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Optimization of protocols for DNA extraction from fecal samples

High-throughput sequencing offers new possibilities in molecular ecology and conservation studies. However, its potential has not yet become fully exploited for noninvasive studies of free–ranging animals, such as those based on feces. High–throughput sequencing allows sequencing of short DNA fragments and could allow simultaneous genotyping of a very large number of samples and markers at a low cost. The application of high throughput genotyping to fecal samples from wildlife has been hindered by several labor intensive steps. Alternative protocols which could allow higher throughput were evaluated for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods were tested on grey wolf (Canis lupus) feces. There was high variation in genotyping success rates. The field sampling method based on surface swabbing performed much worse than the extraction from a fecal fragment. In addition, there is a lot of room for improvement in the DNA extraction step. Optimization of protocols can lead to very much more efficient, cheaper and higher throughput noninvasive monitoring. Selection of appropriate markers is still of paramount importance to increase genotyping success. informacion[at]ebd.csic.es: Sarabia et al (2020) Towards high-throughput analyses of fecal samples from wildlife. Animal Biodiver Conserv 43.2: 271–283 Doi 10.32800/abc.2020.43.0271


http://abc.museucienciesjournals.cat/volum-43-2-2020/towards-high-throughput-analyses-of-fecal-samples-from-wildlife/?lang=en
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Determination of anthropogenic contamination in surface waters using helophytes

Determination of anthropogenic contamination in surface waters using helophytes

Nitrogen (N) loading from anthropogenic activities is contributing to the eutrophication and degradation of wetlands worldwide. Doñana (southwestern Spain), includes a dynamic marshland protected as a UNESCO World Heritage Site, which has a catchment area exposed to increasing N inputs from intensive agriculture and poorly treated urban wastewaters. Identifying the sources of N entering this iconic wetland complex is vital for its conservation. To this end, multiyear (2014–2016), spatially-explicit data on N concentration in water samples were combined with measurements on the relative abundance of N stable isotopes (d15N) in Bolboschoenus maritimus and Typha domingensis, two dominant helophytes (i.e. emergent macrophytes) in the Doñana marsh and entry streams. Overall, plant tissues from entry streams showed higher d15N values than those from the marsh, particularly in those streams most affected by urban wastewaters. Isotopic values did not differ between plant species. Water samples affected by isotopically-enriched urban wastewaters and other diffuse organic N inputs (e.g. livestock farming) had relatively high Dissolved Inorganic Nitrogen (DIN) concentrations. In contrast, in streams mainly affected by diffuse N pollution from greenhouse crops, high DIN values were related to isotopically-depleted N sources (e.g., inorganic fertilizers). Thus, helophytes, in combination with other parameters such as N concentration in water or land cover, can be valuable indicators of anthropogenic pressures in Mediterranean wetlands. Helophytes have widespread distributions, and can be readily sampled even when water is no longer present. However, identification of specific N sources through helophyte d15N values is limited when key potential N sources are isotopically undistinguishable (e.g. fertilizers vs. atmospheric sources). informacion[at]ebd.csic.es: Paredes et al (2019) Stable isotopes in helophytes reflect anthropogenic nitrogen pollution in entry streams at the Doñana World Heritage Site. Ecol Indicators 97: 130-140. Doi 10.1016/j.ecolind.2018.10.0009


https://www.sciencedirect.com/science/article/pii/S1470160X18307702