatic ecosystems. Since diatom-based monitoring of water quality is required by European legislation, the search for methods that facilitate this task has become more relevant. The aim of this study was to test the reliability of DNA metabarcoding combined with high-throughput sequencing (HTS) techniques in the bioassessment of 22 Mediterranean shallow ponds in Spain. For each pond, Trophic Diatom Index (TDI) was calculated from inventories obtained by using light microscopy, and then molecular (HTS) methods. Ponds were subsequently classified into five water quality classes. Our results showed a good correspondence between both methods, especially after applying a correction factor depending on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, mainly those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Therefore, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to traditional ones in Mediterranean shallow ponds.

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 Vulnerability of diatom communities in the Peace–Athabasca Delta to environmental change

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5447
Author(s):  
Stephanie J. Connor ◽  
Alexa C. Alexander-Trusiak ◽  
Donald J. Baird
Keyword(s):  
Community Composition ◽  
Gradient Analysis ◽  
Habitat Degradation ◽  
Region Of Interest ◽  
Specific Conductance ◽  
Environmental Drivers ◽  
Limited Information ◽  
Diatom Community ◽  
Dissolved Phosphorus ◽  
Diatom Community Composition

Habitat degradation associated with resource development is a major ecological concern, particularly in Canada’s boreal zone where limited information on biodiversity is available. Habitat degradation can lead to reductions in biodiversity and ecosystem function, especially when drivers of variability and diversity patterns have not been identified for a region of interest. In this study, the distribution of diatom genera in the Peace–Athabasca Delta in northeastern Alberta was examined in relation to seasonal, geographic, and alkalinity gradients. Grab samples of six abiotic variables (total dissolved nitrogen, total dissolved phosphorus, dissolved iron, turbidity, pH, and specific conductance (SPC)) were taken from 12 remote wetlands over three sampling periods, and regressed against an ordination of diatom community composition to identify key environmental drivers of diatom community variation. Indirect gradient analysis identified two major gradients among sites. First, separation of sites among sampling periods showed successional seasonal changes in diatom community composition. Second, separation of sites from the Peace sub-delta and Birch sub-delta showed a gradient of geographic separation. Direct gradient analysis failed to explain the underlying drivers of these two gradients, but did show that alkalinity is a key driver of diatom community composition in the Embarras sub-delta, and that these sites could be particularly vulnerable to community changes associated with acidification.

scholarly journals Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass - sequence relationships with an innovative metabarcoding protocol

2015 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
High Throughput ◽  
Statistical Power ◽  
High Throughput Sequencing ◽  
Species Abundance ◽  
Reference Database ◽  
Dna Metabarcoding ◽  
Coi Barcoding ◽  
Species Abundances ◽  
Species Specific ◽  
Sequence Relationships

Metabarcoding is an emerging genetic tool to rapidly assess biodiversity in ecosystems. It involves high-throughput sequencing of a standard gene from an environmental sample and comparison to a reference database. However, no consensus has emerged regarding laboratory pipelines to screen species diversity and infer species abundances from environmental samples. In particular, the effect of primer bias and the detection limit for specimens with a low biomass has not been systematically examined, when processing samples in bulk. We developed and tested a DNA metabarcoding protocol that utilises the standard cytochrome c oxidase subunit I (COI) barcoding fragment to detect freshwater macroinvertebrate taxa. DNA was extracted in bulk, amplified in a single PCR step, and purified, and the libraries were directly sequenced in two independent MiSeq runs (300-bp paired-end reads). Specifically, we assessed the influence of specimen biomass on sequence read abundance by sequencing 31 specimens of a stonefly species with known haplotypes spanning three orders of magnitude in biomass (experiment I). Then, we tested the recovery of 52 different freshwater invertebrate taxa of similar biomass using the same standard barcoding primers (experiment II). Each experiment was replicated ten times to maximise statistical power. The results of both experiments were consistent across replicates. We found a distinct positive correlation between species biomass and resulting numbers of MiSeq reads. Furthermore, we reliably recovered 83% of the 52 taxa used to test primer bias. However, sequence abundance varied by four orders of magnitudes between taxa despite the use of similar amounts of biomass. Our metabarcoding approach yielded reliable results for high-throughput assessments. However, the results indicated that primer efficiency is highly species-specific, which would prevent straightforward assessments of species abundance and biomass in a sample. Thus, PCR-based metabarcoding assessments of biodiversity should rely on presence-absence metrics.

