Skunk River Review 2016-2018

https://openspace.dmacc.edu/skunkriver/1025/thumbnail.jp

Soundscape monitoring acoustic data collected in July of 2017 during an in situ larval coral settlement experiment in St. John, US Virgin Islands

Dataset: Soundscape monitoring acoustic dataMatlab R2016 was used to process acoustic data from raw wave audio files. Mean power spectral densities were estimated (Hamming window, non-overlapping 0.5-sec windows, frequency resolution: 1.47 Hz) within 1-minute samples across the total experiment length (62 hours). For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/742573NSF Division of Ocean Sciences (NSF OCE) OCE-153678

Soundscapes influence the settlement of the common caribbean coral porites astreoides irrespective of light conditions

Author Posting. © Royal Society, 2018. This article is posted here by permission of Royal Society for personal use, not for redistribution. The definitive version was published in Proceedings of the Royal Society Open Science 5(12) (2018): 181358. doi: 10.1098/rsos.181358.The settlement of reef-building corals is critical to the survival and recovery of reefs. Recent evidence indicates that coral larvae orient towards reef sound, yet the components of the acoustic environment that may attract coral larvae and induce settlement are unknown. Here we investigated the effects of ambient soundscapes on settlement of Porites astreoides coral larvae using in situ chambers on reefs differing in habitat quality (coral and fish abundance). Mean larval settlement was twice as high in an acoustic environment with high levels of low-frequency sounds, typical of a high-quality, healthy reef; this result was observed in both natural light and dark treatments. Overall, the enhancement of coral settlement by soundscapes typical of healthy reefs suggests a positive feedback where soundscape properties of reefs with elevated coral and fish abundance may facilitate coral recruitment.This study is funded by NSF Biological Oceanography award 15-36782 which supported all authors

Solute Fluxes Through Restored Prairie and Intensively Managed Critical Zones in Nebraska and Iowa

Agricultural activities in the Midwestern United States have potentially altered geochemical fluxes within the critical zone (CZ) compared to native prairie systems that previously dominated the region. To quantify the impact of agricultural land use on soil and stream solute behavior, we are studying two watersheds in the region: Glacier Creek Preserve (GCP) in eastern Nebraska and the Intensively Managed Landscapes Critical Zone Observatory (IML-CZO) in eastern Iowa. Both watersheds were initially under agricultural land use for over 100 years, but part of each watershed was restored to prairie 20 – 50 years ago. Soils at both sites formed in thick Peoria loess (≥6 m) overlying glacial till with similar mean annual temperatures (∼10∘C) but slightly higher mean annual precipitation in Iowa (89 cm) compared to Nebraska (78 cm). At both sites, soil pore water and precipitation were collected every 2–4 weeks to measure anions, cations, and alkalinity; stream waters draining either restored prairie or agriculture were sampled similarly in Nebraska. Both soil moisture content and electrical conductivity were consistently higher in the upper one meter of agricultural soils compared to prairie soils in Nebraska, implying slower drainage and higher solute concentrations in the agricultural soils. At both sites, soil pore water Ca2+ and Mg2+ concentrations and annual fluxes were significantly higher in agricultural soils compared to restored prairie. Conversely, streams draining restored prairie have significantly higher Ca2+and Mg2+ concentrations than the agricultural streams. Fluxes from agricultural streams, however, were higher than the prairie, pointing to a potential dilution effect of runoff from the agricultural land use. These observations lead to a conceptual model where deeply infiltrating water in restored prairie soils interacts with minerals present deeper in the soil before reaching the stream whereas in agricultural soils water does not infiltrate as deeply and thus experiences more shallow flowpaths to the stream. Furthermore, changes in geochemical and hydrologic fluxes have been realized in just a few decades since switching land use from agriculture to prairie. Thus, intensive agricultural land use may alter soil function and solute transport to streams compared to critical zones hosting tallgrass prairie vegetation

Rabies Management Implications Based on Raccoon Population Density Indexes

An estimate or index of target species density is important in determining oral rabies vaccination (ORV) bait densities to control and eliminate specific rabies variants. From 1997–2011, we indexed raccoon (Procyon lotor) densities 253 times based on cumulative captures on 163 sites from Maine to Alabama, USA, near ORV zones created to prevent raccoon rabies from spreading to new areas. We conducted indexing under a common cage trapping protocol near the time of annual ORV to aid in bait density decisions. Unique raccoons (n = 8,415) accounted for 68.0% of captures (n = 12,367). We recaptured raccoons 2,669 times. We applied Schnabel and Huggins mark‐recapture models on sites with ≥3 years of capture data and ≥25% recaptures as context for raccoon density indexes (RDIs). Simple linear relationships between RDIs and mark‐recapture estimates supported application of our 2 index. Raccoon density indexes ranged from 0.0–56.9 raccoons/km . For bait density decisions, we evaluated RDIs in the following 4 raccoon density groups, which were statistically different: (0.0–5.0 [n = 70], 5.1–15.0 [n = 129], 15.1–25.0 [n = 31], and \u3e25.0 raccoons/km2 [n = 23]). Mean RDI was positively associated with a higher percentage of developed land cover and a lower percentage of evergreen forest. Non‐target species composition (excluding recaptured raccoons) accounted for 32.0% of captures. Potential bait competitors accounted for 76.5% of non‐targets. The opossum (Didelphis virginiana) was the primary potential bait competitor from 27°N to 44°N latitude, north of which it was numerically replaced by the striped skunk (Mephitis mephitis). We selected the RDI approach over mark-recapture methods because of costs, geographic scope, staff availability, and the need for supplemental serologic samples. The 4 density groups provided adequate sensitivity to support bait density decisions for the current 2 bait density options. Future improvements to the method include providing random trapping locations to field personnel to prevent trap clustering and marking non‐targets to better characterize bait competitors

