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Macroinvertebrate surveys are commonly used for assessing the health of freshwater systems around the world. Traditionally, surveying involves morphologically identifying the families, and sometimes genera, present in samples. Biological indices, derived from taxonomic lists, provide convenient ways to summarise community data and may be fairly ins...
Contexts in source publication
Context 1
... were collected from 7 sites in 3 freshwater creeks (Tributary of Devlins, Lalor and Vineyard) in Sydney, Australia (Fig. 1) on multiple occasions between December 2016 and July 2017 (see Supplementary Table S1). On each sampling occasion, three replicate samples were taken from the edges of pools. ...Context 2
... instance, the AIA analysis with a 0.05% read number filter had only 6 samples that disagreed with the morphological classification and four of these either ascribing mild pollution to moderately polluted reaches or vice versa. The percentage of cases where the molecular classification agreed with the morphological classification at the generic level, when read number filtering greater than 0 was applied, was between 67.6 and 86.5% in the AIA analyses, 67.6-78.4 in the BoBW analysis and 35.1-48.6% in the GenBank analysis (Table 1). The family level analyses were in much greater agreement. ...Context 3
... all but one sample was morphologically categorised as severely polluted. The percentage of cases where the molecular classification agreed with the morphological classification at the family level was between 89.2 and 97.3% in the AIA analyses, 94.6-100 in the BoBW analysis and 97.3% across all read number thresholds in the GenBank analysis (Table 1). ...Similar publications
Background
Triple-negative breast cancer (TNBC) is a clinically aggressive disease with abundant variants that cause homologous recombination repair deficiency (HRD). Whether TNBC patients with HRD are sensitive to anthracycline, cyclophosphamide and taxane (ACT), and whether the combination of HRD and tumour immunity can improve the recognition of...
Citations
... Nevertheless, generating accurate species lists from MBC data is challenging [60]. Thus, the availability of reference sequences linked to known species needs to be developed [17,61]. Several researchers have found that MBC was superior to MOI in single-sample comparisons [62,63]. ...
Background:
The water level of Poyang Lake (China) fluctuates seasonally. Shahu Lake, a smaller body of water connected to Poyang Lake during the wet season, is separated in the dry season. Due to a special fishing method termed 'lake enclosed in autumn', the water level is lowered and reaches its lowest point in January, which is <0.5 m deep in the middle of the lake. Our research investigated the effect of water level changes on the zooplankton community composition in Shahu Lake.
Methods:
We used both DNA metabarcoding method (MBC) (18S rRNA gene V4 region) and morphological method (MOI) to track the zooplankton community structure over four seasons in Shahu Lake (China).
Results:
Totals of 90 and 98 species of zooplankton were detected by MOI and MBC, respectively, with rotifers being the main zooplankton component. The α-diversity index of both methods increased from spring to summer and decreased from summer to autumn, reaching the lowest value in winter. NMDS and a cluster analysis showed that all zooplankton communities detected by MOI and MBC were significantly separated by season. The zooplankton community in winter was separated from that of the other three seasons, but the summer and autumn communities were more similar.
Conclusions:
Changes in the water level had significant effects on the zooplankton community composition. We found that MBC was more able to detect the differences in the zooplankton composition than MOI. MBC also had more advantages in copepod recognition. In our study, 37 species of copepods were detected by MBC, but only 11 species were detected by MOI. We concluded that MBC should be used to research the seasonal variations of zooplankton.
... Sequences with a minimum overlap of 25 bp and homology of at least 80% were merged and only sequences between 301 and 313 bp (i.e. close to the target amplicon length) were retained for further analyses 41 . Sequences were clustered into OTUs, using a 97% clustering threshold as this threshold corresponds reasonably well with COI delimitation between invertebrate species 42 . ...
... gov/ genba nk/, accessed 10th of June 2021). We then refined this taxonomic assignment using percent homology thresholds, arbitrarily assigned as part of the GHAP pipeline: 97% or greater for species, 95 to < 97% for genus, 90 to < 95% for family, 85-< 90% for order, and those with < 85% were not assigned because of taxonomic uncertainty 41 . ...
Platypuses ( Ornithorhynchus anatinus ) forage for macroinvertebrate prey exclusively in freshwater habitats. Because food material in their faeces is well digested and mostly unidentifiable, previous dietary studies have relied on cheek pouch assessments and stable isotope analysis. Given DNA metabarcoding can identify species composition from only fragments of genetic material, we investigated its effectiveness in analysing the diet of platypuses, and to assess variation across seasons and sexes. Of the 18 orders and 60 families identified, Ephemeroptera and Diptera were the most prevalent orders, detected in 100% of samples, followed by Trichoptera, Pulmonata, and Odonata (86.21% of samples). Caenidae and Chironomidae were the most common families. Diptera had a high average DNA read, suggesting it is an important dietary component that may have been underestimated in previous studies. We found no variation in diet between sexes and only minimal changes between seasons. DNA metabarcoding proved to be a highly useful tool for assessing platypus diet, improving prey identification compared to cheek pouch analysis, which can underestimate soft-bodied organisms, and stable isotope analysis which cannot distinguish all taxa isotopically. This will be a useful tool for investigating how platypus prey diversity is impacted by habitat degradation as a result of anthropogenic stressors.
... Astonishingly, these rapid advances in eDNA-based technologies are rather timidly implemented in routine biomonitoring (Hering et al., 2018;Shackleton et al., 2021). Although the concept of Biomonitoring 2.0 is widely endorsed, its acceptance in practice is hampered for various reasons. ...
... Astonishingly, these rapid advances in eDNA-based technologies are rather timidly implemented in routine biomonitoring (Hering et al., 2018;Shackleton et al., 2021). Although the concept of Biomonitoring 2.0 is widely endorsed, its acceptance in practice is hampered for various reasons. ...
