Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows.

Different second-generation sequencing technologies may have taxon-specific biases when DNA metabarcoding prey in predator faeces. Our major objective was to examine differences in prey recovery from bat guano across two different sequencing workflows using the same faecal DNA extracts. We compared results between the Ion Torrent PGM and the Illumina MiSeq with similar library preparations and the same analysis pipeline. We focus on repeatability and provide an R Notebook in an effort towards transparency for future methodological improvements. Full documentation of each step enhances the accessibility of our analysis pipeline. We tagged DNA from insectivorous bat faecal samples, targeted the arthropod cytochrome c oxidase I minibarcode region and sequenced the product on both second-generation sequencing platforms. We developed an analysis pipeline with a high operational taxonomic unit (OTU) clustering threshold (i.e., ≥98.5%) followed by copy number filtering to avoid merging rare but genetically similar prey into the same OTUs. With this workflow, we detected 297 unique prey taxa, of which 74% were identified at the species level. Of these, 104 (35%) prey OTUs were detected by both platforms, 176 (59%) OTUs were detected by the Illumina MiSeq system only, and 17 (6%) OTUs were detected using the Ion Torrent system only. Costs were similar between platforms but the Illumina MiSeq recovered six times more reads and four additional insect orders than did Ion Torrent. The considerations we outline are particularly important for long-term ecological monitoring; a more standardized approach will facilitate comparisons between studies and allow faster recognition of changes within ecological communities.

Presence of artisanal gold mining predicts mercury bioaccumulation in five genera of bats (Chiroptera).

Mercury, a toxic trace metal, has been used extensively as an inexpensive and readily available method of extracting gold from fine-grained sediment. Worldwide, artisanal mining is responsible for one third of all mercury released into the environment. By testing bat hair from museum specimens and field collected samples from areas both impacted and unimpacted by artisanal gold mining in Perú, we show monomethylmercury (MMHg) has increased in the last 100 years. MMHg concentrations were also greatest in the highest bat trophic level (insectivores), and in areas experiencing extractive artisanal mining. Reproductive female bats had higher MMHg concentrations, and both juvenile and adult bats from mercury contaminated sites had more MMHg than those from uncontaminated sites. Bats have important ecological functions, providing vital ecosystem services such as pollination, seed dispersal, and insect control. Natural populations can act as environmental sentinels and offer the chance to expand our understanding of, and responses to, environmental and human health concerns.

Bioaccumulation and biomagnification of mercury and methylmercury in four sympatric coastal sharks in a protected subtropical lagoon.

Mercury bioaccumulation is frequently observed in marine ecosystems, often with stronger effects at higher trophic levels. We compared total mercury (THg) and methylmercury (MeHg) from muscle with length, comparative isotopic niche, and diet (via δ13C and δ15N) among four sympatric coastal sharks in Florida Bay (USA): blacknose, blacktip, bull, and lemon. Mercury in blacknose and blacktip sharks increased significantly with size, whereas bull and lemon sharks had a high variance in mercury relative to size. Both δ13C and δ15N were consistent with general resource use and trophic position relationships across all species. A significant relationship was observed between δ13C and mercury in blacktip sharks, suggesting an ontogenetic shift isotopic niche, possibly a dietary change. Multiple regression showed that δ13C and δ15N were the strongest factors regarding mercury bioaccumulation in individuals across all species. Additional research is recommended to resolve the mechanisms that determine mercury biomagnification in individual shark species.

Cyanobacterial Neurotoxin BMAA and Mercury in Sharks.

Sharks have greater risk for bioaccumulation of marine toxins and mercury (Hg), because they are long-lived predators. Shark fins and cartilage also contain ß-N-methylamino-l-alanine (BMAA), a ubiquitous cyanobacterial toxin linked to neurodegenerative diseases. Today, a significant number of shark species have found their way onto the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. Many species of large sharks are threatened with extinction due in part to the growing high demand for shark fin soup and, to a lesser extent, for shark meat and cartilage products. Recent studies suggest that the consumption of shark parts may be a route to human exposure of marine toxins. Here, we investigated BMAA and Hg concentrations in fins and muscles sampled in ten species of sharks from the South Atlantic and Pacific Oceans. BMAA was detected in all shark species with only seven of the 55 samples analyzed testing below the limit of detection of the assay. Hg concentrations measured in fins and muscle samples from the 10 species ranged from 0.05 to 13.23 ng/mg. These analytical test results suggest restricting human consumption of shark meat and fins due to the high frequency and co-occurrence of two synergistic environmental neurotoxic compounds.

Mercury in bats from the northeastern United States.

This study examines mercury exposure in bats across the northeast U.S. from 2005 to 2009. We collected 1,481 fur and 681 blood samples from 8 states and analyzed them for total Hg. A subset (n = 20) are also analyzed for methylmercury (MeHg). Ten species of bats from the northeast U.S. are represented in this study of which two are protected by the Endangered Species Act (ESA 1973) and two other species are pending review. There are four objectives in this paper: (1) to examine correlates to differences in fur-Hg levels among all of the sampling sites, including age, sex, species, and presence of a Hg point source; (2) define the relationship between blood and fur-Hg levels and the factors that influence that relationship including age, sex, species, reproductive status, and energetic condition; (3) determine the relationships between total Hg and MeHg in five common eastern bat species; and (4) assess the distribution of Hg across bat populations in the northeast. We found total blood and fur mercury was eight times higher in bats captured near point sources compared to nonpoint sources. Blood-Hg and fur-Hg were well correlated with females on average accumulating two times more Hg in fur than males. On average fur MeHg accounted for 86 % (range 71-95 %) of the total Hg in bat fur. Considering that females had high Hg concentrations, beyond that of established levels of concern, suggests there could be negative implications for bat populations from high Hg exposure since Hg is readily transferred to pups via breast milk. Bats provide an integral part of the ecosystem and their protection is considered to be of high priority. More research is needed to determine if Hg is a stressor that is negatively impacting bat populations.

Offshore observations of eastern red bats (Lasiurus borealis) in the Mid-Atlantic United States using multiple survey methods.

Little is known about the migration and movements of migratory tree-roosting bat species in North America, though anecdotal observations of migrating bats over the Atlantic Ocean have been reported since at least the 1890s. Aerial surveys and boat-based surveys of wildlife off the Atlantic Seaboard detected a possible diurnal migration event of eastern red bats (Lasiurus borealis) in September 2012. One bat was sighted approximately 44 km east of Rehoboth Beach, Delaware during a boat-based survey. Eleven additional bats were observed between 16.9 and 41.8 km east of New Jersey, Delaware, and Virginia in high definition video footage collected during digital aerial surveys. Observations were collected incidentally as part of a large baseline study of seabird, marine mammal, and sea turtle distributions and movements in the offshore environment. Digital survey methods also allowed for altitude estimation for several of these bats at >100 m above sea level. These observations provide new evidence of bat movements offshore, and offer insight into their flight heights above sea level and the times of day at which such migrations may occur.