scholarly journals Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0130324 ◽  
Author(s):  
Vasco Elbrecht ◽  
Florian Leese
Keyword(s):  
Species Abundance ◽  
Ecosystem Assessments ◽  
Sequence Relationships

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.

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.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

STUDYING OF TERSKO-SULAKSKAYA LOWLAND VEGETATION UNDER THE RESULTS OF GROUND-BASED RESEARCH AND AUTOMATED INTERPRETATION

1970 ◽  
pp. 29-32
Author(s):  
M. I. Dzhalalova ◽  
A. B. Biarslanov ◽  
D. B. Asgerova
Keyword(s):  
Plant Communities ◽  
Satellite Imagery ◽  
Vegetation Cover ◽  
Anthropogenic Impacts ◽  
Species Abundance ◽  
Remote Sensing Data ◽  
Indigenous Communities ◽  
The State ◽  
Anthropogenic Factors ◽  
Internet Resource

The state of plant communities in areas located in the Tersko-Sulak lowland was studied by assessing phytocenotic indicators: the structure of vegetation cover, projective cover, species diversity, species abundance and elevated production, as well as automated decoding methods. There are almost no virgin soils and natural phytocenoses here; all of them have been transformed into agrocenoses (irrigated arable lands and hayfields, rice-trees and pastures). The long-term impact on pasture ecosystems of natural and anthropogenic factors leads to significant changes in the indigenous communities of this region. Phytocenoses are formed mainly by dry-steppe types of cereals with the participation of feather grass, forbs and ephemera, a semi-desert haloxerophytic shrub - Taurida wormwood. At the base of the grass stand is common coastal wormwood and Taurida wormwood - species resistant to anthropogenic influences. Anthropogenic impacts have led to a decrease in the number of species of feed-rich grain crops and a decrease in the overall productivity of pastures. Plant communities in all areas are littered with ruderal species. The seasonal dynamics of the land cover of the sites was estimated by the methods of automatic decoding of satellite images of the Landsat8 OLI series satellite for 2015, dated by the periods: spring - May 20, summer - July 23, autumn - October 20. Satellite imagery data obtained by Landsat satellite with a resolution in the multispectral image of 30 m per pixel, and in the panchromatic image - 10 m per pixel, which correspond to the requirements for satellite imagery to assess the dynamics of soil and vegetation cover. Lower resolution data, for example, NDVI MODIS, does not provide a reliable reflection of the state of soil and vegetation cover under arid conditions. In this regard, remote sensing data obtained from the Internet resource https://earthexplorer.usgs.gov/ was used.

To the flora of сonjugates (Streptophyta, Conjugatophyceae) of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia)

2014 ◽  
Vol 48 ◽  
pp. 81-88
Author(s):  
A. F. Luknitskaya
Keyword(s):  
Species Distribution ◽  
National Park ◽  
Species Abundance ◽  
Water Bodies ◽  
Number Of Species ◽  
First Time

76 species, 3 varieties and 1 form from 21 genera of Streptophyta, Conjugatophyceae (Actinotaenium, Bambusina, Closterium, Cosmarium, Cylindrocystis, Euastrum, Gonatozygon, Haplotaenium, Micrasterias, Mougeotia, Netrium, Penium, Planotaenium, Pleurotaenium, Raphidiastrum, Spirogyra, Spirotaenia, Staurastrum, Staurodesmus, Tetmemorus, Xanthidium) were found in the basins of the Valdai District area of the National Park «Valdaiskiy» (Novgorod Region, Russia). The list of species is annotated with data on the species distribution in 55 collecting sites of 29 water bodies of the national park, and species abundance in collected samples according to Luknitskaya (2009). Among above mentioned genera, the genus Cosmarium is represented by the greatest number of species (20). Staurastrum chaetoceros has been found for the first time for the Novgorod Region.

Sign in / Sign up

Export Citation Format

Share Document