Genetic variation within Vermont was greater within the westward-trending Winooski River watershed than in the Passumpsic River watershed, which drains east into the Connecticut River. Within hemisphere, patterned genetic variation was evident only in the AFLP data and only locally. These two clades have little to no variation even at large geographic scales. Matteuccia struthiopteris segregates globally into minimally divergent (0.3%) Eurasian and American lineages. ![]() Here we use DNA sequences and AFLP data to investigate the genetic variation of the fiddlehead fern at two geographic scales to infer the historical biogeography of the species. Much of its current North American and European distribution was covered in ice or uninhabitable tundra during the Pleistocene. Matteuccia struthiopteris (Onocleaceae) has a present-day distribution across much of the north-temperate and boreal regions of the world. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locusâspecific validation efforts. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. Specifically, we use a taxonomy crossâvalidation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.DNA metabarcoding is an important tool for molecular ecology. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples they diverged strongly in composition. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. To compare the abilities of seawater and sedimentary microbial. ![]() Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean.
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