Project description:The meiofauna is an important part of the marine ecosystem, but its composition and distribution patterns are relatively unexplored. Here we assessed the biodiversity and community structure of meiofauna from five locations on the Swedish western and southern coasts using a high-throughput DNA sequencing (metabarcoding) approach. The mitochondrial cytochrome oxidase 1 (COI) mini-barcode and nuclear 18S small ribosomal subunit (18S) V1-V2 region were amplified and sequenced using Illumina MiSeq technology. Our analyses revealed a higher number of species than previously found in other areas: thirteen samples comprising 6.5 dm3 sediment revealed 708 COI and 1,639 18S metazoan OTUs. Across all sites, the majority of the metazoan biodiversity was assigned to Arthropoda, Nematoda and Platyhelminthes. Alpha and beta diversity measurements showed that community composition differed significantly amongst sites. OTUs initially assigned to Acoela, Gastrotricha and the two Platyhelminthes sub-groups Macrostomorpha and Rhabdocoela were further investigated and assigned to species using a phylogeny-based taxonomy approach. Our results demonstrate that there is great potential for discovery of new meiofauna species even in some of the most extensively studied locations.
Project description:A fast and reliable method for obtaining a species-level identification is a fundamental requirement for a wide range of activities, from plant protection and invasive species management to biodiversity assessments and ecological studies. For insects, novel molecular techniques such as DNA metabarcoding have emerged as a rapid alternative to traditional morphological identification, reducing the dependence on limited taxonomic experts. Until recently, molecular techniques have required a destructive DNA extraction, precluding the possibility of preserving voucher specimens for future studies, or species descriptions. Here we paired insect metabarcoding with two recent non-destructive DNA extraction protocols, to obtain a rapid and high-throughput taxonomic identification of diverse insect taxa while retaining a physical voucher specimen. The aim of this work was to explore how non-destructive extraction protocols impact the semi-quantitative nature of metabarcoding, which alongside species presence/absence also provides a quantitative, but biased, representation of their relative abundances. By using a series of mock communities representing each stage of a typical metabarcoding workflow we were able to determine how different morphological (i.e., insect biomass and exoskeleton hardness) and molecular traits (i.e., primer mismatch and amplicon GC%), interact with different protocol steps to introduce quantitative bias into non-destructive metabarcoding results. We discuss the relevance of taxonomic bias to metabarcoding identification of insects and potential approaches to account for it.
Project description:Seed of 4 lines of S. tuberosum var andigena were sown and, after transplanting, grown in 3 gal nursery containers in a greenhouse with natural daylight. The seeds were sown in July and the drought stress experiment began in September. Drought stress was administered by withholding water and monitored by measuring the rate of photosynthesis (PS; LiCor 6400). We found that loss of photosynthetic capability (ie a PS rate of 0-2 mM CO2/m2/sec) correlated with a severe drought stress. Control plants were watered normally and maintained a PS rate of 18-20 mM CO2/m2/sec. After drought stress, the treated plants were re-watered and PS measurements taken again. After the first cycles of stress, control and treated plants were harvested and roots, tubers and shoots were stored at –80°C for RNA extractions. The drought experiment was then repeated for the remaining plants such that they were exposed to a second cycle of stress. For each line of S. andigena, there were 2 control and 2 treated plants per cycle of stress. RNA was extracted following the acid phenol protocol of TIGR. Keywords: Direct comparison, loop design
Project description:Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, a limitation of eDNA surveys is that detected DNA molecules may originate from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding has recently been proposed as a complementary tool for more localized assessments of the biological community. In this study, we evaluated the effectiveness of eDNA and eRNA metabarcoding for inferring the richness and species distribution patterns of vertebrates and invertebrates in a Central European lowland river. We collected water samples and analyzed them using a 12S marker for vertebrates and a COI marker for invertebrates. We detected 31 fish, 16 mammal, 10 bird and one lamprey species in the vertebrate dataset. While results were largely consistent, we detected a higher number of species when analysing eRNA (mean = 30.89) than eDNA (mean = 26.16). Also, eRNA detections had a stronger local signature than eDNA detections when compared against species distribution patterns from traditional fish monitoring data. For invertebrates, we detected 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan and four cnidarian species. In contrast to the pattern of vertebrate richness, we detected a higher richness using eDNA (mean = 41.37) compared to eRNA (mean = 22.42). Our findings primarily show that eDNA and eRNA-based detections are comparable for vertebrate and invertebrate taxa. Biological replication was important for both template molecules studied. Signal detections for vertebrates were more localized for eRNA compared to eDNA. Overall, the advantages of the extra steps needed for eRNA analyses depend on the study question but both methods provide important data for biodiversity monitoring and research.
Project description:The biodiversity crisis is one of the greatest challenges facing humanity, but our understanding of the drivers remains limited. Thus, after decades of studies and regulation efforts, it remains unknown whether to what degree and at what concentrations modern agricultural pesticides cause regional-scale species losses. We analyzed the effects of pesticides on the regional taxa richness of stream invertebrates in Europe (Germany and France) and Australia (southern Victoria). Pesticides caused statistically significant effects on both the species and family richness in both regions, with losses in taxa up to 42% of the recorded taxonomic pools. Furthermore, the effects in Europe were detected at concentrations that current legislation considers environmentally protective. Thus, the current ecological risk assessment of pesticides falls short of protecting biodiversity, and new approaches linking ecology and ecotoxicology are needed.
| S-EPMC3704006 | biostudies-literature
Project description:Metabarcoding benthic macroinvertebrates - assessing biodiversity at small spatial scales