Extreme streams: flow intermittency as a control on diatom communities in meltwater streams in the McMurdo Dry Valleys, Antarctica1This article is derived from a special session entitled “A New Hydrology: Inflow Effects on Ecosystem Form and Functioning” that took place at the February 2011 ASLO Aquatic Sciences conference in San Juan, Puerto Rico.

2012 ◽  
Vol 69 (8) ◽  
pp. 1405-1419 ◽  
Author(s):  
Lee F. Stanish ◽  
Tyler J. Kohler ◽  
Rhea M.M. Esposito ◽  
Breana L. Simmons ◽  
Uffe N. Nielsen ◽  
...  
Keyword(s):  
Community Composition ◽  
Endemic Species ◽  
Mcmurdo Dry Valleys ◽  
Dry Valleys ◽  
Intermittent Streams ◽  
Diatom Community ◽  
Diatom Communities ◽  
Dry Valley ◽  
Flow Intermittency ◽  
Diatom Community Composition

In the McMurdo Dry Valleys of Antarctica, stream biota is limited by the brief availability of liquid water. The benthic microbial mats harbor diatoms that have adapted to hydrologic stresses, including numerous endemic species. We found a strong relationship between diatom community composition and flow intermittency in a data set including seven streams that spanned a gradient in flow intermittency. In particular, two genera represented by numerous endemic species in Dry Valley habitats, Hantzschia and Luticola , had high abundances in moderately and highly intermittent streams, respectively. The Shannon Index of diversity was greatest in streams with intermediate flow intermittency, with lower diversity in more stable streams resulting from lower evenness, and lower diversity in highly intermittent streams resulting from lower richness. These results indicate that multiple metrics of biodiversity may be useful in assessing the response of diatom communities to changing hydrologic regime. We propose that flow intermittency acts as a species filter that increases habitat heterogeneity in Dry Valley streams and may allow endemic species to persist. Future Antarctic warming may alter diatom community composition and habitats that act as refugia for desiccation-tolerant taxa.

scholarly journals Diversity and Seasonality Dynamics of Ciliate Communities in Four Estuaries of Shenzhen, China (South China Sea)

2021 ◽  
Vol 9 (3) ◽  
pp. 260
Author(s):  
Chuanqi Jiang ◽  
Bin Liu ◽  
Jing Zhang ◽  
Siyu Gu ◽  
Zhencheng Liu ◽  
...  
Keyword(s):  
South China Sea ◽  
Community Composition ◽  
South China ◽  
Seasonal Changes ◽  
High Throughput Sequencing ◽  
Seasonal Patterns ◽  
Molecular Tools ◽  
Specific Primers ◽  
China Sea ◽  
Dna Metabarcoding

Ciliates are fundamental components of microzooplankton, with important ecological roles. However, ciliate communities are particularly difficult to monitor using conventional morphological approaches. New molecular tools, such as DNA metabarcoding, can facilitate the study of these communities. This study used high-throughput sequencing to examine the diversity and seasonal dynamics of ciliate communities in four estuarine ecosystems in the South China Sea from June 2019 to March 2020. The amplification of the V4 region of 18S rDNA using ciliate-specific primers identified a total of 1645 amplicon sequence variants (ASVs), corresponding to 13 ciliate classes, 97 families, and 157 genera. The dominant species across all four sampling stations were spirotrichs (including choreotrichs, oligotrichs, and stichotrichs), oligohymenophorean scuticociliates, litostomateans Didinium, and prostomateans Cryptocaryon. Significant differences in ciliate diversity and community composition in the four stations were mainly due to differences in rare, rather than abundant, ASVs. Analysis of the ciliate communities and seasonal patterns in their composition revealed that variations in habitat and environmental conditions have a greater effect than seasonal changes on community composition.

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