Multiscale spatio-temporal patterns of boat noise on U.S. Virgin Island coral reefs

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Marine Pollution Bulletin 136 (2018): 282-290, doi:10.1016/j.marpolbul.2018.09.009.Sound-sensitive organisms are abundant on coral reefs. Accordingly, experiments suggest that boat noise could elicit adverse effects on coral reef organisms. Yet, there are few data quantifying boat noise prevalence on coral reefs. We use long-term passive acoustic recordings at nine coral reefs and one sandy comparison site in a marine protected area to quantify spatio-temporal variation in boat noise and its effect on the soundscape. Boat noise was most common at reefs with high coral cover and fish density, and temporal patterns reflected patterns of human activity. Boat noise significantly increased low-frequency sound levels at the monitored sites. With boat noise present, the peak frequencies of the natural soundscape shifted from higher frequencies to the lower frequencies frequently used in fish communication. Taken together, the spectral overlap between boat noise and fish communication and the elevated boat detections on reefs with biological densities raises concern for coral reef organisms.This research was funded by the National Science Foundation Biological Oceanography Program (award OCE-1536782) and the WHOI Summer Student Fellowship Program

Solute Fluxes Through Restored Prairie and Intensively Managed Critical Zones in Nebraska and Iowa

Agricultural activities in the Midwestern United States have potentially altered geochemical fluxes within the critical zone (CZ) compared to native prairie systems that previously dominated the region. To quantify the impact of agricultural land use on soil and stream solute behavior, we are studying two watersheds in the region: Glacier Creek Preserve (GCP) in eastern Nebraska and the Intensively Managed Landscapes Critical Zone Observatory (IML-CZO) in eastern Iowa. Both watersheds were initially under agricultural land use for over 100 years, but part of each watershed was restored to prairie 20 – 50 years ago. Soils at both sites formed in thick Peoria loess (≥6 m) overlying glacial till with similar mean annual temperatures (∼10°C) but slightly higher mean annual precipitation in Iowa (89 cm) compared to Nebraska (78 cm). At both sites, soil pore water and precipitation were collected every 2–4 weeks to measure anions, cations, and alkalinity; stream waters draining either restored prairie or agriculture were sampled similarly in Nebraska. Both soil moisture content and electrical conductivity were consistently higher in the upper one meter of agricultural soils compared to prairie soils in Nebraska, implying slower drainage and higher solute concentrations in the agricultural soils. At both sites, soil pore water Ca2+ and Mg2+ concentrations and annual fluxes were significantly higher in agricultural soils compared to restored prairie. Conversely, streams draining restored prairie have significantly higher Ca2+ and Mg2+ concentrations than the agricultural streams. Fluxes from agricultural streams, however, were higher than the prairie, pointing to a potential dilution effect of runoff from the agricultural land use. These observations lead to a conceptual model where deeply infiltrating water in restored prairie soils interacts with minerals present deeper in the soil before reaching the stream whereas in agricultural soils water does not infiltrate as deeply and thus experiences more shallow flowpaths to the stream. Furthermore, changes in geochemical and hydrologic fluxes have been realized in just a few decades since switching land use from agriculture to prairie. Thus, intensive agricultural land use may alter soil function and solute transport to streams compared to critical zones hosting tallgrass prairie vegetation

A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1

Background: The major histocompatibility complex (MHC) is present within the genomes of all jawed vertebrates. MHC genes are especially important in regulating immune responses, but even after over 80 years of research on the MHC, much remains to be learned about how it influences adaptive and innate immune responses. In most species, the MHC is highly polymorphic and polygenic. Strong and highly reproducible associations are established for chicken MHC-B haplotypes in a number of infectious diseases. Here, we report (1) the development of a high-density SNP (single nucleotide polymorphism) panel for MHC-B typing that encompasses a 209,296 bp region in which 45 MHC-B genes are located, (2) how this panel was used to define chicken MHC-B haplotypes within a large number of lines/breeds and (3) the detection of recombinants which contributes to the observed diversity. Methods: A SNP panel was developed for the MHC-B region between the BG2 and CD1A1 genes. To construct this panel, each SNP was tested in end-point read assays on more than 7500 DNA samples obtained from inbred and commercially used egg-layer lines that carry known and novel MHC-B haplotypes. One hundred and one SNPs were selected for the panel. Additional breeds and experimentally-derived lines, including lines that carry MHC-B recombinant haplotypes, were then genotyped. Results: MHC-B haplotypes based on SNP genotyping were consistent with the MHC-B haplotypes that were assigned previously in experimental lines that carry B2, B5, B12, B13, B15, B19, B21, and B24 haplotypes. SNP genotyping resulted in the identification of 122 MHC-B haplotypes including a number of recombinant haplotypes, which indicate that crossing-over events at multiple locations within the region lead to the production of new MHC-B haplotypes. Furthermore, evidence of gene duplication and deletion was found. Conclusions: The chicken MHC-B region is highly polymorphic across the surveyed 209-kb region that contains 45 genes. Our results expand the number of identified haplotypes and provide insights into the contribution of recombination events to MHC-B diversity including the identification of recombination hotspots and an estimation of recombination frequency

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

Human-associated microbial communities comprise not only complex mixtures of bacterial species, but also mixtures of conspecific strains, the implications of which are mostly unknown since strain level dynamics are underexplored due to the difficulties of studying them. We introduce the Strain Genome Explorer (StrainGE) toolkit, which deconvolves strain mixtures and characterizes component strains at the nucleotide level from short-read metagenomic sequencing with higher sensitivity and resolution than other tools. StrainGE is able to identify strains at 0.1x coverage and detect variants for multiple conspecific strains within a sample from coverages as low as 0.5x