Effects of time and environmental conditions on the quality of DNA extracted from fecal samples for genotyping of wild deer in a warm temperate broad-leaved forest

Performance of viral and bacterial genetic markers for sewage pollution tracking in tropical Thailand

Identifying sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these marker genes in tropical areas are limited. Therefore, this research evaluated four human-associated MST marker genes (human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21) for tracking sewage pollution in aquatic environments of Thailand. The viral marker genes, HPyV and crAssphage were highly sensitive and specific to sewage from onsite wastewater treatment plants (OWTPs; n = 19), with no cross-detection in 120 composite swine, cattle, chicken, duck, goat, sheep, and buffalo fecal samples. The bacterial marker genes, Lachno3 and BacV6-21, demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in OWTP samples were Lachno3 and BacV6-21 (5.42-8.02 and nondetect-8.05 log₁₀ copies/100 mL), crAssphage (5.28-7.38 log₁₀ copies/100 mL), and HPyVs (3.66-6.53 log₁₀ copies/100 mL), respectively. Due to their increased specificity, the abundance of viral markers were further investigated in environmental waters, in which HPyVs showed greater levels (up to 4.33 log₁₀ copies/100 mL) and greater detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log₁₀ copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log₁₀ copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log₁₀ copies/100 mL and 88.9%). HPyVs and crAssphage marker genes were identified as highly sensitive and specific for tracking sewage pollution in aquatic environments of Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

Factors influencing genotyping success and genotyping error rate of Eurasian otter (Lutra lutra) faeces collected in temperate Central Europe

The use of non-invasively collected DNA source material for genetic and genomic applications is usually characterized by low target DNA concentration and quality, genotyping errors and cost-intensive lab procedures. However, for otters (Lutrinae) as elusive species of conservation concern, genetic non-invasive sampling has become an important tool to study their ecology and demography. To increase cost-efficiency of monitoring programmes and to promote the expansion of genomic approaches to non-invasive samples, we aimed to refine sample collection and preparation. Therefore, we examined the effects of intrinsic sample characteristics (including diet), environmental conditions in the field and sample treatment in the molecular laboratory on the success of genotyping and allelic dropout (ADO) rates using microsatellite markers in 1970 fresh Eurasian otter (Lutra lutra) scats. Using fresh samples only, we probably eliminated one of the most important impediments of genotyping DNA from otter faecal samples beforehand. But, we observed higher genotyping success and lower ADO rates for anal glad secretions and faecal samples containing high proportions of mucus. Moist conditions during sample collection may promote DNA degradation and PCR inhibition, leading to decreased genotyping success rates. ADO was further affected by the type of extraction kit. However, a high proportion of variance remaining unexplained by our models implied that additional parameters were acting (amount of PCR inhibitors, non-uniform distribution of intestinal cells, efficiency of PCRs, specific microclimate at marking sites). We summarized influential factors maximizing genotyping quality of otter scats and give recommendations for sample collection, storage and DNA extraction based on our results and current literature.

Towards high–throughput analyses of fecal samples from wildlife

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. We evaluate alternative protocols which could allow higher throughput for two of these steps: sample collection and DNA extraction. Two different field sampling and seven different DNA extraction methods are tested here 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.

Effect of Quantitative Polymerase Chain Reaction Data Analysis Using Sample Amplification Efficiency on Microbial Source Tracking Assay Performance and Source Attribution

The widely used microbial source tracking (MST) technique, quantitative polymerase chain reaction (qPCR), quantifies host-specific gene abundance in polluted water to identify and prioritize contamination sources. This study characterized the effects of a qPCR data analysis using the sample PCR efficiencies (the LinRegPCR model) on gene abundance and compared them with the standard curve-based method (the mixed model). Five qPCR assays were evaluated: the universal GenBac3, human-specific HF183/BFDrev and CPQ_056, swine-specific Pig-2-Bac, and cattle-specific Bac3qPCR assays. The LinRegPCR model increased the low-copy amplification, especially in the HF183/BFDrev assay, thus lowering the specificity to 0.34. Up to 1.41 log₁₀ copies/g and 0.41 log₁₀ copies/100 mL differences were observed for composite fecal and sewage samples (n = 147) by the LinRegPCR approach, corresponding to an 18.2% increase and 6.4% decrease, respectively. Freshwater samples (n = 48) demonstrated a maximum of 1.95 log₁₀ copies/100 mL difference between the two models. Identical attributing sources by both models were shown in 54.55% of environmental samples; meanwhile, the LinRegPCR approach improved the inability to identify sources by the mixed model in 29.55% of the samples. This study emphasizes the need for a standardized data analysis protocol for qPCR MST assays for interlaboratory consistency and comparability.

A DNA toolbox for non-invasive genetic studies of sambar deer (Rusa unicolor)

Invasive sambar deer (Rusa unicolor) are having significant detrimental impacts on natural environments in south-eastern Australia. Little, however, is known about their ecology, limiting evidence-based management strategies directed at reducing deer impacts. Genetic data, generated from DNA isolated from deer scats, can be used to fill ecological knowledge gaps. This study outlines a non-invasive genetic sampling strategy by which good-quality DNA from a single deer scat can be used to determine (1) species of origin, (2) sex and (3) a unique DNA profile. DNA from deer tissue and sambar deer scat samples were used to develop and optimise molecular methods to collect reliable genetic information. A DNA toolbox is presented that describes how to find, collect and store scat samples, isolate DNA and use molecular markers to generate informative genetic data. Generating genetic data using this approach will support studies aimed at acquiring ecological knowledge about sambar deer. Such knowledge will be critical for developing evidence-based recommendations to improve on-ground management decisions for sambar deer.